5GZJ | pdb_00005gzj

Cyclodeaminase_PA

PDB DOI: https://doi.org/10.2210/pdb5GZJ/pdb

Classification: LYASE
Organism(s): Streptomyces pristinaespiralis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2016-09-28 Released: 2018-01-17
Deposition Author(s): Ying, H., Chen, K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.87 Å
R-Value Free:
0.194 (Depositor), 0.199 (DCC)
R-Value Work:
0.153 (Depositor), 0.164 (DCC)
R-Value Observed:
0.155 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 5GZJ

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Cyclodeaminase_PA

Ying, H., Chen, K.

To be published.

Macromolecule Content

Total Structure Weight: 77.54 kDa
Atom Count: 5,858
Modeled Residue Count: 701
Deposited Residue Count: 718
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysine cyclodeaminase	A, B	359	Streptomyces pristinaespiralis	Mutation(s): 0 Gene Names: pipA, SPRI_0308, SPRI_7045 EC: 4.3.1.12
UniProt
Find proteins for D9UBW0 (Streptomyces pristinaespiralis) Explore D9UBW0 Go to UniProtKB: D9UBW0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D9UBW0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.87 Å
R-Value Free: 0.194 (Depositor), 0.199 (DCC)
R-Value Work: 0.153 (Depositor), 0.164 (DCC)
R-Value Observed: 0.155 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.604	α = 90
b = 93.25	β = 90
c = 118.524	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2018-01-17

Deposition Author(s):

Funding Organization	Location	Grant Number
	China	--

Revision History (Full details and data files)

Version 1.0: 2018-01-17
Type: Initial release
Version 1.1: 2024-03-20
Changes: Data collection, Database references

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.