3E0Z | pdb_00003e0z

Crystal structure of a putative imidazole glycerol phosphate synthase homolog (eubrec_1070) from eubacterium rectale at 1.75 A resolution

PDB DOI: https://doi.org/10.2210/pdb3E0Z/pdb

Classification: UNKNOWN FUNCTION
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-08-01 Released: 2008-08-12
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free:
0.219 (Depositor), 0.225 (DCC)
R-Value Work:
0.171 (Depositor), 0.183 (DCC)
R-Value Observed:
0.174 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3E0Z

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

Literature

Crystal structure of protein of unknown function (RER070207001348) from Eubacterium rectale at 1.75 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 51.22 kDa
Atom Count: 3,980
Modeled Residue Count: 431
Deposited Residue Count: 436
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
protein of unknown function	A, B, C, D	109	N/A	Mutation(s): 0 Gene Names: RER070207001348

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain H [auth C] MOL2 format, chain H [auth C] mmCIF format, chain H [auth C]	H [auth C]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain H [auth C] Interactions & Density Focus chain H [auth C]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A], G [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.219 (Depositor), 0.225 (DCC)
R-Value Work: 0.171 (Depositor), 0.183 (DCC)
R-Value Observed: 0.174 (Depositor)

Diffraction Data:

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.79	α = 90
b = 60.18	β = 98.18
c = 59.86	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2008-08-12

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2008-08-12
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description
Version 1.3: 2019-07-24
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.4: 2024-10-16
Changes: Data collection, Database references, Derived calculations, Refinement description, 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.