3MI5

Axial Ligand Swapping In Double Mutant Maintains Intradiol-cleavage Chemistry in Protocatechuate 3,4-Dioxygenase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.153 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Axial Ligand Swapping In Double Mutant Maintains Intradiol-cleavage Chemistry in Protocatechuate 3,4-Dioxygenase

Purpero, V.M.Lipscomb, J.D.

To be published.

Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protocatechuate 3,4-dioxygenase alpha chainA, C [auth B], E [auth C], G [auth D], I [auth E], K [auth F]200Pseudomonas putidaMutation(s): 0 
Gene Names: pcaG
EC: 1.13.11.3
UniProt
Find proteins for P00436 (Pseudomonas putida)
Explore P00436 
Go to UniProtKB:  P00436
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Protocatechuate 3,4-dioxygenase beta chainB [auth M], D [auth N], F [auth O], H [auth P], J [auth Q], L [auth R]238Pseudomonas putidaMutation(s): 2 
Gene Names: pcaH
EC: 1.13.11.3
UniProt
Find proteins for P00437 (Pseudomonas putida)
Explore P00437 
Go to UniProtKB:  P00437
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CAQ
Query on CAQ

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CC [auth P] , DA [auth M] , HD [auth R] , IB [auth O] , KA [auth B] , KC [auth E] , RC [auth Q] , S [auth A] , 
CC [auth P],  DA [auth M],  HD [auth R],  IB [auth O],  KA [auth B],  KC [auth E],  RC [auth Q],  S [auth A],  SA [auth N],  TB [auth D],  ZA [auth C],  ZC [auth F]
CATECHOL
C6 H6 O2
YCIMNLLNPGFGHC-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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BC [auth P] , CB [auth O] , EC [auth E] , FA [auth B] , GD [auth R] , M [auth A] , MB [auth D] , NA [auth N] , 
BC [auth P],  CB [auth O],  EC [auth E],  FA [auth B],  GD [auth R],  M [auth A],  MB [auth D],  NA [auth N],  NC [auth Q],  QC [auth Q],  UA [auth C],  UC [auth F]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

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AA [auth M] , AB [auth C] , CD [auth R] , DB [auth O] , EB [auth O] , ED [auth R] , FC [auth E] , FD [auth R] , 
AA [auth M],  AB [auth C],  CD [auth R],  DB [auth O],  EB [auth O],  ED [auth R],  FC [auth E],  FD [auth R],  GB [auth O],  GC [auth E],  HA [auth B],  HB [auth O],  IC [auth E],  JA [auth B],  JC [auth E],  LA [auth B],  O [auth A],  OB [auth D],  OC [auth Q],  P [auth A],  PA [auth N],  PB [auth D],  PC [auth Q],  Q [auth A],  QB [auth D],  R [auth A],  RA [auth N],  RB [auth D],  SC [auth Q],  T [auth A],  V [auth M],  VA [auth C],  VC [auth F],  W [auth M],  WA [auth C],  WB [auth P],  WC [auth F],  XA [auth C],  XB [auth P],  XC [auth F],  Z [auth M],  ZB [auth P]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
BME
Query on BME

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AC [auth P] , AD [auth F] , BA [auth M] , DC [auth P] , DD [auth R] , EA [auth M] , FB [auth O] , GA [auth B] , 
AC [auth P],  AD [auth F],  BA [auth M],  DC [auth P],  DD [auth R],  EA [auth M],  FB [auth O],  GA [auth B],  HC [auth E],  IA [auth B],  JB [auth O],  JD [auth R],  LB [auth O],  LC [auth E],  N [auth A],  NB [auth D],  OA [auth N],  QA [auth N],  SB [auth D],  VB [auth P],  X [auth M],  Y [auth M],  YA [auth C],  YB [auth P],  YC [auth F]
BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
 Ligand Interaction
FE
Query on FE

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BB [auth O], BD [auth R], MA [auth N], MC [auth Q], U [auth M], UB [auth P]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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CA [auth M], ID [auth R], KB [auth O], TA [auth N], TC [auth Q]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.153 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 190.543α = 90
b = 167.995β = 132.4
c = 128.342γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-04-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-08
    Changes: Advisory, Refinement description