3K7C | pdb_00003k7c

Crystal structure of Putative NTF2-like transpeptidase (NP_281412.1) from CAMPYLOBACTER JEJUNI at 2.00 A resolution

PDB DOI: https://doi.org/10.2210/pdb3K7C/pdb

Classification: PROTEIN BINDING
Organism(s): Campylobacter jejuni
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-10-12 Released: 2009-11-03
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.256 (Depositor), 0.280 (DCC)
R-Value Work:
0.214 (Depositor), 0.230 (DCC)
R-Value Observed:
0.216 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Crystal structure of Putative NTF2-like transpeptidase (NP_281412.1) from CAMPYLOBACTER JEJUNI at 2.00 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 53.9 kDa
Atom Count: 3,664
Modeled Residue Count: 432
Deposited Residue Count: 456
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative NTF2-like transpeptidase	A, B, C, D	114	Campylobacter jejuni	Mutation(s): 0 Gene Names: Cj0202c
UniProt
Find proteins for Q0PBT7 (Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168)) Explore Q0PBT7 Go to UniProtKB: Q0PBT7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q0PBT7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain X [auth D] SDF format, chain W [auth D] SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain H [auth A] MOL2 format, chain X [auth D] MOL2 format, chain W [auth D] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain H [auth A] mmCIF format, chain X [auth D] mmCIF format, chain W [auth D] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain H [auth A]	H [auth A] L [auth B] M [auth B] N [auth B] W [auth D] H [auth A], L [auth B], M [auth B], N [auth B], W [auth D], X [auth D]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain W [auth D] Focus chain X [auth D] Interactions & Density Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain W [auth D] Focus chain X [auth D]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain Q [auth C] SDF format, chain V [auth D] SDF format, chain U [auth C] SDF format, chain T [auth C] SDF format, chain S [auth C] SDF format, chain R [auth C] SDF format, chain P [auth C] SDF format, chain O [auth C] SDF format, chain K [auth B] SDF format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain V [auth D] MOL2 format, chain U [auth C] MOL2 format, chain T [auth C] MOL2 format, chain S [auth C] MOL2 format, chain R [auth C] MOL2 format, chain P [auth C] MOL2 format, chain O [auth C] MOL2 format, chain K [auth B] MOL2 format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain V [auth D] mmCIF format, chain U [auth C] mmCIF format, chain T [auth C] mmCIF format, chain S [auth C] mmCIF format, chain R [auth C] mmCIF format, chain P [auth C] mmCIF format, chain O [auth C] mmCIF format, chain K [auth B] mmCIF format, chain F [auth A]	F [auth A] G [auth A] I [auth B] J [auth B] K [auth B] F [auth A], G [auth A], I [auth B], J [auth B], K [auth B], O [auth C], P [auth C], Q [auth C], R [auth C], S [auth C], T [auth C], U [auth C], V [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain O [auth C] Focus chain P [auth C] 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 D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain O [auth C] Focus chain P [auth C] 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 D]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]

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: 0.256 (Depositor), 0.280 (DCC)
R-Value Work: 0.214 (Depositor), 0.230 (DCC)
R-Value Observed: 0.216 (Depositor)

Diffraction Data: https://doi.org/10.18430/M33K7C

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.442	α = 90
b = 89.807	β = 110.5
c = 59.665	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
SHELXD	phasing
autoSHARP	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2009-11-03

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2009-11-03
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2017-10-25
Changes: Author supporting evidence, Refinement description
Version 1.3: 2019-07-17
Changes: Data collection, Derived calculations, Refinement description
Version 1.4: 2023-02-01
Changes: Database references, Derived calculations
Version 1.5: 2024-10-16
Changes: Data collection, Refinement description, Structure summary