3AW8 | pdb_00003aw8

Crystal structure of N5-carboxyaminoimidazole ribonucleotide synthetase from Thermus thermophilus HB8

PDB DOI: https://doi.org/10.2210/pdb3AW8/pdb

Classification: LIGASE
Organism(s): Thermus thermophilus HB8
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2011-03-15 Released: 2012-04-11
Deposition Author(s): Okada, K., Tsunoda, S., Taka, H., Baba, S., Kanagawa, M., Nakagawa, N., Ebihara, A., Kuramitsu, S., Yokoyama, S., Kawai, G., Sampei, G., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.255 (Depositor), 0.232 (DCC)
R-Value Work:
0.209 (Depositor), 0.214 (DCC)
R-Value Observed:
0.209 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3AW8

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal structures of N5-carboxyaminoimidazole ribonucleotide synthetase, PurK, from thermophilic bacteria

Okada, K., Taka, H., Tsunoda, S., Tamura, S., Miyazawa, R., Baba, S., Kanagawa, M., Nakagawa, N., Ebihara, A., Kuramitsu, S., Yokoyama, S., Kawai, G., Sampei, G.

To be published.

Macromolecule Content

Total Structure Weight: 81.1 kDa
Atom Count: 5,804
Modeled Residue Count: 720
Deposited Residue Count: 738
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoribosylaminoimidazole carboxylase, ATPase subunit	A, B	369	Thermus thermophilus HB8	Mutation(s): 0 Gene Names: TTHA0513 EC: 6.3.4.18
UniProt
Find proteins for Q5SKY0 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SKY0 Go to UniProtKB: Q5SKY0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5SKY0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AMP Query on AMP 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]	ADENOSINE MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P UDMBCSSLTHHNCD-KQYNXXCUSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain F [auth B] SDF format, chain D [auth A] MOL2 format, chain G [auth B] MOL2 format, chain F [auth B] MOL2 format, chain D [auth A] mmCIF format, chain G [auth B] mmCIF format, chain F [auth B] mmCIF format, chain D [auth A]	D [auth A], F [auth B], G [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain F [auth B] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B] Focus chain G [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.255 (Depositor), 0.232 (DCC)
R-Value Work: 0.209 (Depositor), 0.214 (DCC)
R-Value Observed: 0.209 (Depositor)

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.26	α = 90
b = 81.26	β = 90
c = 203.163	γ = 90

Software Package:

Software Name	Purpose
BSS	data collection
AMoRE	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2012-04-11

Deposition Author(s):

RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History (Full details and data files)

Version 1.0: 2012-04-11
Type: Initial release
Version 1.1: 2024-03-13
Changes: Data collection, Database references, Derived calculations

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