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- PDB-1bx7: HIRUSTASIN FROM HIRUDO MEDICINALIS AT 1.2 ANGSTROMS -

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Basic information

Entry
Database: PDB / ID: 1bx7
TitleHIRUSTASIN FROM HIRUDO MEDICINALIS AT 1.2 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: 1.2 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: Structure / Year: 1997
Title: Erratum. 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.
#3: 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 / diffrn_source / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HIRUSTASIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,0793
Polymers5,8871
Non-polymers1922
Water93752
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
Components on special symmetry positions
IDModelComponents
11A-130-

HOH

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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.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 1.05
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 1996 / Details: BENT CRYSTAL
RadiationMonochromator: GE(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 1.2→25.2 Å / Num. obs: 15928 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 15
Reflection shellResolution: 1.2→1.25 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.376 / Mean I/σ(I) obs: 1.61 / % possible all: 98.1
Reflection shell
*PLUS
% possible obs: 98.1 %

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Processing

Software
NameClassification
MARXDSdata collection
MARSCALEdata reduction
SHELXL-97model building
SHELXL-97refinement
MARXDSdata reduction
MARSCALEdata scaling
SHELXL-97phasing
RefinementMethod to determine structure: AB INITIO / Resolution: 1.2→25.2 Å / Num. parameters: 4045 / Num. restraintsaints: 4895 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 2%
RfactorNum. reflection% reflectionSelection details
Rfree0.2254 792 5 %RANDOM
all0.1803 15894 --
obs0.1794 -99.2 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-2
Refine analyzeNum. disordered residues: 5 / Occupancy sum hydrogen: 342 / Occupancy sum non hydrogen: 417.02
Refinement stepCycle: LAST / Resolution: 1.2→25.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms387 0 10 52 449
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.014
X-RAY DIFFRACTIONs_angle_d0.036
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.029
X-RAY DIFFRACTIONs_zero_chiral_vol0.14
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.12
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.042
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.004
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.097
X-RAY DIFFRACTIONs_approx_iso_adps0.096
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.127 / Rfactor Rwork: 0.1794
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_plane_restr0.375
X-RAY DIFFRACTIONs_chiral_restr0.14

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