3S9X | pdb_00003s9x

High resolution crystal structure of ASCH domain from Lactobacillus crispatus JV V101

PDB DOI: https://doi.org/10.2210/pdb3S9X/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Vibrio cholerae TMA 21
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2011-06-02 Released: 2011-07-27
Deposition Author(s): Nocek, B., Xu, X., Cui, H., Jedrzejczak, R., Edwards, A., Savchenko, A., Mabbutt, B.C., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.35 Å
R-Value Free:
0.172 (Depositor), 0.171 (DCC)
R-Value Work:
0.134 (Depositor), 0.131 (DCC)
R-Value Observed:
0.136 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3S9X

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

Literature

High resolution crystal structure of ASCH domain from Lactobacillus crispatus JV V101

Nocek, B., Xu, X., Cui, H., Jedrzejczak, R., Edwards, A., Savchenko, A., Mabbutt, B.C., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 18.76 kDa
Atom Count: 1,667
Modeled Residue Count: 159
Deposited Residue Count: 159
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ASCH domain	A	159	Vibrio cholerae TMA 21	Mutation(s): 0 Gene Names: VCB_002424
UniProt
Find proteins for A0ABX9FEY2 (Vibrio paracholerae) Explore A0ABX9FEY2 Go to UniProtKB: A0ABX9FEY2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0ABX9FEY2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.35 Å
R-Value Free: 0.172 (Depositor), 0.171 (DCC)
R-Value Work: 0.134 (Depositor), 0.131 (DCC)
R-Value Observed: 0.136 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.855	α = 90
b = 39.689	β = 90
c = 128.594	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	phasing
SHELX	model building
ARP/wARP	model building
MOLREP	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
SHELX	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2011-07-27

Deposition Author(s):

Jedrzejczak, R.

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2011-07-27
Type: Initial release
Version 1.1: 2024-11-20
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.