3A4Y | pdb_00003a4y

Crystal Structure of H61A mutant TTHA0252 from Thermus thermophilus HB8

PDB DOI: https://doi.org/10.2210/pdb3A4Y/pdb
Entry: 3A4Y supersedes: 2ZDW

Classification: HYDROLASE
Organism(s): Thermus thermophilus HB8
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2009-07-22 Released: 2009-08-04
Deposition Author(s): Ishikawa, H., Nakagawa, N., Kuramitsu, S., Yokoyama, S., Masui, R., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.282 (Depositor), 0.270 (DCC)
R-Value Work:
0.239 (Depositor), 0.230 (DCC)

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 H61A mutant TTHA0252 from Thermus thermophilus HB8

Ishikawa, H., Nakagawa, N., Kuramitsu, S., Masui, R.

To be published.

Macromolecule Content

Total Structure Weight: 194.41 kDa
Atom Count: 13,743
Modeled Residue Count: 1,724
Deposited Residue Count: 1,724
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribonuclease TTHA0252	A, B, C, D	431	Thermus thermophilus HB8	Mutation(s): 1 Gene Names: TTHA0252 EC: 3.1
UniProt
Find proteins for Q5SLP1 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SLP1 Go to UniProtKB: Q5SLP1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5SLP1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FLC Query on FLC Download Ideal Coordinates CCD File SDF format, chain X [auth A] SDF format, chain OA [auth B] SDF format, chain DB [auth C] MOL2 format, chain X [auth A] MOL2 format, chain OA [auth B] MOL2 format, chain DB [auth C] mmCIF format, chain X [auth A] mmCIF format, chain OA [auth B] mmCIF format, chain DB [auth C]	DB [auth C], OA [auth B], X [auth A]	CITRATE ANION C₆ H₅ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-K		Interactions Focus chain DB [auth C] Focus chain OA [auth B] Focus chain X [auth A] Interactions & Density Focus chain DB [auth C] Focus chain OA [auth B] Focus chain X [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain ZA [auth C] SDF format, chain Z [auth B] SDF format, chain YA [auth C] SDF format, chain XA [auth C] SDF format, chain WA [auth C] SDF format, chain W [auth A] SDF format, chain VA [auth C] SDF format, chain V [auth A] SDF format, chain UA [auth C] SDF format, chain U [auth A] SDF format, chain TA [auth C] SDF format, chain T [auth A] SDF format, chain SA [auth C] SDF format, chain S [auth A] SDF format, chain RA [auth C] SDF format, chain R [auth A] SDF format, chain QA [auth C] SDF format, chain Q [auth A] SDF format, chain P [auth A] SDF format, chain O [auth A] SDF format, chain NB [auth D] SDF format, chain NA [auth B] SDF format, chain N [auth A] SDF format, chain MB [auth D] SDF format, chain MA [auth B] SDF format, chain M [auth A] SDF format, chain LB [auth D] SDF format, chain LA [auth B] SDF format, chain L [auth A] SDF format, chain KB [auth D] SDF format, chain KA [auth B] SDF format, chain K [auth A] SDF format, chain JB [auth D] SDF format, chain JA [auth B] SDF format, chain J [auth A] SDF format, chain IB [auth D] SDF format, chain IA [auth B] SDF format, chain I [auth A] SDF format, chain HB [auth D] SDF format, chain HA [auth B] SDF format, chain H [auth A] SDF format, chain GB [auth D] SDF format, chain GA [auth B] SDF format, chain G [auth A] SDF format, chain FB [auth D] SDF format, chain FA [auth B] SDF format, chain F [auth A] SDF format, chain EA [auth B] SDF format, chain E [auth A] SDF format, chain DA [auth B] SDF format, chain CB [auth C] SDF format, chain CA [auth B] SDF format, chain BB [auth C] SDF format, chain BA [auth B] SDF format, chain AB [auth C] SDF format, chain AA [auth B] MOL2 format, chain ZA [auth C] MOL2 format, chain Z [auth B] MOL2 format, chain YA [auth C] MOL2 format, chain XA [auth C] MOL2 format, chain WA [auth C] MOL2 format, chain W [auth A] MOL2 format, chain VA [auth C] MOL2 format, chain V [auth A] MOL2 format, chain UA [auth C] MOL2 format, chain U [auth A] MOL2 format, chain TA [auth C] MOL2 format, chain T [auth A] MOL2 format, chain SA [auth C] MOL2 format, chain S [auth A] MOL2 format, chain RA [auth C] MOL2 format, chain R [auth A] MOL2 format, chain QA [auth C] MOL2 format, chain Q [auth A] MOL2 format, chain P [auth A] MOL2 format, chain O [auth A] MOL2 format, chain NB [auth D] MOL2 format, chain NA [auth B] MOL2 format, chain N [auth A] MOL2 format, chain MB [auth D] MOL2 format, chain MA [auth B] MOL2 format, chain M [auth A] MOL2 format, chain LB [auth D] MOL2 format, chain LA [auth B] MOL2 format, chain L [auth A] MOL2 format, chain KB [auth D] MOL2 format, chain KA [auth B] MOL2 format, chain K [auth A] MOL2 format, chain JB [auth D] MOL2 format, chain JA [auth B] MOL2 format, chain J [auth A] MOL2 format, chain IB [auth D] MOL2 format, chain IA [auth B] MOL2 format, chain I [auth A] MOL2 format, chain HB [auth D] MOL2 format, chain HA [auth B] MOL2 format, chain H [auth A] MOL2 format, chain GB [auth D] MOL2 format, chain GA [auth B] MOL2 format, chain G [auth A] MOL2 format, chain FB [auth D] MOL2 format, chain FA [auth B] MOL2 format, chain F [auth A] MOL2 format, chain EA [auth B] MOL2 format, chain E [auth A] MOL2 format, chain DA [auth B] MOL2 format, chain CB [auth C] MOL2 format, chain CA [auth B] MOL2 format, chain BB [auth C] MOL2 format, chain BA [auth B] MOL2 format, chain AB [auth C] MOL2 format, chain AA [auth B] mmCIF format, chain ZA [auth C] mmCIF format, chain Z [auth B] mmCIF format, chain YA [auth C] mmCIF format, chain XA [auth C] mmCIF format, chain WA [auth C] mmCIF format, chain W [auth A] mmCIF format, chain VA [auth C] mmCIF format, chain V [auth A] mmCIF format, chain UA [auth C] mmCIF format, chain U [auth A] mmCIF format, chain TA [auth C] mmCIF format, chain T [auth A] mmCIF format, chain SA [auth C] mmCIF format, chain S [auth A] mmCIF format, chain RA [auth C] mmCIF format, chain R [auth A] mmCIF format, chain QA [auth C] mmCIF format, chain Q [auth A] mmCIF format, chain P [auth A] mmCIF format, chain O [auth A] mmCIF format, chain NB [auth D] mmCIF format, chain NA [auth B] mmCIF format, chain N [auth A] mmCIF format, chain MB [auth D] mmCIF format, chain MA [auth B] mmCIF format, chain M [auth A] mmCIF format, chain LB [auth D] mmCIF format, chain LA [auth B] mmCIF format, chain L [auth A] mmCIF format, chain KB [auth D] mmCIF format, chain KA [auth B] mmCIF format, chain K [auth A] mmCIF format, chain JB [auth D] mmCIF format, chain JA [auth B] mmCIF format, chain J [auth A] mmCIF format, chain IB [auth D] mmCIF format, chain IA [auth B] mmCIF format, chain I [auth A] mmCIF format, chain HB [auth D] mmCIF format, chain HA [auth B] mmCIF format, chain H [auth A] mmCIF format, chain GB [auth D] mmCIF format, chain GA [auth B] mmCIF format, chain G [auth A] mmCIF format, chain FB [auth D] mmCIF format, chain FA [auth B] mmCIF format, chain F [auth A] mmCIF format, chain EA [auth B] mmCIF format, chain E [auth A] mmCIF format, chain DA [auth B] mmCIF format, chain CB [auth C] mmCIF format, chain CA [auth B] mmCIF format, chain BB [auth C] mmCIF format, chain BA [auth B] mmCIF format, chain AB [auth C] mmCIF format, chain AA [auth B]	AA [auth B] AB [auth C] BA [auth B] BB [auth C] CA [auth B] AA [auth B], AB [auth C], BA [auth B], BB [auth C], CA [auth B], CB [auth C], DA [auth B], E [auth A], EA [auth B], F [auth A], FA [auth B], FB [auth D], G [auth A], GA [auth B], GB [auth D], H [auth A], HA [auth B], HB [auth D], I [auth A], IA [auth B], IB [auth D], J [auth A], JA [auth B], JB [auth D], K [auth A], KA [auth B], KB [auth D], L [auth A], LA [auth B], LB [auth D], M [auth A], MA [auth B], MB [auth D], N [auth A], NA [auth B], NB [auth D], O [auth A], P [auth A], Q [auth A], QA [auth C], R [auth A], RA [auth C], S [auth A], SA [auth C], T [auth A], TA [auth C], U [auth A], UA [auth C], V [auth A], VA [auth C], W [auth A], WA [auth C], XA [auth C], YA [auth C], Z [auth B], ZA [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth B] Focus chain AB [auth C] Focus chain BA [auth B] Focus chain BB [auth C] Focus chain CA [auth B] Focus chain CB [auth C] Focus chain DA [auth B] Focus chain E [auth A] Focus chain EA [auth B] Focus chain F [auth A] Focus chain FA [auth B] Focus chain FB [auth D] Focus chain G [auth A] Focus chain GA [auth B] Focus chain GB [auth D] Focus chain H [auth A] Focus chain HA [auth B] Focus chain HB [auth D] Focus chain I [auth A] Focus chain IA [auth B] Focus chain IB [auth D] Focus chain J [auth A] Focus chain JA [auth B] Focus chain JB [auth D] Focus chain K [auth A] Focus chain KA [auth B] Focus chain KB [auth D] Focus chain L [auth A] Focus chain LA [auth B] Focus chain LB [auth D] Focus chain M [auth A] Focus chain MA [auth B] Focus chain MB [auth D] Focus chain N [auth A] Focus chain NA [auth B] Focus chain NB [auth D] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain QA [auth C] Focus chain R [auth A] Focus chain RA [auth C] Focus chain S [auth A] Focus chain SA [auth C] Focus chain T [auth A] Focus chain TA [auth C] Focus chain U [auth A] Focus chain UA [auth C] Focus chain V [auth A] Focus chain VA [auth C] Focus chain W [auth A] Focus chain WA [auth C] Focus chain XA [auth C] Focus chain YA [auth C] Focus chain Z [auth B] Focus chain ZA [auth C] Interactions & Density Focus chain AA [auth B] Focus chain AB [auth C] Focus chain BA [auth B] Focus chain BB [auth C] Focus chain CA [auth B] Focus chain CB [auth C] Focus chain DA [auth B] Focus chain E [auth A] Focus chain EA [auth B] Focus chain F [auth A] Focus chain FA [auth B] Focus chain FB [auth D] Focus chain G [auth A] Focus chain GA [auth B] Focus chain GB [auth D] Focus chain H [auth A] Focus chain HA [auth B] Focus chain HB [auth D] Focus chain I [auth A] Focus chain IA [auth B] Focus chain IB [auth D] Focus chain J [auth A] Focus chain JA [auth B] Focus chain JB [auth D] Focus chain K [auth A] Focus chain KA [auth B] Focus chain KB [auth D] Focus chain L [auth A] Focus chain LA [auth B] Focus chain LB [auth D] Focus chain M [auth A] Focus chain MA [auth B] Focus chain MB [auth D] Focus chain N [auth A] Focus chain NA [auth B] Focus chain NB [auth D] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain QA [auth C] Focus chain R [auth A] Focus chain RA [auth C] Focus chain S [auth A] Focus chain SA [auth C] Focus chain T [auth A] Focus chain TA [auth C] Focus chain U [auth A] Focus chain UA [auth C] Focus chain V [auth A] Focus chain VA [auth C] Focus chain W [auth A] Focus chain WA [auth C] Focus chain XA [auth C] Focus chain YA [auth C] Focus chain Z [auth B] Focus chain ZA [auth C]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain Y [auth A] SDF format, chain PA [auth B] SDF format, chain OB [auth D] SDF format, chain EB [auth C] MOL2 format, chain Y [auth A] MOL2 format, chain PA [auth B] MOL2 format, chain OB [auth D] MOL2 format, chain EB [auth C] mmCIF format, chain Y [auth A] mmCIF format, chain PA [auth B] mmCIF format, chain OB [auth D] mmCIF format, chain EB [auth C]	EB [auth C], OB [auth D], PA [auth B], Y [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain EB [auth C] Focus chain OB [auth D] Focus chain PA [auth B] Focus chain Y [auth A] Interactions & Density Focus chain EB [auth C] Focus chain OB [auth D] Focus chain PA [auth B] Focus chain Y [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.282 (Depositor), 0.270 (DCC)
R-Value Work: 0.239 (Depositor), 0.230 (DCC)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 143.144	α = 90
b = 146.767	β = 109.24
c = 121.123	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
XFIT	data reduction

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2009-08-04

Deposition Author(s):

RIKEN Structural Genomics/Proteomics Initiative (RSGI)

This entry supersedes: 2ZDW

Revision History (Full details and data files)

Version 1.0: 2009-08-04
Type: Initial release
Version 1.1: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.2: 2017-10-11
Changes: Refinement description
Version 1.3: 2021-11-10
Changes: Database references, Derived calculations
Version 1.4: 2023-11-01
Changes: Data collection, Refinement description