4G6Q | pdb_00004g6q

The crystal structure of a functionally unknown protein Kfla_6221 from Kribbella flavida DSM 17836

PDB DOI: https://doi.org/10.2210/pdb4G6Q/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Kribbella flavida DSM 17836
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-07-19 Released: 2012-09-19
Deposition Author(s): Tan, K., Chhor, G., Endres, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.08 Å
R-Value Free:
0.237 (Depositor), 0.234 (DCC)
R-Value Work:
0.189 (Depositor), 0.186 (DCC)
R-Value Observed:
0.192 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

The crystal structure of a functionally unknown protein Kfla_6221 from Kribbella flavida DSM 17836, CASP Target

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

To be published.

Macromolecule Content

Total Structure Weight: 40.78 kDa
Atom Count: 2,865
Modeled Residue Count: 345
Deposited Residue Count: 364
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative uncharacterized protein	A, B	182	Kribbella flavida DSM 17836	Mutation(s): 0 Gene Names: Kfla_6221
UniProt
Find proteins for D2PVI4 (Kribbella flavida (strain DSM 17836 / JCM 10339 / NBRC 14399)) Explore D2PVI4 Go to UniProtKB: D2PVI4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D2PVI4
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 B] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain E [auth B] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain E [auth B] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], E [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.08 Å
R-Value Free: 0.237 (Depositor), 0.234 (DCC)
R-Value Work: 0.189 (Depositor), 0.186 (DCC)
R-Value Observed: 0.192 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.759	α = 90
b = 77.759	β = 90
c = 140.688	γ = 90

Software Package:

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

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2012-09-19

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2012-09-19
Type: Initial release
Version 1.1: 2024-11-27
Changes: Data collection, Database references, Derived calculations, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.