4ZV9

2.00 Angstrom resolution crystal structure of an uncharacterized protein from Escherichia coli O157:H7 str. Sakai

PDB DOI: https://doi.org/10.2210/pdb4ZV9/pdb

Classification: Structural Genomics, Unknown Function
Organism(s): Escherichia coli O157:H7
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2015-05-18 Released: 2015-06-17
Deposition Author(s): Halavaty, A.S., Wawrzak, Z., Filippova, E.V., Kiryukhina, O., Endres, M., Joachimiak, A., Anderson, W.F., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.199
R-Value Work: 0.168
R-Value Observed: 0.169

wwPDB Validation 3D Report Full Report

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

Literature

2.00 Angstrom resolution crystal structure of an uncharacterized protein from Escherichia coli O157:H7 str. Sakai

Halavaty, A.S., Wawrzak, Z., Filippova, E.V., Kiryukhina, O., Endres, M., Joachimiak, A., Anderson, W.F., Midwest Center for Structural Genomics (MCSG)

To be published.

Macromolecule Content

Total Structure Weight: 159.69 kDa
Atom Count: 12,803
Modelled Residue Count: 1,428
Deposited Residue Count: 1,428
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 protein	A, B, C, D, E A, B, C, D, E, F	238	Escherichia coli O157:H7	Mutation(s): 0 Gene Names: ECs3884
UniProt
Find proteins for Q8XBV0 (Escherichia coli O157:H7) Explore Q8XBV0 Go to UniProtKB: Q8XBV0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8XBV0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain O [auth E] MOL2 format, chain O [auth E] mmCIF format, chain O [auth E]	O [auth E]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain O [auth E] Interactions & Density Focus chain O [auth E]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain S [auth F] MOL2 format, chain S [auth F] mmCIF format, chain S [auth F]	S [auth F]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain S [auth F] Interactions & Density Focus chain S [auth F]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain J [auth B] MOL2 format, chain J [auth B] mmCIF format, chain J [auth B]	J [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain J [auth B] Interactions & Density Focus chain J [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain M [auth E] SDF format, chain N [auth E] SDF format, chain P [auth F] SDF format, chain Q [auth F] SDF format, chain R [auth F] SDF format, chain G [auth A] SDF format, chain I [auth A] SDF format, chain K [auth B] SDF format, chain L [auth D] MOL2 format, chain H [auth A] MOL2 format, chain M [auth E] MOL2 format, chain N [auth E] MOL2 format, chain P [auth F] MOL2 format, chain Q [auth F] MOL2 format, chain R [auth F] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth D] mmCIF format, chain H [auth A] mmCIF format, chain M [auth E] mmCIF format, chain N [auth E] mmCIF format, chain P [auth F] mmCIF format, chain Q [auth F] mmCIF format, chain R [auth F] mmCIF format, chain G [auth A] mmCIF format, chain I [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth D]	G [auth A] H [auth A] I [auth A] K [auth B] L [auth D] G [auth A], H [auth A], I [auth A], K [auth B], L [auth D], M [auth E], N [auth E], P [auth F], Q [auth F], R [auth F]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth D] Focus chain M [auth E] Focus chain N [auth E] Focus chain P [auth F] Focus chain Q [auth F] Focus chain R [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth D] Focus chain M [auth E] Focus chain N [auth E] Focus chain P [auth F] Focus chain Q [auth F] Focus chain R [auth F]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CME Query on CME	A, B, C, D, E A, B, C, D, E, F	L-PEPTIDE LINKING	C₅ H₁₁ N O₃ S₂		CYS
MSE Query on MSE	A, B, C, D, E A, B, C, D, E, F	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: 0.199
R-Value Work: 0.168
R-Value Observed: 0.169
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.615	α = 90
b = 96.341	β = 98.22
c = 129.617	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2015-06-17

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2015-06-17
Type: Initial release
Version 1.1: 2024-10-23
Changes: Advisory, Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary