2PCQ | pdb_00002pcq

Crystal structure of putative dihydrodipicolinate synthase (TTHA0737) from Thermus Thermophilus HB8

• PDB DOI: https://doi.org/10.2210/pdb2PCQ/pdb

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


• Deposited: 2007-03-30 Released: 2007-10-02 
• Deposition Author(s): Jeyakanthan, J., Kanaujia, S.P., Vasuki Ranjani, C., Sekar, K., Kitamura, Y., Ebihara, A., Kuramitsu, S., Shinkai, A., Shiro, Y., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.193 (Depositor), 0.194 (DCC) 
• R-Value Work: 
  0.164 (Depositor), 0.165 (DCC) 
• R-Value Observed: 
  0.164 (Depositor) 

Literature

Crystal structure of putative dihydrodipicolinate synthase (TTHA0737) from Thermus Thermophilus HB8

Jeyakanthan, J., Kanaujia, S.P., Vasuki Ranjani, C., Sekar, K., Kitamura, Y., Ebihara, A., Kuramitsu, S., Shinkai, A., Shiro, Y., Yokoyama, S.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 31.42 kDa 
• Atom Count: 2,644 
• Modeled Residue Count: 283 
• Deposited Residue Count: 283 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative dihydrodipicolinate synthase	A	283	Thermus thermophilus HB8	Mutation(s): 0  EC: 4.2.1.52
UniProt
Find proteins for Q5SKB1 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SKB1  Go to UniProtKB:  Q5SKB1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
K	B [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.193 (Depositor), 0.194 (DCC) 
• R-Value Work:  0.164 (Depositor), 0.165 (DCC) 
• R-Value Observed: 0.164 (Depositor) 

Space Group: P 6₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 159.732	α = 90
b = 159.732	β = 90
c = 72.496	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-10-02 
Deposition Author(s): Jeyakanthan, J., Kanaujia, S.P., Vasuki Ranjani, C., Sekar, K., Kitamura, Y., Ebihara, A., Kuramitsu, S., Shinkai, A., Shiro, Y., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2007-10-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Derived calculations, Source and taxonomy, Version format compliance
• Version 1.2: 2024-11-13
  Changes: Data collection, Database references, Derived calculations, Structure summary