3INN | pdb_00003inn

Crystal structure of pantoate-beta-alanine-ligase in complex with ATP at low occupancy at 2.1 A resolution

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.245 (Depositor), 0.248 (DCC) 
  • R-Value Work: 
    0.194 (Depositor), 0.198 (DCC) 
  • R-Value Observed: 
    0.196 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history. 

Literature

Crystal structure of pantoate-beta-alanine-ligase in complex with ATP at low occupancy at 2.1 A resolution

Seattle Structural Genomics Center for Infectious Disease (SSGCID), Abendroth, J., Davies, D., Staker, B.

To be published.

Macromolecule Content 

  • Total Structure Weight: 140.86 kDa 
  • Atom Count: 9,322 
  • Modeled Residue Count: 1,122 
  • Deposited Residue Count: 1,256 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Pantothenate synthetase
A, B, C, D
314Brucella melitensisMutation(s): 0 
Gene Names: BMEI1593, panC
EC: 6.3.2.1
UniProt
Find proteins for Q8YFC9 (Brucella melitensis biotype 1 (strain ATCC 23456 / CCUG 17765 / NCTC 10094 / 16M))
Explore Q8YFC9 
Go to UniProtKB:  Q8YFC9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8YFC9
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP

Query on ATP


Download:Ideal Coordinates CCD File
E [auth A],
I [auth C],
M [auth D]		ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
UNX

Query on UNX


Download:Ideal Coordinates CCD File
F [auth A]
G [auth A]
H [auth A]
J [auth C]
K [auth C]
F [auth A],
G [auth A],
H [auth A],
J [auth C],
K [auth C],
L [auth C]
UNKNOWN ATOM OR ION
X

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.245 (Depositor), 0.248 (DCC) 
  • R-Value Work:  0.194 (Depositor), 0.198 (DCC) 
  • R-Value Observed: 0.196 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.32α = 90
b = 94.32β = 90
c = 236.93γ = 120
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-10-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description