3NXK | pdb_00003nxk

Crystal Structure of Probable Cytoplasmic L-asparaginase from Campylobacter jejuni

PDB DOI: https://doi.org/10.2210/pdb3NXK/pdb

Classification: HYDROLASE
Organism(s): Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-07-14 Released: 2010-08-04
Deposition Author(s): Kim, Y., Makowska-Grzyska, M., Maltseva, N., Papazisi, L., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.228 (Depositor), 0.220 (DCC)
R-Value Work:
0.166 (Depositor), 0.160 (DCC)
R-Value Observed:
0.169 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Crystal Structure of Probable Cytoplasmic L-asparaginase from Campylobacter jejuni

Kim, Y., Makowska-Grzyska, M., Maltseva, N., Papazisi, L., Anderson, W.F., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 290.58 kDa
Atom Count: 20,657
Modeled Residue Count: 2,577
Deposited Residue Count: 2,672
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytoplasmic L-asparaginase	A, B, C, D, E A, B, C, D, E, F, G, H	334	Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819	Mutation(s): 0 Gene Names: ansA, Cj0029 EC: 3.5.1.1
UniProt
Find proteins for Q0PC96 (Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168)) Explore Q0PC96 Go to UniProtKB: Q0PC96
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q0PC96
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain Z [auth E] SDF format, chain W [auth D] SDF format, chain V [auth D] SDF format, chain S [auth C] SDF format, chain R [auth C] SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain KA [auth H] SDF format, chain JA [auth H] SDF format, chain J [auth A] SDF format, chain IA [auth G] SDF format, chain I [auth A] SDF format, chain HA [auth G] SDF format, chain FA [auth F] SDF format, chain EA [auth F] SDF format, chain AA [auth E] MOL2 format, chain Z [auth E] MOL2 format, chain W [auth D] MOL2 format, chain V [auth D] MOL2 format, chain S [auth C] MOL2 format, chain R [auth C] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain KA [auth H] MOL2 format, chain JA [auth H] MOL2 format, chain J [auth A] MOL2 format, chain IA [auth G] MOL2 format, chain I [auth A] MOL2 format, chain HA [auth G] MOL2 format, chain FA [auth F] MOL2 format, chain EA [auth F] MOL2 format, chain AA [auth E] mmCIF format, chain Z [auth E] mmCIF format, chain W [auth D] mmCIF format, chain V [auth D] mmCIF format, chain S [auth C] mmCIF format, chain R [auth C] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain KA [auth H] mmCIF format, chain JA [auth H] mmCIF format, chain J [auth A] mmCIF format, chain IA [auth G] mmCIF format, chain I [auth A] mmCIF format, chain HA [auth G] mmCIF format, chain FA [auth F] mmCIF format, chain EA [auth F] mmCIF format, chain AA [auth E]	AA [auth E] EA [auth F] FA [auth F] HA [auth G] I [auth A] AA [auth E], EA [auth F], FA [auth F], HA [auth G], I [auth A], IA [auth G], J [auth A], JA [auth H], KA [auth H], M [auth B], N [auth B], R [auth C], S [auth C], V [auth D], W [auth D], Z [auth E]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth E] Focus chain EA [auth F] Focus chain FA [auth F] Focus chain HA [auth G] Focus chain I [auth A] Focus chain IA [auth G] Focus chain J [auth A] Focus chain JA [auth H] Focus chain KA [auth H] Focus chain M [auth B] Focus chain N [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain V [auth D] Focus chain W [auth D] Focus chain Z [auth E] Interactions & Density Focus chain AA [auth E] Focus chain EA [auth F] Focus chain FA [auth F] Focus chain HA [auth G] Focus chain I [auth A] Focus chain IA [auth G] Focus chain J [auth A] Focus chain JA [auth H] Focus chain KA [auth H] Focus chain M [auth B] Focus chain N [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain V [auth D] Focus chain W [auth D] Focus chain Z [auth E]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain X [auth D] SDF format, chain Y [auth D] SDF format, chain T [auth C] SDF format, chain Q [auth B] SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain L [auth A] SDF format, chain DA [auth E] SDF format, chain CA [auth E] SDF format, chain BA [auth E] MOL2 format, chain X [auth D] MOL2 format, chain Y [auth D] MOL2 format, chain T [auth C] MOL2 format, chain Q [auth B] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain L [auth A] MOL2 format, chain DA [auth E] MOL2 format, chain CA [auth E] MOL2 format, chain BA [auth E] mmCIF format, chain X [auth D] mmCIF format, chain Y [auth D] mmCIF format, chain T [auth C] mmCIF format, chain Q [auth B] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain L [auth A] mmCIF format, chain DA [auth E] mmCIF format, chain CA [auth E] mmCIF format, chain BA [auth E]	BA [auth E] CA [auth E] DA [auth E] L [auth A] O [auth B] BA [auth E], CA [auth E], DA [auth E], L [auth A], O [auth B], P [auth B], Q [auth B], T [auth C], X [auth D], Y [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain BA [auth E] Focus chain CA [auth E] Focus chain DA [auth E] Focus chain L [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain T [auth C] Focus chain X [auth D] Focus chain Y [auth D] Interactions & Density Focus chain BA [auth E] Focus chain CA [auth E] Focus chain DA [auth E] Focus chain L [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain T [auth C] Focus chain X [auth D] Focus chain Y [auth D]
ACY Query on ACY Download Ideal Coordinates CCD File SDF format, chain U [auth C] SDF format, chain K [auth A] SDF format, chain GA [auth F] MOL2 format, chain U [auth C] MOL2 format, chain K [auth A] MOL2 format, chain GA [auth F] mmCIF format, chain U [auth C] mmCIF format, chain K [auth A] mmCIF format, chain GA [auth F]	GA [auth F], K [auth A], U [auth C]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain GA [auth F] Focus chain K [auth A] Focus chain U [auth C] Interactions & Density Focus chain GA [auth F] Focus chain K [auth A] Focus chain U [auth C]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E A, B, C, D, E, F, G, H	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.228 (Depositor), 0.220 (DCC)
R-Value Work: 0.166 (Depositor), 0.160 (DCC)
R-Value Observed: 0.169 (Depositor)

Diffraction Data: https://doi.org/10.18430/m33nxk

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.321	α = 90
b = 127.653	β = 103.05
c = 149.832	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	phasing
BALBES	phasing
MOLREP	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2010-08-04

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2010-08-04
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2023-11-22
Changes: Data collection
Version 1.4: 2024-11-27
Changes: Structure summary