8F9X

Cyclase-Phosphotriesterase from Ruegeria pomeroyi DSS-3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.32 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.235 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Cyclase-PTE

Ji, D.Frkic, R.L.Jackson, C.J.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cyclase family protein
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J
230Ruegeria pomeroyi DSS-3Mutation(s): 0 
Gene Names: SPO0761
UniProt
Find proteins for Q5LVE1 (Ruegeria pomeroyi (strain ATCC 700808 / DSM 15171 / DSS-3))
Explore Q5LVE1 
Go to UniProtKB:  Q5LVE1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5LVE1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BTB
Query on BTB

Download Ideal Coordinates CCD File 
EB [auth H]
FA [auth D]
M [auth A]
MB [auth I]
N [auth A]
EB [auth H],
FA [auth D],
M [auth A],
MB [auth I],
N [auth A],
PA [auth F],
PB [auth I],
QA [auth F],
U [auth B],
UB [auth J],
VB [auth J],
X [auth C],
XA [auth G],
YA [auth G]
2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C8 H19 N O5
OWMVSZAMULFTJU-UHFFFAOYSA-N
PG4
Query on PG4

Download Ideal Coordinates CCD File 
BA [auth C]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
TRS
Query on TRS

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DB [auth H]
EA [auth D]
JA [auth E]
LB [auth I]
T [auth B]
DB [auth H],
EA [auth D],
JA [auth E],
LB [auth I],
T [auth B],
TB [auth J]
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
ZN
Query on ZN

Download Ideal Coordinates CCD File 
AB [auth H]
BB [auth H]
CA [auth D]
CB [auth H]
DA [auth D]
AB [auth H],
BB [auth H],
CA [auth D],
CB [auth H],
DA [auth D],
HA [auth E],
IA [auth E],
IB [auth I],
JB [auth I],
K [auth A],
KB [auth I],
L [auth A],
NA [auth F],
OA [auth F],
Q [auth B],
QB [auth J],
R [auth B],
RB [auth J],
S [auth B],
SB [auth J],
UA [auth G],
V [auth C],
VA [auth G],
W [auth C],
WA [auth G]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth C]
FB [auth H]
GA [auth D]
GB [auth H]
HB [auth H]
AA [auth C],
FB [auth H],
GA [auth D],
GB [auth H],
HB [auth H],
KA [auth E],
LA [auth E],
MA [auth E],
NB [auth I],
O [auth A],
OB [auth I],
P [auth A],
RA [auth F],
SA [auth F],
TA [auth F],
WB [auth J],
Y [auth C],
Z [auth C],
ZA [auth G]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.32 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.235 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.08α = 90
b = 68.08β = 90
c = 446.501γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Australian Research Council (ARC)AustraliaCE200100012
Australian Research Council (ARC)AustraliaCE200100029

Revision History  (Full details and data files)

  • Version 1.0: 2023-12-06
    Type: Initial release
  • Version 2.0: 2025-01-29
    Type: Coordinate replacement
    Reason: Atomic clashes
    Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Refinement description, Structure summary