4Q2B

The crystal structure of an endo-1,4-D-glucanase from Pseudomonas putida KT2440

PDB DOI: https://doi.org/10.2210/pdb4Q2B/pdb

Classification: HYDROLASE
Organism(s): Pseudomonas putida KT2440
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2014-04-07 Released: 2014-06-25
Deposition Author(s): Tan, K., Joachimiak, G., Endres, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.12 Å
R-Value Free: 0.198
R-Value Work: 0.163
R-Value Observed: 0.165

wwPDB Validation 3D Report Full Report

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

Literature

The crystal structure of an endo-1,4-D-glucanase from Pseudomonas putida KT2440

Tan, K., Joachimiak, G., Endres, M., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 235.39 kDa
Atom Count: 17,169
Modelled Residue Count: 2,058
Deposited Residue Count: 2,094
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endo-1,4-beta-D-glucanase	A, B, C, D, E A, B, C, D, E, F	349	Pseudomonas putida KT2440	Mutation(s): 0 Gene Names: PP_2637
UniProt
Find proteins for Q88JL2 (Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)) Explore Q88JL2 Go to UniProtKB: Q88JL2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q88JL2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TRS Query on TRS Download Ideal Coordinates CCD File SDF format, chain CA [auth E] SDF format, chain EA [auth F] SDF format, chain H [auth A] SDF format, chain Z [auth D] MOL2 format, chain CA [auth E] MOL2 format, chain EA [auth F] MOL2 format, chain H [auth A] MOL2 format, chain Z [auth D]	CA [auth E], EA [auth F], H [auth A], Z [auth D]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain CA [auth E] Focus chain EA [auth F] Focus chain H [auth A] Focus chain Z [auth D] Interactions & Density Focus chain CA [auth E] Focus chain EA [auth F] Focus chain H [auth A] Focus chain Z [auth D]
MLA Query on MLA Download Ideal Coordinates CCD File SDF format, chain Q [auth C] MOL2 format, chain Q [auth C]	Q [auth C]	MALONIC ACID C₃ H₄ O₄ OFOBLEOULBTSOW-UHFFFAOYSA-N		Interactions Focus chain Q [auth C] Interactions & Density Focus chain Q [auth C]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain BA [auth E] SDF format, chain DA [auth F] SDF format, chain G [auth A] SDF format, chain L [auth B] SDF format, chain O [auth C] SDF format, chain P [auth C] SDF format, chain X [auth D] MOL2 format, chain BA [auth E] MOL2 format, chain DA [auth F] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] MOL2 format, chain X [auth D]	BA [auth E] DA [auth F] G [auth A] L [auth B] O [auth C] BA [auth E], DA [auth F], G [auth A], L [auth B], O [auth C], P [auth C], X [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain BA [auth E] Focus chain DA [auth F] Focus chain G [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain X [auth D] Interactions & Density Focus chain BA [auth E] Focus chain DA [auth F] Focus chain G [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain X [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain Y [auth D] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain Y [auth D]	R [auth C], S [auth C], Y [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain R [auth C] Focus chain S [auth C] Focus chain Y [auth D] Interactions & Density Focus chain R [auth C] Focus chain S [auth C] Focus chain Y [auth D]
IMD Query on IMD Download Ideal Coordinates CCD File SDF format, chain W [auth C] MOL2 format, chain W [auth C]	W [auth C]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain W [auth C] Interactions & Density Focus chain W [auth C]
FMT Query on FMT Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain T [auth C] SDF format, chain U [auth C] SDF format, chain V [auth C] MOL2 format, chain AA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C]	AA [auth D] I [auth A] J [auth A] K [auth A] M [auth B] AA [auth D], I [auth A], J [auth A], K [auth A], M [auth B], N [auth B], T [auth C], U [auth C], V [auth C]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Interactions & Density Focus chain AA [auth D] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [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: 2.12 Å
R-Value Free: 0.198
R-Value Work: 0.163
R-Value Observed: 0.165
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 126.938	α = 90
b = 129.189	β = 90
c = 165.115	γ = 90

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