4QYI | pdb_00004qyi

1.95 Angstrom resolution crystal structure of a hypoxanthine-guanine phosphoribosyltransferase (hpt-2) from Bacillus anthracis str. 'Ames Ancestor' with HEPES molecule in the active site

PDB DOI: https://doi.org/10.2210/pdb4QYI/pdb

Classification: TRANSFERASE
Organism(s): Bacillus anthracis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2014-07-24 Released: 2014-08-27
Deposition Author(s): Halavaty, A.S., Minasov, G., Dubrovska, I., Winsor, J., Shuvalova, L., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.252 (Depositor), 0.257 (DCC)
R-Value Work:
0.221 (Depositor), 0.225 (DCC)
R-Value Observed:
0.223 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

1.95 Angstrom resolution crystal structure of a hypoxanthine-guanine phosphoribosyltransferase (hpt-2) from Bacillus anthracis str. 'Ames Ancestor' with HEPES molecule in the active site

Halavaty, A.S., Minasov, G., Dubrovska, I., Winsor, J., Shuvalova, L., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 107.73 kDa
Atom Count: 7,518
Modeled Residue Count: 850
Deposited Residue Count: 930
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypoxanthine phosphoribosyltransferase	A	186	Bacillus anthracis	Mutation(s): 0 Gene Names: BAS4712, BA_5074, GBAA_5074, hpt-2, hpt2 EC: 2.4.2.8
UniProt
Find proteins for A0A6L8PVA4 (Bacillus anthracis) Explore A0A6L8PVA4 Go to UniProtKB: A0A6L8PVA4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A6L8PVA4
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypoxanthine phosphoribosyltransferase	B, C, D, E	186	Bacillus anthracis	Mutation(s): 0 Gene Names: BAS4712, BA_5074, GBAA_5074, hpt-2, hpt2 EC: 2.4.2.8
UniProt
Find proteins for A0A6L8PVA4 (Bacillus anthracis) Explore A0A6L8PVA4 Go to UniProtKB: A0A6L8PVA4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A6L8PVA4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EPE Query on EPE Download:Ideal Coordinates CCD File SDF format, chain Z [auth E] SDF format, chain P [auth C] SDF format, chain L [auth B] MOL2 format, chain Z [auth E] MOL2 format, chain P [auth C] MOL2 format, chain L [auth B] mmCIF format, chain Z [auth E] mmCIF format, chain P [auth C] mmCIF format, chain L [auth B]	L [auth B], P [auth C], Z [auth E]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain L [auth B] Focus chain P [auth C] Focus chain Z [auth E] Interactions & Density Focus chain L [auth B] Focus chain P [auth C] Focus chain Z [auth E]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain Y [auth E] SDF format, chain X [auth E] SDF format, chain S [auth D] SDF format, chain R [auth D] SDF format, chain O [auth C] SDF format, chain K [auth B] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain Y [auth E] MOL2 format, chain X [auth E] MOL2 format, chain S [auth D] MOL2 format, chain R [auth D] MOL2 format, chain O [auth C] MOL2 format, chain K [auth B] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain Y [auth E] mmCIF format, chain X [auth E] mmCIF format, chain S [auth D] mmCIF format, chain R [auth D] mmCIF format, chain O [auth C] mmCIF format, chain K [auth B] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A] H [auth A] K [auth B] O [auth C] R [auth D] G [auth A], H [auth A], K [auth B], O [auth C], R [auth D], S [auth D], X [auth E], Y [auth E]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain R [auth D] Focus chain S [auth D] Focus chain X [auth E] Focus chain Y [auth E] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain R [auth D] Focus chain S [auth D] Focus chain X [auth E] Focus chain Y [auth E]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain W [auth E] MOL2 format, chain W [auth E] mmCIF format, chain W [auth E]	W [auth E]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain W [auth E] Interactions & Density Focus chain W [auth E]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain V [auth E] SDF format, chain U [auth E] SDF format, chain T [auth E] SDF format, chain Q [auth D] SDF format, chain N [auth C] SDF format, chain M [auth C] SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain F [auth A] MOL2 format, chain V [auth E] MOL2 format, chain U [auth E] MOL2 format, chain T [auth E] MOL2 format, chain Q [auth D] MOL2 format, chain N [auth C] MOL2 format, chain M [auth C] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain F [auth A] mmCIF format, chain V [auth E] mmCIF format, chain U [auth E] mmCIF format, chain T [auth E] mmCIF format, chain Q [auth D] mmCIF format, chain N [auth C] mmCIF format, chain M [auth C] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain F [auth A]	F [auth A] I [auth B] J [auth B] M [auth C] N [auth C] F [auth A], I [auth B], J [auth B], M [auth C], N [auth C], Q [auth D], T [auth E], U [auth E], V [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain Q [auth D] Focus chain T [auth E] Focus chain U [auth E] Focus chain V [auth E] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain Q [auth D] Focus chain T [auth E] Focus chain U [auth E] Focus chain V [auth E]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CME Query on CME	B, C, D, E	L-PEPTIDE LINKING	C₅ H₁₁ N O₃ S₂		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.252 (Depositor), 0.257 (DCC)
R-Value Work: 0.221 (Depositor), 0.225 (DCC)
R-Value Observed: 0.223 (Depositor)

Diffraction Data:

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 172.779	α = 90
b = 117.009	β = 90.96
c = 56.883	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2014-08-27

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2014-08-27
Type: Initial release
Version 1.1: 2017-11-22
Changes: Refinement description
Version 1.2: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2024-11-06
Changes: Structure summary