1VCD | pdb_00001vcd

Crystal Structure of a T.thermophilus HB8 Ap6A hydrolase Ndx1

PDB DOI: https://doi.org/10.2210/pdb1VCD/pdb

Classification: HYDROLASE
Organism(s): Thermus thermophilus HB8
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2004-03-05 Released: 2005-04-26
Deposition Author(s): Iwai, T., Nakagawa, N., Kuramitsu, S., Masui, R., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.237 (Depositor), 0.238 (DCC)
R-Value Work:
0.214 (Depositor), 0.214 (DCC)
R-Value Observed:
0.214 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Crystal Structure of Nudix Protein Ndx1 from Thermus thermophilus HB8 in binary complex with diadenosine hexaphosphate

Iwai, T., Nakagawa, N., Kuramitsu, S., Masui, R.

To be published.

Macromolecule Content

Total Structure Weight: 28.75 kDa
Atom Count: 2,207
Modeled Residue Count: 252
Deposited Residue Count: 252
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ndx1	A, B	126	Thermus thermophilus HB8	Mutation(s): 0 Gene Names: ndx1 EC: 3.6.1.61
UniProt
Find proteins for Q75UV1 (Thermus thermophilus) Explore Q75UV1 Go to UniProtKB: Q75UV1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q75UV1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain C [auth A] MOL2 format, chain E [auth B] MOL2 format, chain C [auth A] mmCIF format, chain E [auth B] mmCIF format, chain C [auth A]	C [auth A], E [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B] mmCIF format, chain D [auth A] mmCIF format, chain F [auth B]	D [auth A], F [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.237 (Depositor), 0.238 (DCC)
R-Value Work: 0.214 (Depositor), 0.214 (DCC)
R-Value Observed: 0.214 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.559	α = 90
b = 52.324	β = 90
c = 114.009	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
MLPHARE	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2005-04-26

Deposition Author(s):

RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History (Full details and data files)

Version 1.0: 2005-04-26
Type: Initial release
Version 1.1: 2008-04-27
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.3: 2023-12-27
Changes: Data collection, Database references, Derived calculations

1VCD | pdb_00001vcd

Crystal Structure of a T.thermophilus HB8 Ap6A hydrolase Ndx1

Literature

Crystal Structure of Nudix Protein Ndx1 from Thermus thermophilus HB8 in binary complex with diadenosine hexaphosphate

Biological Assembly 1

Biological Assembly 2

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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