2TIO

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 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.179 

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This is version 1.2 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: 10.1016/s0167-4838(98)00226-x
  • Primary Citation of 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 ...

    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.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (BETA-TRYPSIN)A223Bos 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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BEN
Query on BEN
Download Ideal Coordinates CCD File 
F [auth A]BENZAMIDINE
C7 H8 N2
PXXJHWLDUBFPOL-UHFFFAOYSA-N		 Ligand Interaction
SO4
Query on SO4
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C [auth A],
D [auth A],
E [auth A]		SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
HEX
Query on HEX
Download Ideal Coordinates CCD File 
G [auth A]HEXANE
C6 H14
VLKZOEOYAKHREP-UHFFFAOYSA-N		 Ligand Interaction
CA
Query on CA
Download Ideal Coordinates CCD File 
B [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.179 
  • 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