1VS1 | pdb_00001vs1

Crystal structure of 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase (DAHP synthase) from Aeropyrum pernix in complex with Mn2+ and PEP

• PDB DOI: https://doi.org/10.2210/pdb1VS1/pdb

• Classification: TRANSFERASE
• Organism(s): Aeropyrum pernix
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2006-03-09 Released: 2006-05-16 
• Deposition Author(s): Shumilin, I.A., Zhou, L., Wu, J., Woodard, R.W., Bauerle, R., Kretsinger, R.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.218 (Depositor), 0.217 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.174 (DCC) 
• R-Value Observed: 
  0.176 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase (DAHP synthase) from Aeropyrum pernix in complex with Mn2+ and PEP

Shumilin, I.A., Zhou, L., Wu, J., Woodard, R.W., Bauerle, R., Kretsinger, R.H.

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 (software)

Macromolecule Content 

• Total Structure Weight: 121.04 kDa 
• Atom Count: 8,422 
• Modeled Residue Count: 1,076 
• Deposited Residue Count: 1,104 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-deoxy-7-phosphoheptulonate synthase	A, B, C, D	276	Aeropyrum pernix	Mutation(s): 0  Gene Names: APE0581 EC: 2.5.1.54
UniProt
Find proteins for Q9YEJ7 (Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1)) Explore Q9YEJ7  Go to UniProtKB:  Q9YEJ7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEP	F [auth A], H [auth B], J [auth C], L [auth D]	PHOSPHOENOLPYRUVATE C3 H5 O6 P DTBNBXWJWCWCIK-UHFFFAOYSA-N
MN	E [auth A], G [auth B], I [auth C], K [auth D]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.218 (Depositor), 0.217 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.174 (DCC) 
• R-Value Observed: 0.176 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.768	α = 90
b = 130.404	β = 110.61
c = 78.362	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
SHELXD	phasing
SHELXE	model building
MLPHARE	phasing
DM	phasing
SOLVE	phasing
RESOLVE	phasing
O	model building
Coot	model building
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-05-16 
Deposition Author(s): Shumilin, I.A., Zhou, L., Wu, J., Woodard, R.W., Bauerle, R., Kretsinger, R.H.

Revision History  

• Version 1.0: 2006-05-16
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description