3MDQ | pdb_00003mdq

Crystal structure of an Exopolyphosphatase (CHU_0316) from Cytophaga hutchinsonii ATCC 33406 at 1.50 A resolution

PDB DOI: https://doi.org/10.2210/pdb3MDQ/pdb

Classification: HYDROLASE
Organism(s): Cytophaga hutchinsonii ATCC 33406
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-03-30 Released: 2010-05-12
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.178 (Depositor), 0.190 (DCC)
R-Value Work:
0.153 (Depositor), 0.160 (DCC)
R-Value Observed:
0.154 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of an Exopolyphosphatase (CHU_0316) from Cytophaga hutchinsonii ATCC 33406 at 1.50 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 36.51 kDa
Atom Count: 3,048
Modeled Residue Count: 312
Deposited Residue Count: 315
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Exopolyphosphatase	A	315	Cytophaga hutchinsonii ATCC 33406	Mutation(s): 0 Gene Names: ppx, CHU_0316 EC: 3.6.1.11
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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 D [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain E [auth A]	D [auth A], E [auth A], F [auth A], G [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A]	H [auth A], I [auth A], J [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A]	B [auth A], C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.178 (Depositor), 0.190 (DCC)
R-Value Work: 0.153 (Depositor), 0.160 (DCC)
R-Value Observed: 0.154 (Depositor)

Diffraction Data: https://doi.org/10.18430/M33MDQ

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.687	α = 90
b = 89.335	β = 90
c = 89.374	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2010-05-12

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2010-05-12
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2017-11-08
Changes: 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: 2024-11-27
Changes: Data collection, Structure summary