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- PDB-5gvt: Crystal structures of the serine protease domain of murine plasma... -

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Basic information

Entry
Database: PDB / ID: 5gvt
TitleCrystal structures of the serine protease domain of murine plasma kallikrein
ComponentsPlasma kallikrein
KeywordsHYDROLASE / serine protease / murine plasma kallikrein
Function / homology
Function and homology information


Intrinsic Pathway of Fibrin Clot Formation / Activation of Matrix Metalloproteinases / plasma kallikrein / blood coagulation, intrinsic pathway / positive regulation of fibrinolysis / zymogen activation / plasminogen activation / fibrinolysis / inflammatory response / serine-type endopeptidase activity ...Intrinsic Pathway of Fibrin Clot Formation / Activation of Matrix Metalloproteinases / plasma kallikrein / blood coagulation, intrinsic pathway / positive regulation of fibrinolysis / zymogen activation / plasminogen activation / fibrinolysis / inflammatory response / serine-type endopeptidase activity / proteolysis / extracellular space
Similarity search - Function
Apple domain. / Apple domain / APPLE domain / PAN/Apple domain profile. / PAN domain / PAN/Apple domain / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. ...Apple domain. / Apple domain / APPLE domain / PAN/Apple domain profile. / PAN domain / PAN/Apple domain / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / 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
beta-D-mannopyranose / alpha-D-mannopyranose / Plasma kallikrein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 Å
AuthorsXu, M. / Jiang, L. / Huang, M.
Funding support China, 1items
OrganizationGrant numberCountry
the Natural Science Foundation of China31570745, 31370737, 31400637 China
CitationJournal: Chin.J.Struct.Chem. / Year: 2017
Title: Crystal Structures of the Serine Protease Domain of Murine Plasma Kallikrein
Authors: Xu, M. / Xu, P. / Zhou, X. / Andreasen, P. / Jiang, L. / Huang, M.
History
DepositionSep 6, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 22, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Plasma kallikrein
B: Plasma kallikrein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4406
Polymers55,7192
Non-polymers7214
Water25214
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1610 Å2
ΔGint5 kcal/mol
Surface area22210 Å2
Unit cell
Length a, b, c (Å)72.231, 85.556, 109.229
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Plasma kallikrein


Mass: 27859.521 Da / Num. of mol.: 2
Fragment: Plasma kallikrein light chain, serine protease domain
Mutation: C122S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Klkb1, Klk3, Pk / Production host: Komagataella pastoris (fungus) / References: UniProt: P26262, plasma kallikrein
#2: Sugar ChemComp-BMA / beta-D-mannopyranose / beta-D-mannose / D-mannose / mannose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-mannopyranoseCOMMON NAMEGMML 1.0
b-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 1

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Sample preparation

CrystalDensity Matthews: 3.03 Å3/Da / Density % sol: 59.41 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 8.5 / Details: PEG 3350 25%, 0.1M Tris-HCl, 0.1M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 21266 / % possible obs: 98.4 % / Redundancy: 3.9 % / Net I/σ(I): 13.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ANY

2any


Resolution: 2.61→46.04 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 28.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.253 1023 4.97 %RANDOM
Rwork0.219 ---
obs0.221 20565 96.7 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.61→46.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3622 0 44 14 3680
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0153759
X-RAY DIFFRACTIONf_angle_d1.695093
X-RAY DIFFRACTIONf_dihedral_angle_d17.6441389
X-RAY DIFFRACTIONf_chiral_restr0.061565
X-RAY DIFFRACTIONf_plane_restr0.007632
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6066-2.74410.37961050.30882231X-RAY DIFFRACTION78
2.7441-2.9160.33141540.29342787X-RAY DIFFRACTION99
2.916-3.14110.32611410.27032863X-RAY DIFFRACTION100
3.1411-3.45710.27061740.24222842X-RAY DIFFRACTION100
3.4571-3.95710.25081520.21172875X-RAY DIFFRACTION100
3.9571-4.98450.21961490.18362906X-RAY DIFFRACTION100
4.9845-46.04190.22861480.2113038X-RAY DIFFRACTION99

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