3NYI | pdb_00003nyi

The crystal structure of a fat acid (stearic acid)-binding protein from Eubacterium ventriosum ATCC 27560.

PDB DOI: https://doi.org/10.2210/pdb3NYI/pdb

Classification: LIPID BINDING PROTEIN
Organism(s): Eubacterium ventriosum ATCC 27560
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-07-15 Released: 2010-09-22
Deposition Author(s): Zhang, R., Tan, K., Li, H., Keigher, L., Babnigg, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.220 (Depositor), 0.212 (DCC)
R-Value Work:
0.168 (Depositor), 0.167 (DCC)
R-Value Observed:
0.171 (Depositor)

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

The crystal structure of a fat acid (stearic acid)-binding protein from Eubacterium ventriosum ATCC 27560.

Zhang, R., Tan, K., Li, H., Keigher, L., Babnigg, G., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 66.71 kDa
Atom Count: 4,990
Modeled Residue Count: 588
Deposited Residue Count: 592
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
fat acid-binding protein	A, B	296	Eubacterium ventriosum ATCC 27560	Mutation(s): 0 Gene Names: EUBVEN_01190
UniProt
Find proteins for A5Z657 (Eubacterium ventriosum ATCC 27560) Explore A5Z657 Go to UniProtKB: A5Z657
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A5Z657
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
STE Query on STE Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	STEARIC ACID C₁₈ H₃₆ O₂ QIQXTHQIDYTFRH-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: 1.90 Å
R-Value Free: 0.220 (Depositor), 0.212 (DCC)
R-Value Work: 0.168 (Depositor), 0.167 (DCC)
R-Value Observed: 0.171 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.725	α = 90
b = 110.221	β = 108.62
c = 57.127	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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2010-09-22

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2010-09-22
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2016-12-21
Changes: Structure summary
Version 1.3: 2024-10-09
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.