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- PDB-5du3: Active form of human C1-inhibitor -

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Basic information

Entry
Database: PDB / ID: 5du3
TitleActive form of human C1-inhibitor
ComponentsPlasma protease C1 inhibitor
Keywordshydrolase inhibitor / Serine protease inhibitor
Function / homology
Function and homology information


negative regulation of complement activation, lectin pathway / Defective SERPING1 causes hereditary angioedema / blood circulation / fibrinolysis / Intrinsic Pathway of Fibrin Clot Formation / complement activation, classical pathway / 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 / fibrinolysis / Intrinsic Pathway of Fibrin Clot Formation / complement activation, classical pathway / platelet alpha granule lumen / Regulation of Complement cascade / serine-type endopeptidase inhibitor activity / blood coagulation / Platelet degranulation / collagen-containing extracellular matrix / blood microparticle / endoplasmic reticulum lumen / innate immune response / extracellular space / extracellular exosome / extracellular region
Similarity search - Function
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
Similarity search - Domain/homology
Plasma protease C1 inhibitor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsPannu, N.S. / Dijk, M. / Holkers, J. / Voskamp, P. / Giannetti, B.M. / Waterreus, W.J. / van Veen, H.A.
CitationJournal: Structure / Year: 2016
Title: How Dextran Sulfate Affects C1-inhibitor Activity: A Model for Polysaccharide Potentiation.
Authors: Dijk, M. / Holkers, J. / Voskamp, P. / Giannetti, B.M. / Waterreus, W.J. / van Veen, H.A. / Pannu, N.S.
History
DepositionSep 18, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 31, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2017Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Plasma protease C1 inhibitor
B: Plasma protease C1 inhibitor


Theoretical massNumber of molelcules
Total (without water)85,5602
Polymers85,5602
Non-polymers00
Water2,720151
1
A: Plasma protease C1 inhibitor


Theoretical massNumber of molelcules
Total (without water)42,7801
Polymers42,7801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Plasma protease C1 inhibitor


Theoretical massNumber of molelcules
Total (without water)42,7801
Polymers42,7801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.410, 75.380, 203.960
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: CYS / Beg label comp-ID: CYS / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: 0 / Auth seq-ID: 101 - 476 / Label seq-ID: 5 - 380

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Plasma protease C1 inhibitor / C1Inh / C1 esterase inhibitor / C1-inhibiting factor / Serpin G1


Mass: 42780.234 Da / Num. of mol.: 2 / Fragment: UNP residues 119-500
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SERPING1, C1IN, C1NH / Production host: Oryctolagus cuniculus (rabbit) / References: UniProt: P05155
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20% PEG3350 w/v and 200 mM KF with a crystallization drop size of 1 microlitre and a protein content of 70% w/v

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.953 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953 Å / Relative weight: 1
ReflectionResolution: 2.1→57.4 Å / Num. obs: 52693 / % possible obs: 100 % / Redundancy: 4.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.042 / Net I/σ(I): 14
Reflection shellResolution: 2.1→2.16 Å / Mean I/σ(I) obs: 1.6 / CC1/2: 0.622 / Rpim(I) all: 0.431 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OAY

2oay


Resolution: 2.1→57.4 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.926 / SU B: 13.723 / SU ML: 0.17 / Cross valid method: THROUGHOUT / ESU R: 0.215 / ESU R Free: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25697 2647 5 %RANDOM
Rwork0.20567 ---
obs0.20818 49868 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.186 Å2
Baniso -1Baniso -2Baniso -3
1--0.78 Å20 Å20 Å2
2---0.92 Å20 Å2
3---1.7 Å2
Refinement stepCycle: 1 / Resolution: 2.1→57.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5946 0 0 151 6097
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0196077
X-RAY DIFFRACTIONr_bond_other_d0.0090.025925
X-RAY DIFFRACTIONr_angle_refined_deg2.0661.978244
X-RAY DIFFRACTIONr_angle_other_deg1.628313676
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2555753
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.45124.819249
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.927151093
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5851522
X-RAY DIFFRACTIONr_chiral_restr0.130.2977
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0216702
X-RAY DIFFRACTIONr_gen_planes_other0.0080.021336
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_it2.42.3853011
X-RAY DIFFRACTIONr_mcbond_other2.42.3843010
X-RAY DIFFRACTIONr_mcangle_it3.9543.5493755
X-RAY DIFFRACTIONr_mcangle_other3.9543.553756
X-RAY DIFFRACTIONr_scbond_it2.6092.6913066
X-RAY DIFFRACTIONr_scbond_other2.6082.6923067
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.423.9024490
X-RAY DIFFRACTIONr_long_range_B_refined6.86918.6896623
X-RAY DIFFRACTIONr_long_range_B_other6.86418.6016591
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 43950 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.16 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 188 -
Rwork0.315 3620 -
obs--99.32 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.14140.22010.21710.41960.30851.46370.04940.00660.04740.061-0.05650.06240.09220.02420.00710.1868-0.00240.02610.3042-0.020.02640.17867.57844.637
20.61960.0379-0.19450.33690.0261.7729-0.092-0.069-0.0498-0.113-0.02580.0331-0.13080.02490.11780.18370.0042-0.02020.29490.00820.01429.32977.7698.023
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A100 - 475
2X-RAY DIFFRACTION2B101 - 475

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