3IE1

Crystal structure of H380A mutant TTHA0252 from Thermus thermophilus HB8 complexed with RNA

PDB DOI: https://doi.org/10.2210/pdb3IE1/pdb
Entry: 3IE1 supersedes: 2ZDE
NAKB: 3IE1

Classification: HYDROLASE/RNA
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: 2.85 Å
R-Value Free: 0.291
R-Value Work: 0.231

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of H380A mutant TTHA0252 from Thermus thermophilus HB8 complexed with RNA

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

To be published.

Macromolecule Content

Total Structure Weight: 199.01 kDa
Atom Count: 13,910
Modelled Residue Count: 1,738
Deposited Residue Count: 1,740
Unique protein chains: 1
Unique nucleic acid 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
Protein Feature View Expand
Reference Sequence

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (5'-R(PUPUPUPU)-3')	E, F, G, H	4	N/A
Protein Feature View 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 AA [auth A] SDF format, chain BA [auth A] MOL2 format, chain AA [auth A] MOL2 format, chain BA [auth A]	AA [auth A], BA [auth A]	CITRATE ANION C₆ H₅ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-K		Ligand Interaction
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain AB [auth C] SDF format, chain BB [auth C] SDF format, chain CB [auth C] SDF format, chain DB [auth C] SDF format, chain EA [auth B] SDF format, chain EB [auth C] SDF format, chain FA [auth B] SDF format, chain FB [auth C] SDF format, chain GA [auth B] SDF format, chain GB [auth C] SDF format, chain HA [auth B] SDF format, chain I [auth A] SDF format, chain IA [auth B] SDF format, chain J [auth A] SDF format, chain JA [auth B] SDF format, chain JB [auth D] SDF format, chain K [auth A] SDF format, chain KA [auth B] SDF format, chain KB [auth D] SDF format, chain L [auth A] SDF format, chain LA [auth B] SDF format, chain LB [auth D] SDF format, chain M [auth A] SDF format, chain MA [auth B] SDF format, chain MB [auth D] SDF format, chain N [auth A] SDF format, chain NA [auth B] SDF format, chain NB [auth D] SDF format, chain O [auth A] SDF format, chain OA [auth B] SDF format, chain OB [auth D] SDF format, chain P [auth A] SDF format, chain PA [auth B] SDF format, chain PB [auth D] SDF format, chain Q [auth A] SDF format, chain QA [auth B] SDF format, chain QB [auth D] SDF format, chain R [auth A] SDF format, chain RA [auth B] SDF format, chain RB [auth D] SDF format, chain S [auth A] SDF format, chain SA [auth B] SDF format, chain T [auth A] SDF format, chain TA [auth B] SDF format, chain U [auth A] SDF format, chain UA [auth B] SDF format, chain V [auth A] SDF format, chain W [auth A] SDF format, chain X [auth A] SDF format, chain XA [auth C] SDF format, chain Y [auth A] SDF format, chain YA [auth C] SDF format, chain Z [auth A] SDF format, chain ZA [auth C] MOL2 format, chain AB [auth C] MOL2 format, chain BB [auth C] MOL2 format, chain CB [auth C] MOL2 format, chain DB [auth C] MOL2 format, chain EA [auth B] MOL2 format, chain EB [auth C] MOL2 format, chain FA [auth B] MOL2 format, chain FB [auth C] MOL2 format, chain GA [auth B] MOL2 format, chain GB [auth C] MOL2 format, chain HA [auth B] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth B] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth B] MOL2 format, chain JB [auth D] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth B] MOL2 format, chain KB [auth D] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth B] MOL2 format, chain LB [auth D] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth B] MOL2 format, chain MB [auth D] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth B] MOL2 format, chain NB [auth D] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth B] MOL2 format, chain OB [auth D] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth B] MOL2 format, chain PB [auth D] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth B] MOL2 format, chain QB [auth D] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth B] MOL2 format, chain RB [auth D] MOL2 format, chain S [auth A] MOL2 format, chain SA [auth B] MOL2 format, chain T [auth A] MOL2 format, chain TA [auth B] MOL2 format, chain U [auth A] MOL2 format, chain UA [auth B] MOL2 format, chain V [auth A] MOL2 format, chain W [auth A] MOL2 format, chain X [auth A] MOL2 format, chain XA [auth C] MOL2 format, chain Y [auth A] MOL2 format, chain YA [auth C] MOL2 format, chain Z [auth A] MOL2 format, chain ZA [auth C]	AB [auth C] BB [auth C] CB [auth C] DB [auth C] EA [auth B] AB [auth C], BB [auth C], CB [auth C], DB [auth C], EA [auth B], EB [auth C], FA [auth B], FB [auth C], GA [auth B], GB [auth C], HA [auth B], I [auth A], IA [auth B], 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], OA [auth B], OB [auth D], P [auth A], PA [auth B], PB [auth D], Q [auth A], QA [auth B], QB [auth D], R [auth A], RA [auth B], RB [auth D], S [auth A], SA [auth B], T [auth A], TA [auth B], U [auth A], UA [auth B], V [auth A], W [auth A], X [auth A], XA [auth C], Y [auth A], YA [auth C], Z [auth A], ZA [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Ligand Interaction
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain CA [auth A] SDF format, chain DA [auth A] SDF format, chain HB [auth C] SDF format, chain IB [auth C] SDF format, chain SB [auth D] SDF format, chain TB [auth D] SDF format, chain VA [auth B] SDF format, chain WA [auth B] MOL2 format, chain CA [auth A] MOL2 format, chain DA [auth A] MOL2 format, chain HB [auth C] MOL2 format, chain IB [auth C] MOL2 format, chain SB [auth D] MOL2 format, chain TB [auth D] MOL2 format, chain VA [auth B] MOL2 format, chain WA [auth B]	CA [auth A] DA [auth A] HB [auth C] IB [auth C] SB [auth D] CA [auth A], DA [auth A], HB [auth C], IB [auth C], SB [auth D], TB [auth D], VA [auth B], WA [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.85 Å
R-Value Free: 0.291
R-Value Work: 0.231
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 143.424	α = 90
b = 148.165	β = 109.61
c = 120.837	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: 2ZDE

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