3CMB

Crystal structure of acetoacetate decarboxylase (YP_001047042.1) from Methanoculleus marisnigri JR1 at 1.60 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.229 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal structure of acetoacetate decarboxylase (YP_001047042.1) from Methanoculleus marisnigri JR1 at 1.60 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Acetoacetate decarboxylaseA, B, C, D283Methanoculleus marisnigri JR1Mutation(s): 0 
Gene Names: YP_001047042.1Memar_1128
Find proteins for A3CUL0 (Methanoculleus marisnigri (strain ATCC 35101 / DSM 1498 / JR1))
Explore A3CUL0 
Go to UniProtKB:  A3CUL0
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PE8
Query on PE8

Download Ideal Coordinates CCD File 
FA [auth D], Z [auth C]3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL
C16 H34 O9
GLZWNFNQMJAZGY-UHFFFAOYSA-N
 Ligand Interaction
P33
Query on P33

Download Ideal Coordinates CCD File 
I [auth A], T [auth B]3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL
C14 H30 O8
XPJRQAIZZQMSCM-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

Download Ideal Coordinates CCD File 
AA [auth C] , GA [auth D] , J [auth A] , K [auth A] , L [auth A] , M [auth A] , N [auth A] , U [auth B] , 
AA [auth C],  GA [auth D],  J [auth A],  K [auth A],  L [auth A],  M [auth A],  N [auth A],  U [auth B],  V [auth B]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
DA [auth D], EA [auth D], H [auth A], Y [auth C]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
BA [auth D] , CA [auth D] , E [auth A] , F [auth A] , G [auth A] , O [auth B] , P [auth B] , Q [auth B] , 
BA [auth D],  CA [auth D],  E [auth A],  F [auth A],  G [auth A],  O [auth B],  P [auth B],  Q [auth B],  R [auth B],  S [auth B],  W [auth C],  X [auth C]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, DL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 129.34α = 90
b = 136.71β = 90
c = 168.12γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXrefinement
SHELXphasing
MolProbitymodel building
XSCALEdata scaling
PDB_EXTRACTdata extraction
MAR345data collection
XDSdata reduction
SHELXDphasing
autoSHARPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-04-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description
  • Version 1.3: 2019-07-24
    Changes: Data collection, Derived calculations, Refinement description