4NOC

The crystal structure of a CBS Domain-containing Protein of Unknown Function from Kribbella flavida DSM 17836.

PDB DOI: https://doi.org/10.2210/pdb4NOC/pdb

Classification: SIGNALING PROTEIN
Organism(s): Kribbella flavida DSM 17836
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2013-11-19 Released: 2013-11-27
Deposition Author(s): Tan, K., Hatzos-Skintges, C., Jedrzejczak, R., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.240
R-Value Work: 0.193
R-Value Observed: 0.195

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

The crystal structure of a CBS Domain-containing Protein of Unknown Function from Kribbella flavida DSM 17836.

Tan, K., Hatzos-Skintges, C., Jedrzejczak, R., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 66.63 kDa
Atom Count: 4,347
Modelled Residue Count: 576
Deposited Residue Count: 604
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative signal transduction protein with CBS domains	A, B, C, D	151	Kribbella flavida DSM 17836	Mutation(s): 0 Gene Names: Kfla_0464
UniProt
Find proteins for D2PVT0 (Kribbella flavida (strain DSM 17836 / JCM 10339 / NBRC 14399)) Explore D2PVT0 Go to UniProtKB: D2PVT0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	D2PVT0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth C] SDF format, chain K [auth C] SDF format, chain L [auth C] SDF format, chain M [auth C] SDF format, chain N [auth C] SDF format, chain O [auth D] SDF format, chain P [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth C] MOL2 format, chain K [auth C] MOL2 format, chain L [auth C] MOL2 format, chain M [auth C] MOL2 format, chain N [auth C] MOL2 format, chain O [auth D] MOL2 format, chain P [auth D]	E [auth A] F [auth A] G [auth A] H [auth B] I [auth B] E [auth A], F [auth A], G [auth A], H [auth B], I [auth B], J [auth C], K [auth C], L [auth C], M [auth C], N [auth C], O [auth D], P [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth C] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth D] Focus chain P [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth C] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth D] Focus chain P [auth D]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.240
R-Value Work: 0.193
R-Value Observed: 0.195
Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.434	α = 90
b = 99.434	β = 90
c = 260.582	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