1VMG | pdb_00001vmg

Crystal structure of MazG nucleotide pyrophosphohydrolase (13816655) from Sulfolobus solfataricus at 1.46 A resolution

PDB DOI: https://doi.org/10.2210/pdb1VMG/pdb

Classification: HYDROLASE
Organism(s): Saccharolobus solfataricus P2
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2004-09-24 Released: 2004-10-05
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.46 Å
R-Value Free:
0.146 (Depositor), 0.161 (DCC)
R-Value Work:
0.142 (Depositor), 0.153 (DCC)
R-Value Observed:
0.142 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 1VMG

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of MazG nucleotide pyrophosphohydrolase (13816655) from Sulfolobus solfataricus at 1.46 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 11.19 kDa
Atom Count: 826
Modeled Residue Count: 83
Deposited Residue Count: 95
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein SSO3215	A	95	Saccharolobus solfataricus P2	Mutation(s): 3 EC: 3.6.1
UniProt
Find proteins for Q97U11 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)) Explore Q97U11 Go to UniProtKB: Q97U11
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q97U11
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LI Query on LI Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	LITHIUM ION Li HBBGRARXTFLTSG-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
UNL Query on UNL Download:Ideal Coordinates CCD File	C [auth A]	Unknown ligand HBBGRARXTFLTSG-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density 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: 1.46 Å
R-Value Free: 0.146 (Depositor), 0.161 (DCC)
R-Value Work: 0.142 (Depositor), 0.153 (DCC)
R-Value Observed: 0.142 (Depositor)

Diffraction Data:

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.749	α = 90
b = 79.749	β = 90
c = 95.909	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
SCALA	data scaling
SHELX	model building
autoSHARP	phasing
REFMAC	refinement
XDS	data reduction
CCP4	data scaling
SHELX	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2004-10-05

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2004-10-05
Type: Initial release
Version 1.1: 2008-04-26
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Derived calculations, Source and taxonomy, Version format compliance
Version 1.3: 2023-12-27
Changes: Data collection, Database references, Derived calculations
Version 1.4: 2024-11-13
Changes: Structure summary

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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.