3I16 | pdb_00003i16

Crystal structure of carbon-sulfur lyase involved in aluminum resistance (YP_878183.1) from Clostridium novyi NT at 2.00 A resolution

PDB DOI: https://doi.org/10.2210/pdb3I16/pdb

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

Deposited: 2009-06-25 Released: 2009-07-21
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.206 (Depositor), 0.211 (DCC)
R-Value Work:
0.165 (Depositor), 0.176 (DCC)
R-Value Observed:
0.168 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 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 2.00 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 193.07 kDa
Atom Count: 14,434
Modeled Residue Count: 1,705
Deposited Residue Count: 1,708
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aluminum resistance protein	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0Q0N1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PLP Query on PLP 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]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Interactions & Density Focus chain J [auth B]
TLA Query on TLA Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain P [auth C] SDF format, chain X [auth D] MOL2 format, chain E [auth A] MOL2 format, chain P [auth C] MOL2 format, chain X [auth D] mmCIF format, chain E [auth A] mmCIF format, chain P [auth C] mmCIF format, chain X [auth D]	E [auth A], P [auth C], X [auth D]	L(+)-TARTARIC ACID C₄ H₆ O₆ FEWJPZIEWOKRBE-JCYAYHJZSA-N		Interactions Focus chain E [auth A] Focus chain P [auth C] Focus chain X [auth D] Interactions & Density Focus chain E [auth A] Focus chain P [auth C] Focus chain X [auth D]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain BA [auth D] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain U [auth C] SDF format, chain V [auth C] SDF format, chain W [auth C] SDF format, chain Y [auth D] SDF format, chain Z [auth D] MOL2 format, chain AA [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] MOL2 format, chain Y [auth D] MOL2 format, chain Z [auth D] mmCIF format, chain AA [auth D] mmCIF format, chain BA [auth D] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C] mmCIF format, chain T [auth C] mmCIF format, chain U [auth C] mmCIF format, chain V [auth C] mmCIF format, chain W [auth C] mmCIF format, chain Y [auth D] mmCIF format, chain Z [auth D]	AA [auth D] BA [auth D] F [auth A] G [auth A] H [auth A] AA [auth D], BA [auth D], F [auth A], G [auth A], H [auth A], I [auth A], K [auth B], L [auth B], M [auth B], N [auth B], O [auth B], Q [auth C], R [auth C], S [auth C], T [auth C], U [auth C], V [auth C], W [auth C], Y [auth D], Z [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain Y [auth D] Focus chain Z [auth D]

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: 2.00 Å
R-Value Free: 0.206 (Depositor), 0.211 (DCC)
R-Value Work: 0.165 (Depositor), 0.176 (DCC)
R-Value Observed: 0.168 (Depositor)

Diffraction Data:

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.645	α = 90
b = 108.999	β = 90
c = 207.556	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2009-07-21

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2009-07-21
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Source and taxonomy, Version format compliance
Version 1.2: 2017-10-25
Changes: Author supporting evidence, Refinement description
Version 1.3: 2019-07-24
Changes: Data collection, Derived calculations, Refinement description
Version 1.4: 2023-02-01
Changes: Database references, Derived calculations