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- PDB-1xx9: Crystal Structure of the FXIa Catalytic Domain in Complex with Ec... -

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Basic information

Entry
Database: PDB / ID: 1xx9
TitleCrystal Structure of the FXIa Catalytic Domain in Complex with EcotinM84R
Components
  • Coagulation factor XI
  • Ecotin
KeywordsBLOOD CLOTTING/HYDROLASE INHIBITOR / FXIa / Catalytic domain / Serine protein / Ecotin / BLOOD CLOTTING-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


coagulation factor XIa / serine-type aminopeptidase activity / Defective F9 activation / positive regulation of fibrinolysis / plasminogen activation / Intrinsic Pathway of Fibrin Clot Formation / serine-type endopeptidase inhibitor activity / blood coagulation / heparin binding / outer membrane-bounded periplasmic space ...coagulation factor XIa / serine-type aminopeptidase activity / Defective F9 activation / positive regulation of fibrinolysis / plasminogen activation / Intrinsic Pathway of Fibrin Clot Formation / serine-type endopeptidase inhibitor activity / blood coagulation / heparin binding / outer membrane-bounded periplasmic space / serine-type endopeptidase activity / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane
Similarity search - Function
Ecotin / Ecotin, C-terminal / Proteinase inhibitor I11, ecotin / Proteinase inhibitor I11, ecotin, gammaproteobacteria / Ecotin superfamily / Ecotin / Apple domain. / Apple domain / APPLE domain / PAN/Apple domain profile. ...Ecotin / Ecotin, C-terminal / Proteinase inhibitor I11, ecotin / Proteinase inhibitor I11, ecotin, gammaproteobacteria / Ecotin superfamily / Ecotin / Apple domain. / Apple domain / APPLE domain / PAN/Apple domain profile. / PAN domain / PAN/Apple domain / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta
Similarity search - Domain/homology
Coagulation factor XI / Ecotin
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsJin, L. / Pandey, P. / Babine, R.E. / Gorga, J.C. / Seidl, K.J. / Gelfand, E. / Weaver, D.T. / Abdel-Meguid, S.S. / Strickler, J.E.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Crystal Structures of the FXIa Catalytic Domain in Complex with Ecotin Mutants Reveal Substrate-like Interactions
Authors: Jin, L. / Pandey, P. / Babine, R.E. / Gorga, J.C. / Seidl, K.J. / Gelfand, E. / Weaver, D.T. / Abdel-Meguid, S.S. / Strickler, J.E.
History
DepositionNov 4, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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.ptnr1_label_seq_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 / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 20, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Coagulation factor XI
B: Coagulation factor XI
C: Ecotin
D: Ecotin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,2595
Polymers86,0384
Non-polymers2211
Water4,684260
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10210 Å2
ΔGint-30 kcal/mol
Surface area33920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.615, 92.669, 186.921
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

#1: Protein Coagulation factor XI / E.C.3.4.21.27 / Plasma thromboplastin antecedent / PTA / FXI


Mass: 26872.562 Da / Num. of mol.: 2 / Fragment: Catalytic Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F11 / Production host: Pichia pastoris (fungus) / References: UniProt: P03951, coagulation factor XIa
#2: Protein Ecotin


Mass: 16146.505 Da / Num. of mol.: 2 / Mutation: M84R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: eco,eti / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P23827
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / 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: 2.1 Å3/Da / Density % sol: 41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: PEG 1000, NaCl, Na/K phosphate, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.1 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Aug 9, 2001 / Details: monochromator
RadiationMonochromator: channel-cut crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 40129 / Num. obs: 36197 / % possible obs: 90.2 % / Observed criterion σ(I): 2 / Redundancy: 4.2 % / Biso Wilson estimate: 9.4 Å2 / Rsym value: 0.073 / Net I/σ(I): 12.3
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.386 / Mean I/σ(I) obs: 2 / Num. unique all: 2715 / % possible all: 69.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNX2002refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1FI8

1fi8


Resolution: 2.2→24.63 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 263306.1 / 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
Rfree0.285 3334 10 %RANDOM
Rwork0.235 ---
all-40389 --
obs-33402 82.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 26.9924 Å2 / ksol: 0.333821 e/Å3
Displacement parametersBiso mean: 39.5 Å2
Baniso -1Baniso -2Baniso -3
1--1.71 Å20 Å20 Å2
2--15.78 Å20 Å2
3----14.06 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.5 Å0.71 Å
Refinement stepCycle: LAST / Resolution: 2.2→24.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5960 0 14 260 6234
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_d25.7
X-RAY DIFFRACTIONc_improper_angle_d0.88
X-RAY DIFFRACTIONc_mcbond_it1.351.5
X-RAY DIFFRACTIONc_mcangle_it2.252
X-RAY DIFFRACTIONc_scbond_it1.942
X-RAY DIFFRACTIONc_scangle_it2.922.5
LS refinement shellResolution: 2.2→2.28 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.415 236 11.2 %
Rwork0.375 1869 -
obs-2715 53.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARWATER_REP.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4CARBOHYDRATE.CARBOHYDRATE.

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