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- PDB-2ol2: High Resolution Structure of Native PCI in Space Group P21 -

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Basic information

Entry
Database: PDB / ID: 2ol2
TitleHigh Resolution Structure of Native PCI in Space Group P21
ComponentsPlasma serine protease inhibitor
Keywordshydrolase inhibitor / serpin
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
Plasma serine protease inhibitor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLi, W. / Huntington, J.A.
Citation
Journal: 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.
#1: Journal: Structure / Year: 2003
Title: Crystal Structure of Protein C Inhibitor Provides Insights into Hormone Binding and Heparin Activation
Authors: Huntington, J.A. / Kjellberg, M. / Stenflo, J.
History
DepositionJan 18, 2007Deposition site: RCSB / Processing site: RCSB
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 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,1513
Polymers89,0592
Non-polymers921
Water5,116284
1
A: Plasma serine protease inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6222
Polymers44,5301
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Plasma serine protease inhibitor


Theoretical massNumber of molelcules
Total (without water)44,5301
Polymers44,5301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.017, 60.074, 133.171
Angle α, β, γ (deg.)90.00, 93.28, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Plasma serine protease inhibitor / PCI / Protein C inhibitor / Serpin A5 / Plasminogen activator inhibitor 3 / PAI-3 / PAI3 / ...PCI / Protein C inhibitor / Serpin A5 / Plasminogen activator inhibitor 3 / PAI-3 / PAI3 / Acrosomal serine protease inhibitor


Mass: 44529.680 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SERPINA5, PCI, PLANH3, PROCI / Plasmid: pET19b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) pLysS / References: UniProt: P05154
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 284 / 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: 2.51 Å3/Da / Density % sol: 51.02 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 6% PEG 3350, 0.04M ammonium citrate,10% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 31, 2006 / Details: Toroidal mirror
RadiationMonochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2→44.37 Å / Num. all: 58771 / Num. obs: 41523 / % possible obs: 67.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.8 % / Biso Wilson estimate: 15.5 Å2 / Rmerge(I) obs: 0.064 / Rsym value: 0.046 / Net I/σ(I): 9.1
Reflection shellResolution: 2→2.11 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 2.7 / Num. unique all: 1696 / Rsym value: 0.21 / % possible all: 19.9

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Processing

Software
NameVersionClassification
CNS1refinement
MxCuBEdata collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HI9

2hi9


Resolution: 2→26.09 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1770869.55 / Data cutoff high rms absF: 1770869.55 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.271 2074 5.1 %RANDOM
Rwork0.225 ---
obs0.225 40772 67.9 %-
all-41523 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 81.1631 Å2 / ksol: 0.362894 e/Å3
Displacement parametersBiso mean: 34.5 Å2
Baniso -1Baniso -2Baniso -3
1--6.36 Å20 Å2-0.14 Å2
2---2.13 Å20 Å2
3---8.49 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2→26.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5406 0 6 284 5696
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.461.5
X-RAY DIFFRACTIONc_mcangle_it2.382
X-RAY DIFFRACTIONc_scbond_it2.112
X-RAY DIFFRACTIONc_scangle_it2.992.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.305 104 5.3 %
Rwork0.27 1857 -
obs--19.9 %

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