4KV7 | pdb_00004kv7

The crystal structure of a possible leucine/isoleucine/valine-binding protein from Rhodopirellula baltica SH 1

PDB DOI: https://doi.org/10.2210/pdb4KV7/pdb

Classification: UNKNOWN FUNCTION
Organism(s): Rhodopirellula baltica SH 1
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2013-05-22 Released: 2013-06-05
Deposition Author(s): Tan, K., Mack, J., Endres, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.20 Å
R-Value Free:
0.163 (Depositor), 0.163 (DCC)
R-Value Work:
0.148 (Depositor), 0.148 (DCC)
R-Value Observed:
0.149 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 4KV7

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

Literature

The crystal structure of a possible leucine/isoleucine/valine-binding protein from Rhodopirellula baltica SH 1

Tan, K., Mack, J., Endres, M., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 41.5 kDa
Atom Count: 3,418
Modeled Residue Count: 369
Deposited Residue Count: 381
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable leucine/isoleucine/valine-binding protein	A	381	Rhodopirellula baltica SH 1	Mutation(s): 1 Gene Names: livK, RB7306
UniProt
Find proteins for Q7UNW4 (Rhodopirellula baltica (strain DSM 10527 / NCIMB 13988 / SH1)) Explore Q7UNW4 Go to UniProtKB: Q7UNW4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q7UNW4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FMT Query on FMT Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.20 Å
R-Value Free: 0.163 (Depositor), 0.163 (DCC)
R-Value Work: 0.148 (Depositor), 0.148 (DCC)
R-Value Observed: 0.149 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.984	α = 76.22
b = 44.483	β = 88.65
c = 57.913	γ = 77.54

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2013-06-05

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2013-06-05
Type: Initial release
Version 1.1: 2024-11-06
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.