2TIO | pdb_00002tio

LOW PACKING DENSITY FORM OF BOVINE BETA-TRYPSIN IN CYCLOHEXANE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 
    0.228 (Depositor) 
  • R-Value Work: 
    0.179 (Depositor), 0.167 (DCC) 
  • R-Value Observed: 
    0.179 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history

Literature

X-ray studies on two forms of bovine beta-trypsin crystals in neat cyclohexane.

Zhu, G.Huang, Q.Wang, Z.Qian, M.Jia, Y.Tang, Y.

(1998) Biochim Biophys Acta 1429: 142-150

  • DOI: https://doi.org/10.1016/s0167-4838(98)00226-x
  • Primary Citation Related Structures: 
    1TIO, 2TIO

  • PubMed Abstract: 

    Two orthorhombic forms (Vm values are 2.3 and 3.0 A3/Da) of bovine beta-trypsin crystals in neat cyclohexane were determined to 1.93 A resolution, by X-ray diffraction. Both structures in organic solvent are similar to those in aqueous solution. In the high packing density form, one cyclohexane molecule is found in a hydrophobic site near the active center. One sulfate locates at the active site with hydrogen or salt bond to the Ser-His catalytic diad, and five more sulfates bind on the molecular surface. The conformation of the side chains near the sulfates changed greatly. In the low packing density form, one cyclohexane and three sulfates are found. In both structures, one benzamidine molecule locates at the hydrophobic pocket of the active center. Most water molecules on the enzyme surface are retained except some with high temperature factors.


  • Organizational Affiliation
    • Department of Chemistry, Peking University, Beijing, PR China.

Macromolecule Content 

  • Total Structure Weight: 23.86 kDa 
  • Atom Count: 1,825 
  • Modeled Residue Count: 223 
  • Deposited Residue Count: 223 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
PROTEIN (BETA-TRYPSIN)223Bos taurusMutation(s): 0 
EC: 3.4.21.4
UniProt
Find proteins for P00760 (Bos taurus)
Explore P00760 
Go to UniProtKB:  P00760
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00760
Sequence Annotations
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Reference Sequence

Small Molecules

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

Query on BEN



Download:Ideal Coordinates CCD File
F [auth A]BENZAMIDINE
C7 H8 N2
PXXJHWLDUBFPOL-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A],
E [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
HEX

Query on HEX



Download:Ideal Coordinates CCD File
G [auth A]HEXANE
C6 H14
VLKZOEOYAKHREP-UHFFFAOYSA-N
CA

Query on CA



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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free:  0.228 (Depositor) 
  • R-Value Work:  0.179 (Depositor), 0.167 (DCC) 
  • R-Value Observed: 0.179 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.02α = 90
b = 63.78β = 90
c = 69.04γ = 90
Software Package:
Software NamePurpose
X-PLORrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-09-30
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2024-11-20
    Changes: Structure summary