3IE1 | pdb_00003ie1

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 (Depositor), 0.280 (DCC)
R-Value Work:
0.231 (Depositor), 0.220 (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 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
Modeled Residue Count: 1,738
Deposited Residue Count: 1,740
Unique protein chains: 1
Unique nucleic acid chains: 1

Macromolecules

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(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

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
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 AA [auth A] SDF format, chain BA [auth A] MOL2 format, chain AA [auth A] MOL2 format, chain BA [auth A] mmCIF format, chain AA [auth A] mmCIF format, chain BA [auth A]	AA [auth A], BA [auth A]	CITRATE ANION C₆ H₅ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-K		Interactions Focus chain AA [auth A] Focus chain BA [auth A] Interactions & Density Focus chain AA [auth A] Focus chain BA [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain CB [auth C] SDF format, chain DB [auth C] SDF format, chain EB [auth C] SDF format, chain FA [auth B] 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 J [auth A] 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 PA [auth B] SDF format, chain QA [auth B] SDF format, chain QB [auth D] SDF format, chain R [auth A] 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 W [auth A] SDF format, chain Y [auth A] SDF format, chain YA [auth C] SDF format, chain Z [auth A] SDF format, chain ZA [auth C] SDF format, chain XA [auth C] SDF format, chain X [auth A] SDF format, chain V [auth A] SDF format, chain RA [auth B] SDF format, chain Q [auth A] SDF format, chain PB [auth D] SDF format, chain P [auth A] SDF format, chain OB [auth D] SDF format, chain OA [auth B] SDF format, chain O [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 IA [auth B] SDF format, chain FB [auth C] SDF format, chain EA [auth B] SDF format, chain BB [auth C] SDF format, chain AB [auth C] MOL2 format, chain CB [auth C] MOL2 format, chain DB [auth C] MOL2 format, chain EB [auth C] MOL2 format, chain FA [auth B] 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 J [auth A] 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 PA [auth B] MOL2 format, chain QA [auth B] MOL2 format, chain QB [auth D] MOL2 format, chain R [auth A] 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 W [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain YA [auth C] MOL2 format, chain Z [auth A] MOL2 format, chain ZA [auth C] MOL2 format, chain XA [auth C] MOL2 format, chain X [auth A] MOL2 format, chain V [auth A] MOL2 format, chain RA [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain PB [auth D] MOL2 format, chain P [auth A] MOL2 format, chain OB [auth D] MOL2 format, chain OA [auth B] MOL2 format, chain O [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 IA [auth B] MOL2 format, chain FB [auth C] MOL2 format, chain EA [auth B] MOL2 format, chain BB [auth C] MOL2 format, chain AB [auth C] mmCIF format, chain CB [auth C] mmCIF format, chain DB [auth C] mmCIF format, chain EB [auth C] mmCIF format, chain FA [auth B] mmCIF format, chain GA [auth B] mmCIF format, chain GB [auth C] mmCIF format, chain HA [auth B] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth B] mmCIF format, chain MB [auth D] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth B] mmCIF format, chain NB [auth D] mmCIF format, chain PA [auth B] mmCIF format, chain QA [auth B] mmCIF format, chain QB [auth D] mmCIF format, chain R [auth A] mmCIF format, chain RB [auth D] mmCIF format, chain S [auth A] mmCIF format, chain SA [auth B] mmCIF format, chain T [auth A] mmCIF format, chain TA [auth B] mmCIF format, chain U [auth A] mmCIF format, chain UA [auth B] mmCIF format, chain W [auth A] mmCIF format, chain Y [auth A] mmCIF format, chain YA [auth C] mmCIF format, chain Z [auth A] mmCIF format, chain ZA [auth C] mmCIF format, chain XA [auth C] mmCIF format, chain X [auth A] mmCIF format, chain V [auth A] mmCIF format, chain RA [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain PB [auth D] mmCIF format, chain P [auth A] mmCIF format, chain OB [auth D] mmCIF format, chain OA [auth B] mmCIF format, chain O [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 IA [auth B] mmCIF format, chain FB [auth C] mmCIF format, chain EA [auth B] mmCIF format, chain BB [auth C] mmCIF format, chain AB [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		Interactions Focus chain AB [auth C] Focus chain BB [auth C] Focus chain CB [auth C] Focus chain DB [auth C] Focus chain EA [auth B] Focus chain EB [auth C] Focus chain FA [auth B] Focus chain FB [auth C] Focus chain GA [auth B] Focus chain GB [auth C] Focus chain HA [auth B] Focus chain I [auth A] Focus chain IA [auth B] 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 OA [auth B] Focus chain OB [auth D] Focus chain P [auth A] Focus chain PA [auth B] Focus chain PB [auth D] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain QB [auth D] Focus chain R [auth A] Focus chain RA [auth B] Focus chain RB [auth D] Focus chain S [auth A] Focus chain SA [auth B] 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 W [auth A] Focus chain X [auth A] Focus chain XA [auth C] Focus chain Y [auth A] Focus chain YA [auth C] Focus chain Z [auth A] Focus chain ZA [auth C] Interactions & Density Focus chain AB [auth C] Focus chain BB [auth C] Focus chain CB [auth C] Focus chain DB [auth C] Focus chain EA [auth B] Focus chain EB [auth C] Focus chain FA [auth B] Focus chain FB [auth C] Focus chain GA [auth B] Focus chain GB [auth C] Focus chain HA [auth B] Focus chain I [auth A] Focus chain IA [auth B] 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 OA [auth B] Focus chain OB [auth D] Focus chain P [auth A] Focus chain PA [auth B] Focus chain PB [auth D] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain QB [auth D] Focus chain R [auth A] Focus chain RA [auth B] Focus chain RB [auth D] Focus chain S [auth A] Focus chain SA [auth B] 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 W [auth A] Focus chain X [auth A] Focus chain XA [auth C] Focus chain Y [auth A] Focus chain YA [auth C] Focus chain Z [auth A] Focus chain ZA [auth C]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain DA [auth A] SDF format, chain SB [auth D] SDF format, chain TB [auth D] SDF format, chain VA [auth B] SDF format, chain WA [auth B] SDF format, chain IB [auth C] SDF format, chain HB [auth C] SDF format, chain CA [auth A] MOL2 format, chain DA [auth A] MOL2 format, chain SB [auth D] MOL2 format, chain TB [auth D] MOL2 format, chain VA [auth B] MOL2 format, chain WA [auth B] MOL2 format, chain IB [auth C] MOL2 format, chain HB [auth C] MOL2 format, chain CA [auth A] mmCIF format, chain DA [auth A] mmCIF format, chain SB [auth D] mmCIF format, chain TB [auth D] mmCIF format, chain VA [auth B] mmCIF format, chain WA [auth B] mmCIF format, chain IB [auth C] mmCIF format, chain HB [auth C] mmCIF format, chain CA [auth A]	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		Interactions Focus chain CA [auth A] Focus chain DA [auth A] Focus chain HB [auth C] Focus chain IB [auth C] Focus chain SB [auth D] Focus chain TB [auth D] Focus chain VA [auth B] Focus chain WA [auth B] Interactions & Density Focus chain CA [auth A] Focus chain DA [auth A] Focus chain HB [auth C] Focus chain IB [auth C] Focus chain SB [auth D] Focus chain TB [auth D] Focus chain VA [auth B] Focus chain WA [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.85 Å
R-Value Free: 0.291 (Depositor), 0.280 (DCC)
R-Value Work: 0.231 (Depositor), 0.220 (DCC)

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
Version 1.4: 2023-11-01
Changes: Data collection, Refinement description