2HX1 | pdb_00002hx1

Crystal structure of possible sugar phosphatase, HAD superfamily (ZP_00311070.1) from CYTOPHAGA HUTCHINSONII ATCC 33406 at 2.10 A resolution

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.234 (Depositor), 0.246 (DCC) 
  • R-Value Work: 
    0.179 (Depositor), 0.189 (DCC) 
  • R-Value Observed: 
    0.181 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 2HX1

This is version 1.5 of the entry. See complete history. 

Literature

Crystal structure of possible sugar phosphatase, HAD superfamily (ZP_00311070.1) from CYTOPHAGA HUTCHINSONII ATCC 33406 at 2.10 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content 

  • Total Structure Weight: 129.65 kDa 
  • Atom Count: 10,057 
  • Modeled Residue Count: 1,136 
  • Deposited Residue Count: 1,136 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Predicted sugar phosphatases of the HAD superfamily
A, B, C, D
284Cytophaga hutchinsoniiMutation(s): 9 
Gene Names: ZP_00311070.1

Small Molecules

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

Query on EPE


Download:Ideal Coordinates CCD File
FA [auth C],
L [auth A],
NA [auth D],
V [auth B]		4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
EDO

Query on EDO


Download:Ideal Coordinates CCD File
AA [auth B]
GA [auth C]
HA [auth C]
IA [auth C]
JA [auth C]
AA [auth B],
GA [auth C],
HA [auth C],
IA [auth C],
JA [auth C],
KA [auth C],
M [auth A],
N [auth A],
O [auth A],
OA [auth D],
PA [auth D],
W [auth B],
X [auth B],
Y [auth B],
Z [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL

Query on CL


Download:Ideal Coordinates CCD File
CA [auth C]
DA [auth C]
EA [auth C]
F [auth A]
G [auth A]
CA [auth C],
DA [auth C],
EA [auth C],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
MA [auth D],
Q [auth B],
R [auth B],
S [auth B],
T [auth B],
U [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG

Query on MG


Download:Ideal Coordinates CCD File
BA [auth C],
E [auth A],
LA [auth D],
P [auth B]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.234 (Depositor), 0.246 (DCC) 
  • R-Value Work:  0.179 (Depositor), 0.189 (DCC) 
  • R-Value Observed: 0.181 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.624α = 90
b = 119.462β = 90
c = 151.274γ = 90
Software Package:
Software NamePurpose
MolProbitymodel building
SHELXphasing
REFMACrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction
CCP4data scaling
SHELXDphasing
autoSHARPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-09-05
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description
  • Version 1.4: 2023-01-25
    Changes: Database references, Derived calculations
  • Version 1.5: 2024-10-30
    Changes: Data collection, Refinement description, Structure summary