3NO4 | pdb_00003no4

Crystal structure of a creatinine amidohydrolase (Npun_F1913) from Nostoc punctiforme PCC 73102 at 2.00 A resolution

PDB DOI: https://doi.org/10.2210/pdb3NO4/pdb

Classification: HYDROLASE
Organism(s): Nostoc punctiforme PCC 73102
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-06-24 Released: 2010-08-25
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.192 (Depositor), 0.200 (DCC)
R-Value Work:
0.151 (Depositor), 0.160 (DCC)
R-Value Observed:
0.153 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of a creatinine amidohydrolase (Npun_F1913) from Nostoc punctiforme PCC 73102 at 2.00 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 88.93 kDa
Atom Count: 6,708
Modeled Residue Count: 770
Deposited Residue Count: 801
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
creatinine amidohydrolase	A, B, C	267	Nostoc punctiforme PCC 73102	Mutation(s): 0 Gene Names: NPUN_22DEC03_CONTIG1_REVISED_GENENPF1913, Npun_F1913
UniProt
Find proteins for B2J3U5 (Nostoc punctiforme (strain ATCC 29133 / PCC 73102)) Explore B2J3U5 Go to UniProtKB: B2J3U5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B2J3U5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain R [auth B] SDF format, chain Z [auth C] SDF format, chain Y [auth C] SDF format, chain X [auth C] SDF format, chain W [auth C] SDF format, chain V [auth C] SDF format, chain S [auth B] SDF format, chain Q [auth B] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain I [auth A] SDF format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain R [auth B] MOL2 format, chain Z [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain X [auth C] MOL2 format, chain W [auth C] MOL2 format, chain V [auth C] MOL2 format, chain S [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain I [auth A] MOL2 format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain R [auth B] mmCIF format, chain Z [auth C] mmCIF format, chain Y [auth C] mmCIF format, chain X [auth C] mmCIF format, chain W [auth C] mmCIF format, chain V [auth C] mmCIF format, chain S [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain I [auth A] mmCIF format, chain G [auth A]	G [auth A] H [auth A] I [auth A] L [auth B] M [auth B] G [auth A], H [auth A], I [auth A], L [auth B], M [auth B], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B], V [auth C], W [auth C], X [auth C], Y [auth C], Z [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C]
NI Query on NI Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain J [auth B] SDF format, chain T [auth C] MOL2 format, chain D [auth A] MOL2 format, chain J [auth B] MOL2 format, chain T [auth C] mmCIF format, chain D [auth A] mmCIF format, chain J [auth B] mmCIF format, chain T [auth C]	D [auth A], J [auth B], T [auth C]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain J [auth B] Focus chain T [auth C] Interactions & Density Focus chain D [auth A] Focus chain J [auth B] Focus chain T [auth C]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
UNL Query on UNL Download Ideal Coordinates CCD File	E [auth A], K [auth B], U [auth C]	Unknown ligand VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain K [auth B] Focus chain U [auth C] Interactions & Density Focus chain E [auth A] Focus chain K [auth B] Focus chain U [auth C]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C	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: 0.192 (Depositor), 0.200 (DCC)
R-Value Work: 0.151 (Depositor), 0.160 (DCC)
R-Value Observed: 0.153 (Depositor)

Diffraction Data: https://doi.org/10.18430/M33NO4

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.085	α = 90
b = 89.085	β = 90
c = 211.563	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SOLVE	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: 2010-08-25

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2010-08-25
Type: Initial release
Version 1.1: 2011-07-13
Changes: 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