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- PDB-1hia: KALLIKREIN COMPLEXED WITH HIRUSTASIN -

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Basic information

Entry
Database: PDB / ID: 1hia
TitleKALLIKREIN COMPLEXED WITH HIRUSTASIN
Components
  • (KALLIKREIN) x 2
  • HIRUSTASIN
KeywordsCOMPLEX (PROTEASE/INHIBITOR) / COMPLEX (PROTEASE-INHIBITOR) / TISSUE KALLIKREIN / SERINE PROTEASE / TRYPSIN / PSA / KININ / SERPIN / COMPLEX (PROTEASE-INHIBITOR) complex
Function / homology
Function and homology information


tissue kallikrein / negative regulation of coagulation / regulation of systemic arterial blood pressure / zymogen activation / secretory granule / serine-type endopeptidase inhibitor activity / heparin binding / serine-type endopeptidase activity / extracellular space / 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 / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site ...Proteinase inhibitor I15, leech antistasin / Antistasin; domain 1 / Antistasin; domain 1 / Antistasin-like domain / Antistasin family / Antistasin-like domain profile. / Hirudin/antistatin / Ribbon / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Glandular kallikrein / Hirustasin
Similarity search - Component
Biological speciesSus scrofa (pig)
Hirudo medicinalis (medicinal leech)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsMittl, P. / Di Marco, S. / Gruetter, M.
Citation
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.
#1: 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.
History
DepositionDec 12, 1996Processing site: BNL
Revision 1.0Dec 24, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Refinement description
Category: database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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: KALLIKREIN
B: KALLIKREIN
I: HIRUSTASIN
X: KALLIKREIN
Y: KALLIKREIN
J: HIRUSTASIN


Theoretical massNumber of molelcules
Total (without water)61,6616
Polymers61,6616
Non-polymers00
Water5,477304
1
A: KALLIKREIN
B: KALLIKREIN
I: HIRUSTASIN


Theoretical massNumber of molelcules
Total (without water)30,8313
Polymers30,8313
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7520 Å2
ΔGint-56 kcal/mol
Surface area12030 Å2
MethodPISA
2
X: KALLIKREIN
Y: KALLIKREIN
J: HIRUSTASIN


Theoretical massNumber of molelcules
Total (without water)30,8313
Polymers30,8313
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7620 Å2
ΔGint-54 kcal/mol
Surface area11970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.900, 86.000, 69.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.99998, -0.00234, 0.00522), (0.00235, -1, 0.00076), (0.00522, 0.00077, 0.99999)58.15774, 57.49194, -34.84722
2given(-0.99998, -0.00234, 0.00522), (0.00235, -1, 0.00076), (0.00522, 0.00077, 0.99999)58.15774, 57.49194, -34.84722

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Components

#1: Protein KALLIKREIN


Mass: 9119.133 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Organ: PANCREAS / References: UniProt: P00752, tissue kallikrein
#2: Protein KALLIKREIN


Mass: 16511.477 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Organ: PANCREAS / References: UniProt: P00752, tissue kallikrein
#3: Protein/peptide HIRUSTASIN


Mass: 5200.117 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hirudo medicinalis (medicinal leech) / Organ: PANCREAS / References: UniProt: P80302
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 304 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.77 Å3/Da / Density % sol: 56.49 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 5
Details: HANGING DROP, RESERVOIR: 23% PEG2000, 180MM AM2SO4, 3.5% DIOXANE 100 MM SODIUM ACETATE, PH 4.6. DROP: 1:1 RATIO OF HIRUSTASIN:KALLIKREIN IN 20MM TRIS-HCL, PH 8.0, pH 5.0, vapor diffusion - hanging drop
PH range: 4.6-8.0
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.5 mMkallikrein1drop
20.85 mMhirustasin1drop
320 mMTris-HCl1drop
423 %PEG20001reservoir
50.18 Mammonium sulfate1reservoir
63.5 %dioxane1reservoir
70.1 Msodium acetate1reservoir

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Data collection

DiffractionMean temperature: 297 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM1A / Wavelength: 0.875
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 1995
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.875 Å / Relative weight: 1
ReflectionResolution: 2.4→25 Å / Num. obs: 27511 / % possible obs: 97.9 % / Redundancy: 3.5 % / Rsym value: 0.126 / Net I/σ(I): 11.2
Reflection shellResolution: 2.4→2.45 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 2.3 / Rsym value: 0.474 / % possible all: 98.6
Reflection
*PLUS
Num. measured all: 96170 / Rmerge(I) obs: 0.126
Reflection shell
*PLUS
% possible obs: 98.6 % / Rmerge(I) obs: 0.474

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Processing

Software
NameVersionClassification
MARXDSdata collection
MARSCALEdata reduction
AMoREphasing
X-PLOR3.1refinement
MARXDSdata reduction
MARSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2PKA

2pka


Resolution: 2.4→8 Å / Rfactor Rfree error: 0 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT
Details: N-TERMINAL RESIDUES (I/J 5-23) OF HIRUSTASIN HAVE HIGH B-FACTORS. NCS-RELATED MOLECULES ARE RELATED BY THE SAME ORIENTATION (IDENTITY MATRIX) AND THE FRACTIONAL TRANSLATION VECTOR (1/2, 1/3, ...Details: N-TERMINAL RESIDUES (I/J 5-23) OF HIRUSTASIN HAVE HIGH B-FACTORS. NCS-RELATED MOLECULES ARE RELATED BY THE SAME ORIENTATION (IDENTITY MATRIX) AND THE FRACTIONAL TRANSLATION VECTOR (1/2, 1/3, 1/2). THIS PACKING EXERTS THE EXTINCTION PATTERN K=3N: H+L=2N.
RfactorNum. reflection% reflectionSelection details
Rfree0.311 2678 9.8 %RANDOM
Rwork0.205 ---
obs0.205 26769 97.9 %-
Displacement parametersBiso mean: 46.2 Å2
Baniso -1Baniso -2Baniso -3
1--6.48 Å20 Å20 Å2
2--4.42 Å20 Å2
3---2.07 Å2
Refinement stepCycle: LAST / Resolution: 2.4→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4280 0 0 304 4584
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
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_deg1.719
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.22
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.379
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_scangle_it2.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.22
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.379

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