2HYK | pdb_00002hyk

The crystal structure of an endo-beta-1,3-glucanase from alkaliphilic Nocardiopsis sp.strain F96

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 
    0.162 (Depositor), 0.176 (DCC) 
  • R-Value Work: 
    0.143 (Depositor), 0.162 (DCC) 
  • R-Value Observed: 
    0.144 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 2HYK

This is version 1.3 of the entry. See complete history. 

Literature

The 1.3 A crystal structure of a novel endo-beta-1,3-glucanase of glycoside hydrolase family 16 from alkaliphilic Nocardiopsis sp. strain F96.

Fibriansah, G., Masuda, S., Koizumi, N., Nakamura, S., Kumasaka, T.

(2007) Proteins 69: 683-690

Macromolecule Content 

  • Total Structure Weight: 27.63 kDa 
  • Atom Count: 2,140 
  • Modeled Residue Count: 237 
  • Deposited Residue Count: 245 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-1,3-glucanase245Nocardiopsis sp. F96Mutation(s): 0 
EC: 3.2.1.39
UniProt
Find proteins for Q2V0H0 (Nocardiopsis sp. F96)
Explore Q2V0H0 
Go to UniProtKB:  Q2V0H0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2V0H0
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4

Query on SO4


Download:Ideal Coordinates CCD File
B [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL


Download:Ideal Coordinates CCD File
F [auth A],
G [auth A],
H [auth A]		GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EOH

Query on EOH


Download:Ideal Coordinates CCD File
D [auth A],
E [auth A]		ETHANOL
C2 H6 O
LFQSCWFLJHTTHZ-UHFFFAOYSA-N
CA

Query on CA


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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free:  0.162 (Depositor), 0.176 (DCC) 
  • R-Value Work:  0.143 (Depositor), 0.162 (DCC) 
  • R-Value Observed: 0.144 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 34.589α = 90
b = 71.843β = 90.21
c = 39.666γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-10-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.2: 2017-10-18
    Changes: Refinement description
  • Version 1.3: 2024-03-13
    Changes: Data collection, Database references, Derived calculations