4EI0

Crystal structure of a DUF4466 family protein (PARMER_03218) from Parabacteroides merdae ATCC 43184 at 2.00 A resolution

PDB DOI: https://doi.org/10.2210/pdb4EI0/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Parabacteroides merdae ATCC 43184
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-04-04 Released: 2012-05-30
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.216
R-Value Work: 0.174
R-Value Observed: 0.176

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of a hypothetical protein (PARMER_03218) from Parabacteroides merdae ATCC 43184 at 2.00 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 69.53 kDa
Atom Count: 5,054
Modelled Residue Count: 603
Deposited Residue Count: 624
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
uncharacterized hypothetical protein	A, B	312	Parabacteroides merdae ATCC 43184	Mutation(s): 0 Gene Names: PARMER_03218
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

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: 2.00 Å
R-Value Free: 0.216
R-Value Work: 0.174
R-Value Observed: 0.176
Space Group: P 2₁ 2₁ 2₁
Diffraction Data: https://doi.org/10.18430/M34EI0

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.749	α = 90
b = 85.879	β = 90
c = 128.695	γ = 90

Software Package:

Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
SHELX	phasing
SHARP	phasing
XSCALE	data scaling
REFMAC	refinement
XDS	data reduction
SHELXD	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2012-05-30

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2012-05-30
Type: Initial release
Version 1.1: 2014-12-24
Changes: Structure summary
Version 1.2: 2017-11-15
Changes: Refinement description
Version 1.3: 2018-01-24
Changes: Database references
Version 1.4: 2023-02-01
Changes: Database references, Derived calculations

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.