2EF5 | pdb_00002ef5

Crystal structure of the arginase from thermus thermophilus

PDB DOI: https://doi.org/10.2210/pdb2EF5/pdb

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

Deposited: 2007-02-20 Released: 2007-04-14
Deposition Author(s): Kumarevel, T.S., Karthe, P., Kuramitsu, S., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.236 (Depositor), 0.223 (DCC)
R-Value Work:
0.233 (Depositor), 0.227 (DCC)
R-Value Observed:
0.233 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of the arginase from thermus thermophilus

Kumarevel, T.S., Karthe, P., Kuramitsu, S., Yokoyama, S.

To be published.

Macromolecule Content

Total Structure Weight: 188.73 kDa
Atom Count: 13,060
Modeled Residue Count: 1,638
Deposited Residue Count: 1,740
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Arginase	A B C [auth D] D [auth E] E [auth F] A, B, C [auth D], D [auth E], E [auth F], F [auth G]	290	Thermus thermophilus	Mutation(s): 0 Gene Names: ttha1496 EC: 3.5.3.1
UniProt
Find proteins for Q5SI78 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SI78 Go to UniProtKB: Q5SI78
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5SI78
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LYS Query on LYS Download Ideal Coordinates CCD File SDF format, chain DA [auth G] SDF format, chain S [auth D] SDF format, chain W [auth E] SDF format, chain Z [auth F] SDF format, chain O [auth B] SDF format, chain K [auth A] MOL2 format, chain DA [auth G] MOL2 format, chain S [auth D] MOL2 format, chain W [auth E] MOL2 format, chain Z [auth F] MOL2 format, chain O [auth B] MOL2 format, chain K [auth A] mmCIF format, chain DA [auth G] mmCIF format, chain S [auth D] mmCIF format, chain W [auth E] mmCIF format, chain Z [auth F] mmCIF format, chain O [auth B] mmCIF format, chain K [auth A]	DA [auth G] K [auth A] O [auth B] S [auth D] W [auth E] DA [auth G], K [auth A], O [auth B], S [auth D], W [auth E], Z [auth F]	LYSINE C₆ H₁₅ N₂ O₂ KDXKERNSBIXSRK-YFKPBYRVSA-O		Interactions Focus chain DA [auth G] Focus chain K [auth A] Focus chain O [auth B] Focus chain S [auth D] Focus chain W [auth E] Focus chain Z [auth F] Interactions & Density Focus chain DA [auth G] Focus chain K [auth A] Focus chain O [auth B] Focus chain S [auth D] Focus chain W [auth E] Focus chain Z [auth F]
GAI Query on GAI Download Ideal Coordinates CCD File SDF format, chain CA [auth G] SDF format, chain I [auth A] SDF format, chain R [auth D] SDF format, chain V [auth E] SDF format, chain N [auth B] SDF format, chain J [auth A] MOL2 format, chain CA [auth G] MOL2 format, chain I [auth A] MOL2 format, chain R [auth D] MOL2 format, chain V [auth E] MOL2 format, chain N [auth B] MOL2 format, chain J [auth A] mmCIF format, chain CA [auth G] mmCIF format, chain I [auth A] mmCIF format, chain R [auth D] mmCIF format, chain V [auth E] mmCIF format, chain N [auth B] mmCIF format, chain J [auth A]	CA [auth G] I [auth A] J [auth A] N [auth B] R [auth D] CA [auth G], I [auth A], J [auth A], N [auth B], R [auth D], V [auth E]	GUANIDINE C H₅ N₃ ZRALSGWEFCBTJO-UHFFFAOYSA-N		Interactions Focus chain CA [auth G] Focus chain I [auth A] Focus chain J [auth A] Focus chain N [auth B] Focus chain R [auth D] Focus chain V [auth E] Interactions & Density Focus chain CA [auth G] Focus chain I [auth A] Focus chain J [auth A] Focus chain N [auth B] Focus chain R [auth D] Focus chain V [auth E]
MN Query on MN Download Ideal Coordinates CCD File SDF format, chain AA [auth G] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain P [auth D] SDF format, chain Y [auth F] SDF format, chain X [auth F] SDF format, chain U [auth E] SDF format, chain T [auth E] SDF format, chain Q [auth D] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain BA [auth G] MOL2 format, chain AA [auth G] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain P [auth D] MOL2 format, chain Y [auth F] MOL2 format, chain X [auth F] MOL2 format, chain U [auth E] MOL2 format, chain T [auth E] MOL2 format, chain Q [auth D] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain BA [auth G] mmCIF format, chain AA [auth G] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain P [auth D] mmCIF format, chain Y [auth F] mmCIF format, chain X [auth F] mmCIF format, chain U [auth E] mmCIF format, chain T [auth E] mmCIF format, chain Q [auth D] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain BA [auth G]	AA [auth G] BA [auth G] G [auth A] H [auth A] L [auth B] AA [auth G], BA [auth G], G [auth A], H [auth A], L [auth B], M [auth B], P [auth D], Q [auth D], T [auth E], U [auth E], X [auth F], Y [auth F]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain AA [auth G] Focus chain BA [auth G] Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain P [auth D] Focus chain Q [auth D] Focus chain T [auth E] Focus chain U [auth E] Focus chain X [auth F] Focus chain Y [auth F] Interactions & Density Focus chain AA [auth G] Focus chain BA [auth G] Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain P [auth D] Focus chain Q [auth D] Focus chain T [auth E] Focus chain U [auth E] Focus chain X [auth F] Focus chain Y [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.236 (Depositor), 0.223 (DCC)
R-Value Work: 0.233 (Depositor), 0.227 (DCC)
R-Value Observed: 0.233 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 150.795	α = 90
b = 97.478	β = 108.66
c = 126.463	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
BSS	data collection
HKL-2000	data reduction
HKL-2000	data scaling
CCP4	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2007-04-14

Deposition Author(s):

RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History (Full details and data files)

Version 1.0: 2007-04-14
Type: Initial release
Version 1.1: 2007-12-03
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.3: 2023-10-25
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.4: 2024-12-25
Changes: Advisory, Derived calculations, Structure summary