3L1W

The crystal structure of a functionally unknown conserved protein from Enterococcus faecalis V583

PDB DOI: https://doi.org/10.2210/pdb3L1W/pdb

Classification: Structural Genomics, Unknown function
Organism(s): Enterococcus faecalis
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2009-12-14 Released: 2010-01-12
Deposition Author(s): Tan, K., Rakowski, E., Jedrzejczak, R., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.198
R-Value Work: 0.167
R-Value Observed: 0.168

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

The crystal structure of a functionally unknown conserved protein from Enterococcus faecalis V583

Tan, K., Rakowski, E., Jedrzejczak, R., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 181.69 kDa
Atom Count: 14,171
Modelled Residue Count: 1,512
Deposited Residue Count: 1,542
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A, B, C, D, E A, B, C, D, E, F	257	Enterococcus faecalis	Mutation(s): 0 Gene Names: EF_1237
UniProt
Find proteins for Q835Y1 (Enterococcus faecalis (strain ATCC 700802 / V583)) Explore Q835Y1 Go to UniProtKB: Q835Y1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q835Y1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain CA [auth D] SDF format, chain DA [auth D] SDF format, chain EA [auth D] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain IA [auth E] SDF format, chain J [auth A] SDF format, chain JA [auth E] SDF format, chain KA [auth E] SDF format, chain LA [auth E] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain PA [auth F] SDF format, chain Q [auth B] SDF format, chain QA [auth F] SDF format, chain RA [auth F] SDF format, chain SA [auth F] SDF format, chain U [auth C] SDF format, chain V [auth C] SDF format, chain W [auth C] SDF format, chain X [auth C] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth E] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth E] MOL2 format, chain KA [auth E] MOL2 format, chain LA [auth E] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain PA [auth F] MOL2 format, chain Q [auth B] MOL2 format, chain QA [auth F] MOL2 format, chain RA [auth F] MOL2 format, chain SA [auth F] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C]	BA [auth D] CA [auth D] DA [auth D] EA [auth D] G [auth A] BA [auth D], CA [auth D], DA [auth D], EA [auth D], G [auth A], H [auth A], I [auth A], IA [auth E], J [auth A], JA [auth E], KA [auth E], LA [auth E], N [auth B], O [auth B], P [auth B], PA [auth F], Q [auth B], QA [auth F], RA [auth F], SA [auth F], U [auth C], V [auth C], W [auth C], X [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain IA [auth E] Focus chain J [auth A] Focus chain JA [auth E] Focus chain KA [auth E] Focus chain LA [auth E] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain PA [auth F] Focus chain Q [auth B] Focus chain QA [auth F] Focus chain RA [auth F] Focus chain SA [auth F] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Interactions & Density Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain IA [auth E] Focus chain J [auth A] Focus chain JA [auth E] Focus chain KA [auth E] Focus chain LA [auth E] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain PA [auth F] Focus chain Q [auth B] Focus chain QA [auth F] Focus chain RA [auth F] Focus chain SA [auth F] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain FA [auth D] SDF format, chain K [auth A] SDF format, chain MA [auth E] SDF format, chain R [auth B] SDF format, chain TA [auth F] SDF format, chain Y [auth C] MOL2 format, chain FA [auth D] MOL2 format, chain K [auth A] MOL2 format, chain MA [auth E] MOL2 format, chain R [auth B] MOL2 format, chain TA [auth F] MOL2 format, chain Y [auth C]	FA [auth D] K [auth A] MA [auth E] R [auth B] TA [auth F] FA [auth D], K [auth A], MA [auth E], R [auth B], TA [auth F], Y [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain FA [auth D] Focus chain K [auth A] Focus chain MA [auth E] Focus chain R [auth B] Focus chain TA [auth F] Focus chain Y [auth C] Interactions & Density Focus chain FA [auth D] Focus chain K [auth A] Focus chain MA [auth E] Focus chain R [auth B] Focus chain TA [auth F] Focus chain Y [auth C]
FMT Query on FMT Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain GA [auth D] SDF format, chain HA [auth D] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain NA [auth E] SDF format, chain OA [auth E] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain UA [auth F] SDF format, chain VA [auth F] SDF format, chain Z [auth C] MOL2 format, chain AA [auth C] MOL2 format, chain GA [auth D] MOL2 format, chain HA [auth D] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain NA [auth E] MOL2 format, chain OA [auth E] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain UA [auth F] MOL2 format, chain VA [auth F] MOL2 format, chain Z [auth C]	AA [auth C] GA [auth D] HA [auth D] L [auth A] M [auth A] AA [auth C], GA [auth D], HA [auth D], L [auth A], M [auth A], NA [auth E], OA [auth E], S [auth B], T [auth B], UA [auth F], VA [auth F], Z [auth C]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain GA [auth D] Focus chain HA [auth D] Focus chain L [auth A] Focus chain M [auth A] Focus chain NA [auth E] Focus chain OA [auth E] Focus chain S [auth B] Focus chain T [auth B] Focus chain UA [auth F] Focus chain VA [auth F] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain GA [auth D] Focus chain HA [auth D] Focus chain L [auth A] Focus chain M [auth A] Focus chain NA [auth E] Focus chain OA [auth E] Focus chain S [auth B] Focus chain T [auth B] Focus chain UA [auth F] Focus chain VA [auth F] Focus chain Z [auth C]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E A, B, C, D, E, F	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.198
R-Value Work: 0.167
R-Value Observed: 0.168
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.565	α = 89.88
b = 68.558	β = 89.79
c = 104.245	γ = 60.07

Software Package:

Software Name	Purpose
SBC-Collect	data collection
SHELXD	phasing
MLPHARE	phasing
DM	model building
ARP	model building
WARP	model building
HKL-3000	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing