1GW9 | pdb_00001gw9

Tri-iodide derivative of Xylose Isomerase from Streptomyces Rubiginosus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 
    0.188 (Depositor), 0.185 (DCC) 
  • R-Value Work: 
    0.164 (Depositor), 0.163 (DCC) 
  • R-Value Observed: 
    0.165 (Depositor) 

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

Triiodide Derivatization and Combinatorial Counter-Ion Replacement: Two Methods for Enhancing Phasing Signal Using Laboratory Cu Kalpha X-Ray Equipment

Evans, G.Bricogne, G.

(2002) Acta Crystallogr D Biol Crystallogr 58: 976

  • DOI: https://doi.org/10.1107/s0907444902005486
  • Primary Citation Related Structures: 
    1GW9, 1GWA, 1GWD, 1GWG

  • PubMed Abstract: 

    A series of experiments performed at Cu Kalpha wavelength on in-house X-ray equipment are presented which investigate two possibilities for enhancing the experimental phasing signal by means of (i) triiodide/iodide soaks using KI/I(2) and (ii) combinations of counter-ions introduced using the short cryosoak method. Triiodide-derivative crystal structures for five test proteins have been refined and reveal that iodine can bind as polyiodide and single iodide ions through hydrophobic and hydrogen-bonding interactions both at the molecular surface and in intramolecular and intermolecular cavities. In three cases, the structures could be automatically determined with autoSHARP using in-house SAD and SIRAS data. The investigation of combinatorial counter-ion replacement using multiple salts with Na(+) and Cs(+) as cations and I(-) and Cl(-) as anions reveals that, for the case of hen egg-white lysozyme, significant improvement in phasing signal is obtained by the combined use of salts compared with SIRAS methods using native and single short-soak derivative data sets.


  • Organizational Affiliation
    • Global Phasing Limited, Cambridge, England.

Macromolecule Content 

  • Total Structure Weight: 47.31 kDa 
  • Atom Count: 3,458 
  • Modeled Residue Count: 385 
  • Deposited Residue Count: 388 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
XYLOSE ISOMERASE388Streptomyces pseudogriseolusMutation(s): 0 
EC: 5.3.1.5
UniProt
Find proteins for P24300 (Streptomyces pseudogriseolus)
Explore P24300 
Go to UniProtKB:  P24300
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP24300
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LXC

Query on LXC



Download:Ideal Coordinates CCD File
D [auth A],
E [auth A]
beta-L-xylopyranose
C5 H10 O5
SRBFZHDQGSBBOR-QTBDOELSSA-N
IOD

Query on IOD



Download:Ideal Coordinates CCD File
AA [auth A]
BA [auth A]
CA [auth A]
DA [auth A]
EA [auth A]
AA [auth A],
BA [auth A],
CA [auth A],
DA [auth A],
EA [auth A],
F [auth A],
FA [auth A],
G [auth A],
GA [auth A],
H [auth A],
HA [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
T [auth A],
U [auth A],
V [auth A],
W [auth A],
X [auth A],
Y [auth A],
Z [auth A]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
CA

Query on CA



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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free:  0.188 (Depositor), 0.185 (DCC) 
  • R-Value Work:  0.164 (Depositor), 0.163 (DCC) 
  • R-Value Observed: 0.165 (Depositor) 
Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.354α = 90
b = 98.54β = 90
c = 102.507γ = 90
Software Package:
Software NamePurpose
BUSTER-TNTrefinement
d*TREKdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-06-06
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Other, Structure summary
  • Version 1.4: 2024-05-08
    Changes: Data collection, Database references, Structure summary