1WL8 | pdb_00001wl8

Crystal structure of PH1346 protein from Pyrococcus horikoshii

• PDB DOI: https://doi.org/10.2210/pdb1WL8/pdb

• Classification: LIGASE
• Organism(s): Pyrococcus horikoshii
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2004-06-21 Released: 2005-08-16 
• Deposition Author(s): Lokanath, N.K., Kunishima, N., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.174 (Depositor), 0.170 (DCC) 
• R-Value Work: 
  0.155 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.156 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Glutamide Amido Transferase from Pyrococcus horikoshii OT3

Lokanath, N.K., Kunishima, N.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 21.64 kDa 
• Atom Count: 1,720 
• Modeled Residue Count: 188 
• Deposited Residue Count: 189 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GMP synthase [glutamine-hydrolyzing] subunit A	A	189	Pyrococcus horikoshii	Mutation(s): 2  EC: 6.3.5.2
UniProt
Find proteins for O59071 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O59071  Go to UniProtKB:  O59071

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACY	C [auth A]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N
CL	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO	A	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS
SNN	A	L-PEPTIDE LINKING	C4 H6 N2 O2		ASN

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free:  0.174 (Depositor), 0.170 (DCC) 
• R-Value Work:  0.155 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.156 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.808	α = 90
b = 63.48	β = 90
c = 65.161	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-08-16 
Deposition Author(s): Lokanath, N.K., Kunishima, N., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2005-08-16
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Derived calculations
• Version 2.1: 2024-10-16
  Changes: Structure summary