6KZW

Crystal structure of YggS family pyridoxal phosphate-dependent enzyme PipY from Fusobacterium nucleatum

PDB DOI: https://doi.org/10.2210/pdb6KZW/pdb

Classification: PROTEIN BINDING
Organism(s): Fusobacterium nucleatum subsp. nucleatum
Expression System: Escherichia coli K-12
Mutation(s): Yes

Deposited: 2019-09-25 Released: 2019-10-16
Deposition Author(s): Chen, Y., Wang, L., Shang, F., Lan, J., Liu, W., Xu, Y.
Funding Organization(s): National Natural Science Foundation of China

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.08 Å
R-Value Free: 0.217
R-Value Work: 0.173
R-Value Observed: 0.174

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of YggS family pyridoxal phosphate-dependent enzyme PipY from Fusobacterium nucleatum

Chen, Y., Wang, L., Shang, F., Lan, J., Liu, W., Xu, Y.

To be published.

Macromolecule Content

Total Structure Weight: 78.92 kDa
Atom Count: 6,055
Modelled Residue Count: 665
Deposited Residue Count: 669
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyridoxal phosphate homeostasis protein	A, B, C	223	Fusobacterium nucleatum subsp. nucleatum	Mutation(s): 2 Gene Names: RO03_02185
UniProt
Find proteins for Q8RFW9 (Fusobacterium nucleatum subsp. nucleatum (strain ATCC 25586 / DSM 15643 / BCRC 10681 / CIP 101130 / JCM 8532 / KCTC 2640 / LMG 13131 / VPI 4355)) Explore Q8RFW9 Go to UniProtKB: Q8RFW9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8RFW9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 (Subject of Investigation/LOI) Query on PO4 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth B] SDF format, chain F [auth C] MOL2 format, chain D [auth A] MOL2 format, chain E [auth B] MOL2 format, chain F [auth C]	D [auth A], E [auth B], F [auth C]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth B] Focus chain F [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: 2.08 Å
R-Value Free: 0.217
R-Value Work: 0.173
R-Value Observed: 0.174
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.929	α = 90
b = 146.375	β = 93.355
c = 74.128	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2019-10-16

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	31200556
National Natural Science Foundation of China	China	21272031

Revision History (Full details and data files)

Version 1.0: 2019-10-16
Type: Initial release
Version 1.1: 2019-12-25
Changes: Derived calculations
Version 1.2: 2021-01-13
Changes: Data collection, Refinement description

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.