4LJS | pdb_00004ljs

The crystal structure of a periplasmic binding protein from Veillonella parvula DSM 2008

PDB DOI: https://doi.org/10.2210/pdb4LJS/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Veillonella parvula DSM 2008
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2013-07-05 Released: 2013-07-24
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: 2.32 Å
R-Value Free:
0.208 (Depositor), 0.206 (DCC)
R-Value Work:
0.154 (Depositor), 0.157 (DCC)
R-Value Observed:
0.156 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 4LJS

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

Literature

The crystal structure of a periplasmic binding protein from Veillonella parvula DSM 2008

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

To be published.

Macromolecule Content

Total Structure Weight: 37.31 kDa
Atom Count: 2,628
Modeled Residue Count: 316
Deposited Residue Count: 324
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Periplasmic binding protein	A	324	Veillonella parvula DSM 2008	Mutation(s): 0 Gene Names: Vpar_0062

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
GOL Query on GOL 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]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-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: 2.32 Å
R-Value Free: 0.208 (Depositor), 0.206 (DCC)
R-Value Work: 0.154 (Depositor), 0.157 (DCC)
R-Value Observed: 0.156 (Depositor)

Space Group: P 6₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.994	α = 90
b = 82.994	β = 90
c = 110.419	γ = 120

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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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2013-07-24

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2013-07-24
Type: Initial release
Version 1.1: 2024-11-20
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.