3G74 | pdb_00003g74

Crystal structure of a functionally unknown protein from Eubacterium ventriosum ATCC 27560

PDB DOI: https://doi.org/10.2210/pdb3G74/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Eubacterium ventriosum ATCC 27560
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-02-09 Released: 2009-03-03
Deposition Author(s): Tan, K., Sather, A., Marshall, N., Freeman, L., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.43 Å
R-Value Free:
0.263 (Depositor), 0.245 (DCC)
R-Value Work:
0.209 (Depositor), 0.233 (DCC)
R-Value Observed:
0.211 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

The crystal structure of a functionally unknown protein from Eubacterium ventriosum ATCC 27560

Tan, K., Sather, A., Marshall, N., Freeman, L., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 94.89 kDa
Atom Count: 5,820
Modeled Residue Count: 707
Deposited Residue Count: 800
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein of unknown function	A, B, C, D, E A, B, C, D, E, F, G, H	100	Eubacterium ventriosum ATCC 27560	Mutation(s): 0 Gene Names: EUBVEN_02336
UniProt
Find proteins for A5Z9E1 (Eubacterium ventriosum ATCC 27560) Explore A5Z9E1 Go to UniProtKB: A5Z9E1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A5Z9E1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain Y [auth H] SDF format, chain X [auth H] SDF format, chain W [auth G] SDF format, chain V [auth G] SDF format, chain U [auth F] SDF format, chain T [auth F] SDF format, chain S [auth E] SDF format, chain R [auth E] SDF format, chain Q [auth E] SDF format, chain P [auth E] SDF format, chain O [auth D] SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] MOL2 format, chain Y [auth H] MOL2 format, chain X [auth H] MOL2 format, chain W [auth G] MOL2 format, chain V [auth G] MOL2 format, chain U [auth F] MOL2 format, chain T [auth F] MOL2 format, chain S [auth E] MOL2 format, chain R [auth E] MOL2 format, chain Q [auth E] MOL2 format, chain P [auth E] MOL2 format, chain O [auth D] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] mmCIF format, chain Y [auth H] mmCIF format, chain X [auth H] mmCIF format, chain W [auth G] mmCIF format, chain V [auth G] mmCIF format, chain U [auth F] mmCIF format, chain T [auth F] mmCIF format, chain S [auth E] mmCIF format, chain R [auth E] mmCIF format, chain Q [auth E] mmCIF format, chain P [auth E] mmCIF format, chain O [auth D] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A]	I [auth A] J [auth A] K [auth A] L [auth A] M [auth B] I [auth A], J [auth A], K [auth A], L [auth A], M [auth B], N [auth B], O [auth D], P [auth E], Q [auth E], R [auth E], S [auth E], T [auth F], U [auth F], V [auth G], W [auth G], X [auth H], Y [auth H]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth D] Focus chain P [auth E] Focus chain Q [auth E] Focus chain R [auth E] Focus chain S [auth E] Focus chain T [auth F] Focus chain U [auth F] Focus chain V [auth G] Focus chain W [auth G] Focus chain X [auth H] Focus chain Y [auth H] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth D] Focus chain P [auth E] Focus chain Q [auth E] Focus chain R [auth E] Focus chain S [auth E] Focus chain T [auth F] Focus chain U [auth F] Focus chain V [auth G] Focus chain W [auth G] Focus chain X [auth H] Focus chain Y [auth H]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.43 Å
R-Value Free: 0.263 (Depositor), 0.245 (DCC)
R-Value Work: 0.209 (Depositor), 0.233 (DCC)
R-Value Observed: 0.211 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.996	α = 90
b = 107.961	β = 92.28
c = 67.691	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
SHELXD	phasing
MLPHARE	phasing
DM	model building
RESOLVE	model building
HKL-3000	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing
RESOLVE	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2009-03-03

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2009-03-03
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2024-11-20
Changes: Data collection, Database references, Derived calculations, Structure summary