3IDZ | pdb_00003idz

Crystal Structure of S378Q mutant TTHA0252 from Thermus thermophilus HB8

PDB DOI: https://doi.org/10.2210/pdb3IDZ/pdb
Entry: 3IDZ supersedes: 2ZDF

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:
0.278 (Depositor), 0.272 (DCC)
R-Value Work:
0.240 (Depositor), 0.235 (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 S378Q mutant TTHA0252 from Thermus thermophilus HB8

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

To be published.

Macromolecule Content

Total Structure Weight: 196.07 kDa
Atom Count: 13,823
Modeled Residue Count: 1,724
Deposited Residue Count: 1,724
Unique protein chains: 1

Macromolecules

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| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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 BB [auth B] SDF format, chain AB [auth B] SDF format, chain AA [auth A] MOL2 format, chain BB [auth B] MOL2 format, chain AB [auth B] MOL2 format, chain AA [auth A] mmCIF format, chain BB [auth B] mmCIF format, chain AB [auth B] mmCIF format, chain AA [auth A]	AA [auth A], AB [auth B], BB [auth B]	CITRATE ANION C₆ H₅ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-K		Interactions Focus chain AA [auth A] Focus chain AB [auth B] Focus chain BB [auth B] Interactions & Density Focus chain AA [auth A] Focus chain AB [auth B] Focus chain BB [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain AC [auth D] SDF format, chain EA [auth B] SDF format, chain EB [auth C] SDF format, chain GB [auth C] SDF format, chain H [auth A] SDF format, chain HA [auth B] SDF format, chain HB [auth C] SDF format, chain I [auth A] SDF format, chain IA [auth B] SDF format, chain IB [auth C] SDF format, chain JA [auth B] SDF format, chain JB [auth C] SDF format, chain K [auth A] SDF format, chain KA [auth B] SDF format, chain KB [auth C] SDF format, chain LA [auth B] SDF format, chain LB [auth C] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain NA [auth B] SDF format, chain NB [auth C] SDF format, chain OB [auth C] SDF format, chain P [auth A] SDF format, chain PA [auth B] SDF format, chain Q [auth A] SDF format, chain QB [auth C] SDF format, chain R [auth A] SDF format, chain RA [auth B] SDF format, chain S [auth A] SDF format, chain SA [auth B] SDF format, chain SB [auth C] SDF format, chain T [auth A] SDF format, chain TA [auth B] SDF format, chain V [auth A] SDF format, chain VB [auth D] SDF format, chain XA [auth B] SDF format, chain XB [auth D] SDF format, chain Y [auth A] SDF format, chain ZB [auth D] SDF format, chain ZA [auth B] SDF format, chain Z [auth A] SDF format, chain YB [auth D] SDF format, chain YA [auth B] SDF format, chain X [auth A] SDF format, chain WB [auth D] SDF format, chain WA [auth B] SDF format, chain W [auth A] SDF format, chain VA [auth B] SDF format, chain UA [auth B] SDF format, chain U [auth A] SDF format, chain RB [auth C] SDF format, chain QA [auth B] SDF format, chain PB [auth C] SDF format, chain OA [auth B] SDF format, chain O [auth A] SDF format, chain MB [auth C] SDF format, chain MA [auth B] SDF format, chain L [auth A] SDF format, chain J [auth A] SDF format, chain GA [auth B] SDF format, chain G [auth A] SDF format, chain FB [auth C] SDF format, chain FA [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain DA [auth B] MOL2 format, chain AC [auth D] MOL2 format, chain EA [auth B] MOL2 format, chain EB [auth C] MOL2 format, chain GB [auth C] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth B] MOL2 format, chain HB [auth C] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth B] MOL2 format, chain IB [auth C] MOL2 format, chain JA [auth B] MOL2 format, chain JB [auth C] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth B] MOL2 format, chain KB [auth C] MOL2 format, chain LA [auth B] MOL2 format, chain LB [auth C] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth B] MOL2 format, chain NB [auth C] MOL2 format, chain OB [auth C] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain QB [auth C] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth B] MOL2 format, chain S [auth A] MOL2 format, chain SA [auth B] MOL2 format, chain SB [auth C] MOL2 format, chain T [auth A] MOL2 format, chain TA [auth B] MOL2 format, chain V [auth A] MOL2 format, chain VB [auth D] MOL2 format, chain XA [auth B] MOL2 format, chain XB [auth D] MOL2 format, chain Y [auth A] MOL2 format, chain ZB [auth D] MOL2 format, chain ZA [auth B] MOL2 format, chain Z [auth A] MOL2 format, chain YB [auth D] MOL2 format, chain YA [auth B] MOL2 format, chain X [auth A] MOL2 format, chain WB [auth D] MOL2 format, chain WA [auth B] MOL2 format, chain W [auth A] MOL2 format, chain VA [auth B] MOL2 format, chain UA [auth B] MOL2 format, chain U [auth A] MOL2 format, chain RB [auth C] MOL2 format, chain QA [auth B] MOL2 format, chain PB [auth C] MOL2 format, chain OA [auth B] MOL2 format, chain O [auth A] MOL2 format, chain MB [auth C] MOL2 format, chain MA [auth B] MOL2 format, chain L [auth A] MOL2 format, chain J [auth A] MOL2 format, chain GA [auth B] MOL2 format, chain G [auth A] MOL2 format, chain FB [auth C] MOL2 format, chain FA [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain DA [auth B] mmCIF format, chain AC [auth D] mmCIF format, chain EA [auth B] mmCIF format, chain EB [auth C] mmCIF format, chain GB [auth C] mmCIF format, chain H [auth A] mmCIF format, chain HA [auth B] mmCIF format, chain HB [auth C] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth B] mmCIF format, chain IB [auth C] mmCIF format, chain JA [auth B] mmCIF format, chain JB [auth C] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth B] mmCIF format, chain KB [auth C] mmCIF format, chain LA [auth B] mmCIF format, chain LB [auth C] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth B] mmCIF format, chain NB [auth C] mmCIF format, chain OB [auth C] mmCIF format, chain P [auth A] mmCIF format, chain PA [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain QB [auth C] mmCIF format, chain R [auth A] mmCIF format, chain RA [auth B] mmCIF format, chain S [auth A] mmCIF format, chain SA [auth B] mmCIF format, chain SB [auth C] mmCIF format, chain T [auth A] mmCIF format, chain TA [auth B] mmCIF format, chain V [auth A] mmCIF format, chain VB [auth D] mmCIF format, chain XA [auth B] mmCIF format, chain XB [auth D] mmCIF format, chain Y [auth A] mmCIF format, chain ZB [auth D] mmCIF format, chain ZA [auth B] mmCIF format, chain Z [auth A] mmCIF format, chain YB [auth D] mmCIF format, chain YA [auth B] mmCIF format, chain X [auth A] mmCIF format, chain WB [auth D] mmCIF format, chain WA [auth B] mmCIF format, chain W [auth A] mmCIF format, chain VA [auth B] mmCIF format, chain UA [auth B] mmCIF format, chain U [auth A] mmCIF format, chain RB [auth C] mmCIF format, chain QA [auth B] mmCIF format, chain PB [auth C] mmCIF format, chain OA [auth B] mmCIF format, chain O [auth A] mmCIF format, chain MB [auth C] mmCIF format, chain MA [auth B] mmCIF format, chain L [auth A] mmCIF format, chain J [auth A] mmCIF format, chain GA [auth B] mmCIF format, chain G [auth A] mmCIF format, chain FB [auth C] mmCIF format, chain FA [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain DA [auth B]	AC [auth D] DA [auth B] E [auth A] EA [auth B] EB [auth C] AC [auth D], DA [auth B], E [auth A], EA [auth B], EB [auth C], F [auth A], FA [auth B], FB [auth C], G [auth A], GA [auth B], GB [auth C], H [auth A], HA [auth B], HB [auth C], I [auth A], IA [auth B], IB [auth C], J [auth A], JA [auth B], JB [auth C], K [auth A], KA [auth B], KB [auth C], L [auth A], LA [auth B], LB [auth C], M [auth A], MA [auth B], MB [auth C], N [auth A], NA [auth B], NB [auth C], O [auth A], OA [auth B], OB [auth C], P [auth A], PA [auth B], PB [auth C], Q [auth A], QA [auth B], QB [auth C], R [auth A], RA [auth B], RB [auth C], S [auth A], SA [auth B], SB [auth C], T [auth A], TA [auth B], U [auth A], UA [auth B], V [auth A], VA [auth B], VB [auth D], W [auth A], WA [auth B], WB [auth D], X [auth A], XA [auth B], XB [auth D], Y [auth A], YA [auth B], YB [auth D], Z [auth A], ZA [auth B], ZB [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AC [auth D] Focus chain DA [auth B] Focus chain E [auth A] Focus chain EA [auth B] Focus chain EB [auth C] Focus chain F [auth A] Focus chain FA [auth B] Focus chain FB [auth C] Focus chain G [auth A] Focus chain GA [auth B] Focus chain GB [auth C] Focus chain H [auth A] Focus chain HA [auth B] Focus chain HB [auth C] Focus chain I [auth A] Focus chain IA [auth B] Focus chain IB [auth C] Focus chain J [auth A] Focus chain JA [auth B] Focus chain JB [auth C] Focus chain K [auth A] Focus chain KA [auth B] Focus chain KB [auth C] Focus chain L [auth A] Focus chain LA [auth B] Focus chain LB [auth C] Focus chain M [auth A] Focus chain MA [auth B] Focus chain MB [auth C] Focus chain N [auth A] Focus chain NA [auth B] Focus chain NB [auth C] Focus chain O [auth A] Focus chain OA [auth B] Focus chain OB [auth C] Focus chain P [auth A] Focus chain PA [auth B] Focus chain PB [auth C] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain QB [auth C] Focus chain R [auth A] Focus chain RA [auth B] Focus chain RB [auth C] Focus chain S [auth A] Focus chain SA [auth B] Focus chain SB [auth C] Focus chain T [auth A] Focus chain TA [auth B] Focus chain U [auth A] Focus chain UA [auth B] Focus chain V [auth A] Focus chain VA [auth B] Focus chain VB [auth D] Focus chain W [auth A] Focus chain WA [auth B] Focus chain WB [auth D] Focus chain X [auth A] Focus chain XA [auth B] Focus chain XB [auth D] Focus chain Y [auth A] Focus chain YA [auth B] Focus chain YB [auth D] Focus chain Z [auth A] Focus chain ZA [auth B] Focus chain ZB [auth D] Interactions & Density Focus chain AC [auth D] Focus chain DA [auth B] Focus chain E [auth A] Focus chain EA [auth B] Focus chain EB [auth C] Focus chain F [auth A] Focus chain FA [auth B] Focus chain FB [auth C] Focus chain G [auth A] Focus chain GA [auth B] Focus chain GB [auth C] Focus chain H [auth A] Focus chain HA [auth B] Focus chain HB [auth C] Focus chain I [auth A] Focus chain IA [auth B] Focus chain IB [auth C] Focus chain J [auth A] Focus chain JA [auth B] Focus chain JB [auth C] Focus chain K [auth A] Focus chain KA [auth B] Focus chain KB [auth C] Focus chain L [auth A] Focus chain LA [auth B] Focus chain LB [auth C] Focus chain M [auth A] Focus chain MA [auth B] Focus chain MB [auth C] Focus chain N [auth A] Focus chain NA [auth B] Focus chain NB [auth C] Focus chain O [auth A] Focus chain OA [auth B] Focus chain OB [auth C] Focus chain P [auth A] Focus chain PA [auth B] Focus chain PB [auth C] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain QB [auth C] Focus chain R [auth A] Focus chain RA [auth B] Focus chain RB [auth C] Focus chain S [auth A] Focus chain SA [auth B] Focus chain SB [auth C] Focus chain T [auth A] Focus chain TA [auth B] Focus chain U [auth A] Focus chain UA [auth B] Focus chain V [auth A] Focus chain VA [auth B] Focus chain VB [auth D] Focus chain W [auth A] Focus chain WA [auth B] Focus chain WB [auth D] Focus chain X [auth A] Focus chain XA [auth B] Focus chain XB [auth D] Focus chain Y [auth A] Focus chain YA [auth B] Focus chain YB [auth D] Focus chain Z [auth A] Focus chain ZA [auth B] Focus chain ZB [auth D]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain CB [auth B] SDF format, chain CC [auth D] SDF format, chain DB [auth B] SDF format, chain TB [auth C] SDF format, chain UB [auth C] SDF format, chain CA [auth A] SDF format, chain BC [auth D] SDF format, chain BA [auth A] MOL2 format, chain CB [auth B] MOL2 format, chain CC [auth D] MOL2 format, chain DB [auth B] MOL2 format, chain TB [auth C] MOL2 format, chain UB [auth C] MOL2 format, chain CA [auth A] MOL2 format, chain BC [auth D] MOL2 format, chain BA [auth A] mmCIF format, chain CB [auth B] mmCIF format, chain CC [auth D] mmCIF format, chain DB [auth B] mmCIF format, chain TB [auth C] mmCIF format, chain UB [auth C] mmCIF format, chain CA [auth A] mmCIF format, chain BC [auth D] mmCIF format, chain BA [auth A]	BA [auth A] BC [auth D] CA [auth A] CB [auth B] CC [auth D] BA [auth A], BC [auth D], CA [auth A], CB [auth B], CC [auth D], DB [auth B], TB [auth C], UB [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain BA [auth A] Focus chain BC [auth D] Focus chain CA [auth A] Focus chain CB [auth B] Focus chain CC [auth D] Focus chain DB [auth B] Focus chain TB [auth C] Focus chain UB [auth C] Interactions & Density Focus chain BA [auth A] Focus chain BC [auth D] Focus chain CA [auth A] Focus chain CB [auth B] Focus chain CC [auth D] Focus chain DB [auth B] Focus chain TB [auth C] Focus chain UB [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.278 (Depositor), 0.272 (DCC)
R-Value Work: 0.240 (Depositor), 0.235 (DCC)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 142.841	α = 90
b = 147.197	β = 109.52
c = 121.172	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

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2009-08-04

Deposition Author(s):

RIKEN Structural Genomics/Proteomics Initiative (RSGI)

This entry supersedes: 2ZDF

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: 2017-11-01
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