2Z1A | pdb_00002z1a

Crystal structure of 5'-nucleotidase precursor from Thermus thermophilus HB8

• PDB DOI: https://doi.org/10.2210/pdb2Z1A/pdb

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


• Deposited: 2007-05-08 Released: 2007-11-13 
• Deposition Author(s): Nakagawa, N., Kishishita, S., Yokoyama, S., Kuramitsu, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.209 (Depositor), 0.208 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.179 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of 5'-nucleotidase precursor from Thermus thermophilus HB8

Nakakaga, N., Kishishita, S., Yokoyama, S., Kuramitsu, S.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 60.51 kDa 
• Atom Count: 4,521 
• Modeled Residue Count: 507 
• Deposited Residue Count: 552 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5'-nucleotidase	A	552	Thermus thermophilus HB8	Mutation(s): 0  EC: 3.1.3.5
UniProt
Find proteins for Q5SIP1 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SIP1  Go to UniProtKB:  Q5SIP1

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
THM	E [auth A]	THYMIDINE C10 H14 N2 O5 IQFYYKKMVGJFEH-XLPZGREQSA-N
PO4	B [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
ZN	C [auth A], D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.209 (Depositor), 0.208 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.179 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.426	α = 90
b = 57.832	β = 105.95
c = 81.96	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-11-13 
Deposition Author(s): Nakagawa, N., Kishishita, S., Yokoyama, S., Kuramitsu, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2007-11-13
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description