4RCK | pdb_00004rck

Crystal Structure of Uncharacterized Membrane Spanning Protein from Vibrio fischeri

PDB DOI: https://doi.org/10.2210/pdb4RCK/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Aliivibrio fischeri ES114
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2014-09-16 Released: 2014-11-26
Deposition Author(s): Kim, Y., Tesar, C., Bearden, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free:
0.237 (Depositor), 0.236 (DCC)
R-Value Work:
0.195 (Depositor), 0.199 (DCC)
R-Value Observed:
0.197 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 4RCK

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

Literature

Crystal Structure of Uncharacterized Membrane Spanning Protein from Vibrio fischeri

Kim, Y., Tesar, C., Bearden, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

To be published.

Macromolecule Content

Total Structure Weight: 49.07 kDa
Atom Count: 3,174
Modeled Residue Count: 406
Deposited Residue Count: 440
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical membrane spanning protein	A, B	220	Aliivibrio fischeri ES114	Mutation(s): 0 Gene Names: VF_A0681
UniProt
Find proteins for Q5DZP5 (Aliivibrio fischeri (strain ATCC 700601 / ES114)) Explore Q5DZP5 Go to UniProtKB: Q5DZP5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5DZP5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [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: 3.00 Å
R-Value Free: 0.237 (Depositor), 0.236 (DCC)
R-Value Work: 0.195 (Depositor), 0.199 (DCC)
R-Value Observed: 0.197 (Depositor)

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.734	α = 90
b = 49.734	β = 90
c = 343.88	γ = 120

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	data collection
HKL-3000	phasing
SHELXS	phasing
MLPHARE	phasing
DM	model building
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: 2014-11-26

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2014-11-26
Type: Initial release
Version 1.1: 2024-10-30
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.