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- PDB-1skz: PROTEASE INHIBITOR -

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Basic information

Entry
Database: PDB / ID: 1skz
TitlePROTEASE INHIBITOR
ComponentsANTISTASIN
KeywordsSERINE PROTEASE INHIBITOR / ANTISTASIN / FACTOR XA INHIBITOR / THROMBOSIS
Function / homology
Function and homology information


negative regulation of coagulation / serine-type endopeptidase inhibitor activity / blood coagulation / 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 speciesHaementeria officinalis (Mexican leech)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.9 Å
AuthorsKrengel, U. / Dijkstra, B.W.
Citation
Journal: EMBO J. / Year: 1997
Title: X-ray structure of antistasin at 1.9 A resolution and its modelled complex with blood coagulation factor Xa.
Authors: Lapatto, R. / Krengel, U. / Schreuder, H.A. / Arkema, A. / de Boer, B. / Kalk, K.H. / Hol, W.G. / Grootenhuis, P.D. / Mulders, J.W. / Dijkema, R. / Theunissen, H.J. / Dijkstra, B.W.
#1: Journal: Hasylab Jahresbericht / Year: 1996
Title: Refined X-Ray Structure of Antistasin at 1.9 A Resolution
Authors: Krengel, U. / Lapatto, R. / Dijkstra, B.W.
#2: Journal: J.Mol.Biol. / Year: 1993
Title: Crystallization and Preliminary Crystallographic Analysis of Antistasin, a Leech-Derived Inhibitor of Blood Coagulation Factor Xa
Authors: Schreuder, H. / Arkema, A. / De Boer, B. / Kalk, K. / Dijkema, R. / Mulders, J. / Theunissen, H. / Hol, W.
History
DepositionApr 16, 1997Processing site: BNL
Revision 1.0Oct 22, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ANTISTASIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4112
Polymers13,3761
Non-polymers351
Water1,58588
1
A: ANTISTASIN
hetero molecules

A: ANTISTASIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8224
Polymers26,7512
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555x,-y,-z1
Unit cell
Length a, b, c (Å)76.500, 76.500, 86.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

#1: Protein ANTISTASIN / FACTOR XA INHIBITOR


Mass: 13375.696 Da / Num. of mol.: 1 / Mutation: Q1E, G2D, M35V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haementeria officinalis (Mexican leech)
Organ: BLOOD / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P15358
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.8 %
Description: THE FINAL HIGH RESOLUTION DATA SET WAS OBTAINED BY SCALING 3 PARTIAL DATA SETS, ONE FROM DESY (TO 1.9 A) AND TWO DATA SETS COLLECTED IN HOUSE (BOTH TO 2.5 A).
Crystal growMethod: vapor diffusion, hanging drop / pH: 6
Details: EQUILIBRATION AGAINST 100 MM NA CITRATE (PH6.0), 1MM PMSF, 10 MM NA AZIDE, 31% (W/V) AMMONIUM SULFATE, 2.75 M NA CHLORIDE IN HANGING DROPS. FOR CRYO EXPERIMENTS TRANSFER TO 100 MM NA CITRATE ...Details: EQUILIBRATION AGAINST 100 MM NA CITRATE (PH6.0), 1MM PMSF, 10 MM NA AZIDE, 31% (W/V) AMMONIUM SULFATE, 2.75 M NA CHLORIDE IN HANGING DROPS. FOR CRYO EXPERIMENTS TRANSFER TO 100 MM NA CITRATE (PH6.0), 30% (W/V) AMMONIUM SULFATE, 2.2 M NA CHLORIDE, 20% GLYCEROL, AFTER PREEQUILIBRATION AGAINST THIS SOLUTION., vapor diffusion - hanging drop
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: Schreuder, H., (1993) J.Mol.Biol., 231, 1137.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlprotein1drop
255 mMsodium citrate1drop
31 mMPMSF1drop
410 mMsodium azide1drop
52.75 M1dropNaCl
715.5 %(w/v)satammonium sulfate1drop
8100 mMsodium citrate1reservoir
91 mMPMSF1reservoir
1010 mMsodium azide1reservoir
1131 %(w/v)satammonium sulfate1reservoir
122.75 M1reservoirNaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, Hamburg / Beamline: BW7A / Wavelength: 0.99
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 1, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 1.9→9.9 Å / Num. obs: 10300 / % possible obs: 95 % / Observed criterion σ(I): 0 / Redundancy: 9.7 % / Rmerge(I) obs: 0.08 / Rsym value: 0.38 / Net I/σ(I): 173
Reflection shellResolution: 1.9→2 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.071 / Mean I/σ(I) obs: 110 / Rsym value: 0.071 / % possible all: 92
Reflection
*PLUS
Num. measured all: 100326 / Rmerge(I) obs: 0.08

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Processing

Software
NameVersionClassification
XDSdata scaling
XSCALEdata scaling
X-PLOR3.843model building
X-PLOR3.843refinement
XDSdata reduction
X-PLOR3.843phasing
RefinementMethod to determine structure: MIR / Resolution: 1.9→5 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: DURING THE REFINEMENT, 10% OF THE REFLECTIONS WERE SET ASIDE TO CALCULATE THE FREE R-FACTOR. THE LAST ROUND OF REFINEMENT, WHICH RESULTED IN AN R-FACTOR 0.215 AND A FREE R-FACTOR OF 0.274, ...Details: DURING THE REFINEMENT, 10% OF THE REFLECTIONS WERE SET ASIDE TO CALCULATE THE FREE R-FACTOR. THE LAST ROUND OF REFINEMENT, WHICH RESULTED IN AN R-FACTOR 0.215 AND A FREE R-FACTOR OF 0.274, WAS THEN REPEATED WITH ALL THE REFLECTIONS FOR THE FINAL RESULTS.
RfactorNum. reflection% reflection
Rwork0.217 --
obs0.217 9103 94 %
Rfree--10 %
Displacement parametersBiso mean: 26 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: LAST / Resolution: 1.9→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms790 0 1 88 879
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.49
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.6
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2.5
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2
X-RAY DIFFRACTIONx_mcangle_it3.3
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_scangle_it3.3
LS refinement shellResolution: 1.9→1.98 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rwork0.323 1083 -
obs--92 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.WATTOPH19.WAT
X-RAY DIFFRACTION3PARAM.CLTOPH.CL

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