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- PDB-1bx8: HIRUSTASIN FROM HIRUDO MEDICINALIS AT 1.4 ANGSTROMS -

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Basic information

Entry
Database: PDB / ID: 1bx8
TitleHIRUSTASIN FROM HIRUDO MEDICINALIS AT 1.4 ANGSTROMS
ComponentsHIRUSTASIN
KeywordsANTI-COAGULANT / PEPTIDIC INHIBITORS / CONFORMATIONAL FLEXIBILITY / SERINE PROTEASE INHIBITOR
Function / homology
Function and homology information


negative regulation of coagulation / serine-type endopeptidase inhibitor activity / heparin binding / extracellular region
Similarity search - Function
Proteinase inhibitor I15, leech antistasin / Antistasin; domain 1 / Antistasin; domain 1 / Antistasin-like domain / Antistasin family / Antistasin-like domain profile. / Hirudin/antistatin / Ribbon / Mainly Beta
Similarity search - Domain/homology
Biological speciesHirudo medicinalis (medicinal leech)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO / Resolution: 1.4 Å
AuthorsUson, I. / Sheldrick, G.M. / De La Fortelle, E. / Bricogne, G. / Di Marco, S. / Priestle, J.P. / Gruetter, M.G. / Mittl, P.R.E.
Citation
Journal: Structure Fold.Des. / Year: 1999
Title: The 1.2 A crystal structure of hirustasin reveals the intrinsic flexibility of a family of highly disulphide-bridged inhibitors.
Authors: Uson, I. / Sheldrick, G.M. / de La Fortelle, E. / Bricogne, G. / Di Marco, S. / Priestle, J.P. / Grutter, M.G. / Mittl, P.R.
#1: Journal: Structure / Year: 1997
Title: A New Structural Class of Serine Protease Inhibitors Revealed by the Structure of the Hirustasin-Kallikrein Complex
Authors: Mittl, P.R. / Di Marco, S. / Fendrich, G. / Pohlig, G. / Heim, J. / Sommerhoff, C. / Fritz, H. / Priestle, J.P. / Grutter, M.G.
#2: Journal: Protein Sci. / Year: 1997
Title: Recombinant Hirustasin: Production in Yeast, Crystallization, and Interaction with Serine Proteases
Authors: Di Marco, S. / Fendrich, G. / Knecht, R. / Strauss, A. / Pohlig, G. / Heim, J. / Priestle, J.P. / Sommerhoff, C.P. / Grutter, M.G.
History
DepositionOct 14, 1998Processing site: BNL
Revision 1.0Apr 27, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HIRUSTASIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,9832
Polymers5,8871
Non-polymers961
Water66737
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.713, 37.713, 67.812
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein HIRUSTASIN


Mass: 5886.788 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hirudo medicinalis (medicinal leech) / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P80302
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 40 %
Description: TWO DIFFERENT INDEPENDENT METHODS WERE USED FOR STRUCTURE SOLUTION
Crystal growpH: 5.45 / Details: pH 5.45
Crystal
*PLUS
Crystal grow
*PLUS
Method: unknown / Details: Di Marco, S., (1997) Protein Sci., 6, 109.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.1 Msodium citrate11
22 Mammonium sulfate11
30.2 Msodium potassium phosphate11tartrate

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM1A / Wavelength: 0.873
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 1, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 1.4→7.1 Å / Num. obs: 10468 / % possible obs: 98.6 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 50.5
Reflection shellResolution: 1.4→1.45 Å / Rmerge(I) obs: 0.376 / Mean I/σ(I) obs: 8.5 / % possible all: 73.4
Reflection
*PLUS
Redundancy: 6.8 %
Reflection shell
*PLUS
% possible obs: 97.7 % / Rmerge(I) obs: 0.174 / Mean I/σ(I) obs: 3.4

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Processing

Software
NameClassification
MARXDSdata collection
MARSCALEdata reduction
SHELXmodel building
SHELXrefinement
MARXDSdata reduction
MARSCALEdata scaling
SHELXphasing
RefinementMethod to determine structure: AB INITIO / Resolution: 1.4→7.1 Å / Num. parameters: 1641 / Num. restraintsaints: 1470 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC REFINEMENT OF THE SULPHUR ATOMS REDUCED FREE R (NO CUTOFF) BY 1%.
RfactorNum. reflection% reflectionSelection details
Rfree0.2066 545 5 %RANDOM (SAME SET AS FOR THE 1.2 A DATA, WHEN AVAILABLE)
all0.178 10468 --
obs0.1768 -98.7 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-2
Refine analyzeNum. disordered residues: 1 / Occupancy sum hydrogen: 323 / Occupancy sum non hydrogen: 390.5
Refinement stepCycle: LAST / Resolution: 1.4→7.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms355 0 10 37 402
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.012
X-RAY DIFFRACTIONs_angle_d0.03
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.028
X-RAY DIFFRACTIONs_zero_chiral_vol0.159
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.116
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.036
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.003
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.116
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.178 / Rfactor obs: 0.1648 / Rfactor Rwork: 0.1768
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_plane_restr0.361
X-RAY DIFFRACTIONs_chiral_restr0.159

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