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- PDB-6a8o: Crystal structures of the serine protease domain of murine plasma... -

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Basic information

Entry
Database: PDB / ID: 6a8o
TitleCrystal structures of the serine protease domain of murine plasma kallikrein with peptide inhibitor mupain-1-16
Components
  • Plasma kallikrein
  • peptide inhibitor,
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
alpha-D-mannopyranose / piperidine-1-carboximidamide / Plasma kallikrein
Similarity search - Component
Biological speciesMus musculus (house mouse)
Synthemiopsis (insect)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.77 Å
AuthorsXu, M. / Jiang, L. / Huang, M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31370737, 31400637, 31170707, 31570745, 31670739, 21603033, U1405229 China
CitationJournal: Febs Lett. / Year: 2018
Title: Crystal structure of plasma kallikrein reveals the unusual flexibility of the S1 pocket triggered by Glu217.
Authors: Xu, M. / Chen, Y. / Xu, P. / Andreasen, P.A. / Jiang, L. / Li, J. / Huang, M.
History
DepositionJul 9, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 10, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 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 1.3Nov 22, 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
P: peptide inhibitor,
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8836
Polymers56,3963
Non-polymers4883
Water0
1
B: Plasma kallikrein
P: peptide inhibitor,
hetero molecules

A: Plasma kallikrein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8836
Polymers56,3963
Non-polymers4883
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x+1/2,-y+1/2,-z1
Buried area2770 Å2
ΔGint-10 kcal/mol
Surface area22180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.260, 82.450, 105.320
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 / / Fletcher factor / Kininogenin / Plasma prekallikrein


Mass: 27645.303 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Klkb1, Klk3, Pk / Variant: C122S / Production host: Pichia (fungus) / References: UniProt: P26262, plasma kallikrein
#2: Protein/peptide peptide inhibitor,


Mass: 1105.242 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synthemiopsis (insect) / Production host: Synthesiomyia (fry)
#3: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / 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: Chemical ChemComp-MRZ / piperidine-1-carboximidamide


Mass: 127.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13N3

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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: 2.95 Å3/Da / Density % sol: 58.31 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 4, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.77→52.66 Å / Num. obs: 16315 / % possible obs: 99.8 % / Redundancy: 7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.039 / Net I/σ(I): 15.73
Reflection shellResolution: 2.77→2.87 Å / Rmerge(I) obs: 0.09 / Mean I/σ(I) obs: 15.73 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
xia2data reduction
xia2data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ANY

2any


Resolution: 2.77→52.66 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.864 / SU B: 17.263 / SU ML: 0.344 / Cross valid method: THROUGHOUT / ESU R: 2.536 / ESU R Free: 0.42 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.3 814 5 %RANDOM
Rwork0.212 ---
obs0.217 15501 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 69.17 Å2
Baniso -1Baniso -2Baniso -3
1--2 Å20 Å20 Å2
2--2.53 Å20 Å2
3----0.54 Å2
Refinement stepCycle: LAST / Resolution: 2.77→52.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3799 0 22 0 3821
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0133915
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173580
X-RAY DIFFRACTIONr_angle_refined_deg1.6421.6575310
X-RAY DIFFRACTIONr_angle_other_deg1.2071.5938361
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.55467
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.56324.057175
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.42915666
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3541512
X-RAY DIFFRACTIONr_chiral_restr0.0630.2519
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024227
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02757
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it6.3187.0451909
X-RAY DIFFRACTIONr_mcbond_other6.3027.041908
X-RAY DIFFRACTIONr_mcangle_it9.55410.5492362
X-RAY DIFFRACTIONr_mcangle_other9.55510.5542363
X-RAY DIFFRACTIONr_scbond_it7.1757.8162006
X-RAY DIFFRACTIONr_scbond_other7.1737.8162006
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other10.92111.4072949
X-RAY DIFFRACTIONr_long_range_B_refined14.35782.0354326
X-RAY DIFFRACTIONr_long_range_B_other14.35582.0654327
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.77→2.84 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.417 47 -
Rwork0.325 1142 -
obs--99.83 %

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