7XIN | pdb_00007xin

Crystal structure of DODC from Pseudomonas

PDB DOI: https://doi.org/10.2210/pdb7XIN/pdb

Classification: LYASE
Organism(s): Pseudomonas
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2022-04-13 Released: 2023-04-19
Deposition Author(s): Li, X., Zhou, Y.L., Liao, L.J., Liu, X.K., Liu, B., Guo, Y., Feng, Z., Sun, D.Y., Zeng, Z.X.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.521 (Depositor), 0.513 (DCC)
R-Value Work:
0.473 (Depositor), 0.469 (DCC)
R-Value Observed:
0.475 (Depositor)

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of DODC from Pseudomonas

Li, X., Zhou, Y.L., Liao, L.J., Liu, X.K., Liu, B., Guo, Y., Feng, Z., Sun, D.Y., Zeng, Z.X.

To be published.

Macromolecule Content

Total Structure Weight: 157.4 kDa
Atom Count: 10,953
Modeled Residue Count: 1,410
Deposited Residue Count: 1,428
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DOPA decarboxylase	A, B [auth C], C [auth E]	476	Pseudomonas	Mutation(s): 0 EC: 4.1.1.28
UniProt
Find proteins for Q88JU5 (Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)) Explore Q88JU5 Go to UniProtKB: Q88JU5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q88JU5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PLP (Subject of Investigation/LOI) Query on PLP Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth C] SDF format, chain F [auth E] MOL2 format, chain D [auth A] MOL2 format, chain E [auth C] MOL2 format, chain F [auth E] mmCIF format, chain D [auth A] mmCIF format, chain E [auth C] mmCIF format, chain F [auth E]	D [auth A], E [auth C], F [auth E]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth C] Focus chain F [auth E] Interactions & Density Focus chain D [auth A] Focus chain E [auth C] Focus chain F [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.521 (Depositor), 0.513 (DCC)
R-Value Work: 0.473 (Depositor), 0.469 (DCC)
R-Value Observed: 0.475 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.767	α = 90.27
b = 67.014	β = 92.38
c = 168.576	γ = 90.36

Software Package:

Software Name	Purpose
HKL-2000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
xia2	data reduction
PHENIX	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-04-19

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History (Full details and data files)

Version 1.0: 2023-04-19
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Refinement description

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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.