3IEL | pdb_00003iel

Crystal Structure of TTHA0252 from Thermus thermophilus HB8 complexed with UMP

• PDB DOI: https://doi.org/10.2210/pdb3IEL/pdb

• Classification: HYDROLASE
• Organism(s): Thermus thermophilus HB8
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-07-23 Released: 2010-07-28 
• Deposition Author(s): Ishikawa, H., Nakagawa, N., Kuramitsu, S., Yokoyama, S., Masui, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 
  0.259 (Depositor), 0.258 (DCC) 
• R-Value Work: 
  0.222 (Depositor), 0.222 (DCC) 

Starting Model: experimental

Literature

Crystal Structure of TTHA0252 from Thermus thermophilus HB8 complexed with UMP

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

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 200.87 kDa 
• Atom Count: 14,251 
• Modeled Residue Count: 1,724 
• Deposited Residue Count: 1,724 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribonuclease TTHA0252	A, B, C, D	431	Thermus thermophilus HB8	Mutation(s): 0  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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
U5P	KD [auth D], LA [auth A], MA [auth A], NA [auth A], OB [auth B], PB [auth B], RC [auth C]	URIDINE-5'-MONOPHOSPHATE C9 H13 N2 O9 P DJJCXFVJDGTHFX-XVFCMESISA-N
FLC	KA [auth A], NB [auth B]	CITRATE ANION C6 H5 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-K
SO4	AA [auth A], AB [auth B], AC [auth C], AD [auth D], BA [auth A], BB [auth B], BC [auth C], BD [auth D], CA [auth A], CB [auth B], CC [auth C], CD [auth D], DA [auth A], DB [auth B], DC [auth C], DD [auth D], E [auth A], EA [auth A], EB [auth B], EC [auth C], ED [auth D], F [auth A], FA [auth A], FB [auth B], FC [auth C], FD [auth D], G [auth A], GA [auth A], GB [auth B], GC [auth C], GD [auth D], H [auth A], HA [auth A], HB [auth B], HC [auth C], HD [auth D], I [auth A], IA [auth A], IB [auth B], IC [auth C], ID [auth D], J [auth A], JA [auth A], JB [auth B], JC [auth C], JD [auth D], K [auth A], KB [auth B], KC [auth C], L [auth A], LB [auth B], LC [auth C], M [auth A], MB [auth B], MC [auth C], N [auth A], NC [auth C], O [auth A], OC [auth C], P [auth A], PC [auth C], Q [auth A], QA [auth B], QC [auth C], R [auth A], RA [auth B], S [auth A], SA [auth B], SB [auth C], T [auth A], TA [auth B], TB [auth C], U [auth A], UA [auth B], UB [auth C], UC [auth D], V [auth A], VA [auth B], VB [auth C], VC [auth D], W [auth A], WA [auth B], WB [auth C], WC [auth D], X [auth A], XA [auth B], XB [auth C], XC [auth D], Y [auth A], YA [auth B], YB [auth C], YC [auth D], Z [auth A], ZA [auth B], ZB [auth C], ZC [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	LD [auth D], MD [auth D], OA [auth A], PA [auth A], QB [auth B], RB [auth B], SC [auth C], TC [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free:  0.259 (Depositor), 0.258 (DCC) 
• R-Value Work:  0.222 (Depositor), 0.222 (DCC) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 145.238	α = 90
b = 146.677	β = 110.11
c = 120.349	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

Entry History 

Deposition Data

• Released Date: 2010-07-28 
Deposition Author(s): Ishikawa, H., Nakagawa, N., Kuramitsu, S., Yokoyama, S., Masui, R.

Revision History  

• Version 1.0: 2010-07-28
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description