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- PDB-2oay: Crystal structure of latent human C1-inhibitor -

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Basic information

Entry
Database: PDB / ID: 2oay
TitleCrystal structure of latent human C1-inhibitor
ComponentsPlasma protease C1 inhibitor
KeywordsIMMUNE SYSTEM / HYDROLASE INHIBITOR / LATENT SERPIN / RCL INSERTION
Function / homology
Function and homology information


negative regulation of complement activation, lectin pathway / Defective SERPING1 causes hereditary angioedema / blood circulation / complement activation, classical pathway / fibrinolysis / Intrinsic Pathway of Fibrin Clot Formation / platelet alpha granule lumen / Regulation of Complement cascade / serine-type endopeptidase inhibitor activity / blood coagulation ...negative regulation of complement activation, lectin pathway / Defective SERPING1 causes hereditary angioedema / blood circulation / complement activation, classical pathway / fibrinolysis / Intrinsic Pathway of Fibrin Clot Formation / platelet alpha granule lumen / Regulation of Complement cascade / serine-type endopeptidase inhibitor activity / blood coagulation / Platelet degranulation / : / blood microparticle / endoplasmic reticulum lumen / innate immune response / extracellular space / extracellular exosome / extracellular region
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 protease C1 inhibitor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsHarmat, V. / Beinrohr, L. / Gal, P. / Dobo, J.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: C1 inhibitor serpin domain structure reveals the likely mechanism of heparin potentiation and conformational disease
Authors: Beinrohr, L. / Harmat, V. / Dobo, J. / Lorincz, Z. / Gal, P. / Zavodszky, P.
History
DepositionDec 18, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / diffrn_source ...chem_comp / diffrn_source / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Aug 30, 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
Revision 1.6Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Plasma protease C1 inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4015
Polymers43,9031
Non-polymers4974
Water1,26170
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.903, 98.903, 94.684
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Plasma protease C1 inhibitor / C1-INHIBITOR / C1 Inh / C1Inh / C1 esterase inhibitor / C1-inhibiting factor


Mass: 43903.484 Da / Num. of mol.: 1 / Fragment: serpin domain / Mutation: allele V458M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SERPING1, C1IN, C1NH / Plasmid: pPic9K / Production host: Pichia pastoris (fungus) / Strain (production host): GS115 / References: UniProt: P05155
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 70 / 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: 1

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Sample preparation

CrystalDensity Matthews: 3.04 Å3/Da / Density % sol: 59.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.85 M NaH2PO4, 0.85 M KH2PO4, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8162 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 3, 2006 / Details: mirrors
RadiationMonochromator: Si [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8162 Å / Relative weight: 1
ReflectionResolution: 2.35→84.52 Å / Num. obs: 21930 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 14.6 % / Biso Wilson estimate: 32.4 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 20.29
Reflection shellResolution: 2.35→2.4 Å / Redundancy: 9.54 % / Rmerge(I) obs: 0.652 / Mean I/σ(I) obs: 3.89 / Num. unique all: 1341 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345data collection
MOLREPphasing
REFMAC5.1.24refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Ensemble of truncated serpin structures. PDB codes: 4CAA, 1QMB, 1E05, 1DVM, 1C8O, 1JTI, 1JJO, 1MTP, 1HLE, 1JRR

4caa

1qmb

1e05

1dvm

1c8o

1jti

1jjo

1mtp

1hle

1jrr


Resolution: 2.35→84.52 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.948 / SU B: 6.574 / SU ML: 0.154 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.239 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21794 1125 5.1 %RANDOM
Rwork0.17363 ---
all0.17595 20803 --
obs0.17595 20803 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 32.433 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å20.14 Å20 Å2
2--0.29 Å20 Å2
3----0.43 Å2
Refinement stepCycle: LAST / Resolution: 2.35→84.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2845 0 32 70 2947
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0222952
X-RAY DIFFRACTIONr_bond_other_d0.0010.022693
X-RAY DIFFRACTIONr_angle_refined_deg1.7641.9674015
X-RAY DIFFRACTIONr_angle_other_deg0.80436265
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4795370
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0980.2481
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023204
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02558
X-RAY DIFFRACTIONr_nbd_refined0.2160.3599
X-RAY DIFFRACTIONr_nbd_other0.2560.33056
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.10.51927
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.5148
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2730.313
X-RAY DIFFRACTIONr_symmetry_vdw_other0.390.345
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1860.59
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0721852
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.23833006
X-RAY DIFFRACTIONr_scbond_it2.12321100
X-RAY DIFFRACTIONr_scangle_it3.36731006
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.32 78
Rwork0.227 1546
Refinement TLS params.Method: refined / Origin x: -14.7946 Å / Origin y: 71.6738 Å / Origin z: -0.6784 Å
111213212223313233
T0.106 Å20.0229 Å2-0.0025 Å2-0.038 Å20.0519 Å2--0.1121 Å2
L1.5314 °20.1233 °20.1272 °2-2.5613 °21.5387 °2--2.821 °2
S-0.022 Å °-0.0272 Å °0.047 Å °-0.0132 Å °-0.0308 Å °-0.0146 Å °-0.1414 Å °-0.2032 Å °0.0528 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA101 - 47613 - 388
2X-RAY DIFFRACTION1AB500

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