3GWP | pdb_00003gwp

Crystal structure of carbon-sulfur lyase involved in aluminum resistance (YP_878183.1) from CLOSTRIDIUM NOVYI NT at 2.90 A resolution

PDB DOI: https://doi.org/10.2210/pdb3GWP/pdb

Classification: LYASE
Organism(s): Clostridium novyi NT
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-04-01 Released: 2009-04-14
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free:
0.271 (Depositor), 0.270 (DCC)
R-Value Work:
0.223 (Depositor), 0.230 (DCC)
R-Value Observed:
0.225 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.6 of the entry. See complete history.

Literature

Crystal structure of carbon-sulfur lyase involved in aluminum resistance (YP_878183.1) from CLOSTRIDIUM NOVYI NT at 2.90 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 192.05 kDa
Atom Count: 12,910
Modeled Residue Count: 1,696
Deposited Residue Count: 1,708
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
carbon-sulfur lyase involved in aluminum resistance	A, B, C, D	427	Clostridium novyi NT	Mutation(s): 0 Gene Names: NT01CX_2110, YP_878183.1
UniProt
Find proteins for A0Q0N1 (Clostridium novyi (strain NT)) Explore A0Q0N1 Go to UniProtKB: A0Q0N1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0Q0N1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP Query on LLP	A, B, C, D	L-PEPTIDE LINKING	C₁₄ H₂₂ N₃ O₇ P		LYS
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: 2.90 Å
R-Value Free: 0.271 (Depositor), 0.270 (DCC)
R-Value Work: 0.223 (Depositor), 0.230 (DCC)
R-Value Observed: 0.225 (Depositor)

Diffraction Data: https://doi.org/10.18430/M33GWP

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.74	α = 90
b = 108.948	β = 90
c = 207.642	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2009-04-14

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2009-04-14
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 1.3: 2019-07-24
Changes: Data collection, Derived calculations, Refinement description
Version 1.4: 2023-02-01
Changes: Database references
Version 1.5: 2023-09-20
Changes: Data collection, Refinement description
Version 1.6: 2023-11-22
Changes: Data collection

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.