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- PDB-5duq: Active human c1-inhibitor in complex with dextran sulfate -

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Basic information

Entry
Database: PDB / ID: 5duq
TitleActive human c1-inhibitor in complex with dextran sulfate
ComponentsPlasma protease C1 inhibitor
KeywordsHYDROLASE / Serine protein inhibitor / Complex with Glycosaminoglycan
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 / platelet alpha granule lumen / complement activation, classical pathway / 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 / platelet alpha granule lumen / complement activation, classical pathway / 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
alpha-cellobiose / alpha-D-glucopyranose / SULFITE ION / Plasma protease C1 inhibitor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.9 Å
AuthorsDijk, M. / Holkers, J. / Voskamp, P. / Giannetti, B.M. / Waterreus, W.J. / van Veen, H.A. / Pannu, N.S.
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 20, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 31, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2017Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)86,8727
Polymers85,8272
Non-polymers1,0455
Water43224
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2370 Å2
ΔGint5 kcal/mol
Surface area31830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.100, 197.424, 56.779
Angle α, β, γ (deg.)90.00, 103.31, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A115 - 475
2010B115 - 475

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 42913.410 Da / Num. of mol.: 2
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

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Sugars , 3 types, 4 molecules

#2: Polysaccharide beta-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-cellobiose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-cellobiose
DescriptorTypeProgram
DGlcpb1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1a_1-5][a2122h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][b-D-Glcp]{}}LINUCSPDB-CARE
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: isolated from a natural 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
#4: Sugar ChemComp-GLC / alpha-D-glucopyranose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 25 molecules

#5: Chemical ChemComp-SO3 / SULFITE ION


Mass: 80.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 3.64 Å3/Da / Density % sol: 66.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 11 mg/ml of C1-inhibitor was mixed with 5kDa dextran sulfate in a 1:2 molar ratio and incubated on ice for an hour. Crystals grew in0.1 M SPG (pH 9), 25% w/v PEG 1500 0.1 M MgCl hexahydrate after 10 days.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.9→44.36 Å / Num. obs: 26376 / % possible obs: 98.6 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.113 / Net I/σ(I): 7.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementResolution: 2.9→44.36 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.903 / SU B: 27.283 / SU ML: 0.442 / Cross valid method: THROUGHOUT / ESU R: 1.31 / ESU R Free: 0.399 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27829 1294 4.9 %RANDOM
Rwork0.22846 ---
obs0.23084 24919 98.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 94.406 Å2
Baniso -1Baniso -2Baniso -3
1-7.7 Å20 Å21.33 Å2
2---5.72 Å2-0 Å2
3----2.34 Å2
Refinement stepCycle: LAST / Resolution: 2.9→44.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5749 0 67 24 5840
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0195940
X-RAY DIFFRACTIONr_bond_other_d0.0050.025775
X-RAY DIFFRACTIONr_angle_refined_deg1.5891.988056
X-RAY DIFFRACTIONr_angle_other_deg1.175313337
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4345725
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.06724.917242
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.997151066
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5511520
X-RAY DIFFRACTIONr_chiral_restr0.0780.2965
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216511
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021295
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_it6.5029.1762906
X-RAY DIFFRACTIONr_mcbond_other6.5019.1762905
X-RAY DIFFRACTIONr_mcangle_it10.41213.7533629
X-RAY DIFFRACTIONr_mcangle_other10.41113.7533630
X-RAY DIFFRACTIONr_scbond_it6.4339.7883032
X-RAY DIFFRACTIONr_scbond_other6.4249.7823029
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other10.50914.4214425
X-RAY DIFFRACTIONr_long_range_B_refined15.28571.7836374
X-RAY DIFFRACTIONr_long_range_B_other15.28471.7966375
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 47194 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.06 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.446 111 -
Rwork0.436 1856 -
obs--99.54 %

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