5XWK | pdb_00005xwk

Crystal Structure of SPAP, an alkaline phosphatase from Sphingomonas in complex with inorganic phosphate

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.203 (Depositor), 0.206 (DCC) 
  • R-Value Work: 
    0.167 (Depositor), 0.174 (DCC) 
  • R-Value Observed: 
    0.169 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 5XWK

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

Literature

Crystal Structure of SPAP, an alkaline phosphatase from Sphingomonas in complex with

Bihani, S.C.

To be published.

Macromolecule Content 

  • Total Structure Weight: 61.85 kDa 
  • Atom Count: 4,482 
  • Modeled Residue Count: 530 
  • Deposited Residue Count: 567 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:
|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Alkaline phosphatase PhoK567Sphingomonas sp.Mutation(s): 0 
Gene Names: phoK
EC: 3.1.3.1
UniProt
Find proteins for A1YYW7 (Sphingomonas sp)
Explore A1YYW7 
Go to UniProtKB:  A1YYW7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA1YYW7
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PO4

Query on PO4


Download:Ideal Coordinates CCD File
F [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL

Query on GOL


Download:Ideal Coordinates CCD File
B [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A]		GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN

Query on ZN


Download:Ideal Coordinates CCD File
C [auth A],
D [auth A]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA

Query on CA


Download:Ideal Coordinates CCD File
E [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.203 (Depositor), 0.206 (DCC) 
  • R-Value Work:  0.167 (Depositor), 0.174 (DCC) 
  • R-Value Observed: 0.169 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.99α = 90
b = 86.99β = 90
c = 165.484γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-07-18
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.2: 2024-11-13
    Changes: Structure summary