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- PDB-2hi9: Crystal Structure of human native protein C inhibitor -

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Basic information

Entry
Database: PDB / ID: 2hi9
TitleCrystal Structure of human native protein C inhibitor
ComponentsPlasma serine protease inhibitor
KeywordsHYDROLASE inhibitor / Serpin / coagulation / haemostasis / thrombin inhibitor / activated protein C inhibitor / acrosin inhibitor / serine protease inhibitor
Function / homology
Function and homology information


protein C inhibitor-TMPRSS7 complex / protein C inhibitor-TMPRSS11E complex / protein C inhibitor-PLAT complex / protein C inhibitor-PLAU complex / protein C inhibitor-thrombin complex / protein C inhibitor-KLK3 complex / protein C inhibitor-plasma kallikrein complex / protein C inhibitor-coagulation factor V complex / protein C inhibitor-coagulation factor Xa complex / protein C inhibitor-coagulation factor XI complex ...protein C inhibitor-TMPRSS7 complex / protein C inhibitor-TMPRSS11E complex / protein C inhibitor-PLAT complex / protein C inhibitor-PLAU complex / protein C inhibitor-thrombin complex / protein C inhibitor-KLK3 complex / protein C inhibitor-plasma kallikrein complex / protein C inhibitor-coagulation factor V complex / protein C inhibitor-coagulation factor Xa complex / protein C inhibitor-coagulation factor XI complex / acrosin binding / platelet dense tubular network / fusion of sperm to egg plasma membrane involved in single fertilization / acrosomal membrane / platelet alpha granule / phosphatidylcholine binding / glycosaminoglycan binding / negative regulation of hydrolase activity / retinoic acid binding / lipid transport / Common Pathway of Fibrin Clot Formation / Intrinsic Pathway of Fibrin Clot Formation / serine-type endopeptidase inhibitor activity / heparin binding / spermatogenesis / protease binding / external side of plasma membrane / protein-containing complex / extracellular space / extracellular exosome / extracellular region / membrane
Similarity search - Function
Antithrombin; Chain I, domain 2 / Antithrombin, subunit I, domain 2 / Alpha-1-antitrypsin; domain 1 / Alpha-1-antitrypsin, domain 1 / Serpin, conserved site / Serpins signature. / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily ...Antithrombin; Chain I, domain 2 / Antithrombin, subunit I, domain 2 / Alpha-1-antitrypsin; domain 1 / Alpha-1-antitrypsin, domain 1 / Serpin, conserved site / Serpins signature. / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily / Serpin superfamily, domain 1 / Serpin (serine protease inhibitor) / SERine Proteinase INhibitors / Roll / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / Plasma serine protease inhibitor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLi, W. / Adams, T.E. / Huntington, J.A.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Structure of native protein C inhibitor provides insight into its multiple functions.
Authors: Li, W. / Adams, T.E. / Kjellberg, M. / Stenflo, J. / Huntington, J.A.
History
DepositionJun 29, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 13, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Plasma serine protease inhibitor
B: Plasma serine protease inhibitor
C: Plasma serine protease inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,4767
Polymers122,8073
Non-polymers6684
Water6,882382
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)198.590, 70.950, 123.880
Angle α, β, γ (deg.)90.000, 127.920, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1125-

HOH

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Components

#1: Protein Plasma serine protease inhibitor / PCI / Protein C inhibitor / Plasminogen activator inhibitor 3 / PAI-3 / PAI3 / Acrosomal serine ...PCI / Protein C inhibitor / Plasminogen activator inhibitor 3 / PAI-3 / PAI3 / Acrosomal serine protease inhibitor


Mass: 40935.816 Da / Num. of mol.: 3 / Fragment: residues 25-387
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SERPINA5 / Production host: Escherichia coli (E. coli) / References: UniProt: P05154
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 382 / 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: 2.8 Å3/Da / Density % sol: 56.11 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 66.7mM tri-potassium citrate, 6.7% PEG3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 16, 2005
Details: monochromator is one of two assymetric cut Si (111) crytals
RadiationMonochromator: Si (111) crytals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2.3→35 Å / Num. all: 60705 / Num. obs: 60523 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 28.2 Å2 / Rmerge(I) obs: 0.083
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.396 / Mean I/σ(I) obs: 2.9 / Num. unique all: 8725 / % possible all: 99

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Processing

Software
NameVersionClassificationNB
CNS1refinement
PDB_EXTRACT2data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→20 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2317208.5 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.269 2449 4.1 %RANDOM
Rwork0.227 ---
all0.229 62663 --
obs0.227 60214 99.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.583 Å2 / ksol: 0.338 e/Å3
Displacement parametersBiso mean: 42.8 Å2
Baniso -1Baniso -2Baniso -3
1--3.99 Å20 Å23.54 Å2
2--6.08 Å20 Å2
3----2.08 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.44 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8270 0 45 382 8697
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.9
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_mcbond_it1.571.5
X-RAY DIFFRACTIONc_mcangle_it2.652
X-RAY DIFFRACTIONc_scbond_it2.232
X-RAY DIFFRACTIONc_scangle_it3.342.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.376 400 4.1 %
Rwork0.339 9434 -
obs-9834 98.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water.paramwater.top
X-RAY DIFFRACTION3carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION4citrate2.paramcitrate2.top
X-RAY DIFFRACTION5glycerol.paramglycerol.top

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