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- PDB-1zrk: Factor XI complexed with 3-hydroxypropyl 3-(7-amidinonaphthalene-... -

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Basic information

Entry
Database: PDB / ID: 1zrk
TitleFactor XI complexed with 3-hydroxypropyl 3-(7-amidinonaphthalene-1-carboxamido)benzenesulfonate
ComponentsCoagulation factor XIFactor XI
KeywordsHYDROLASE / serine protease / coagulation
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 / blood coagulation / heparin binding / serine-type endopeptidase activity / extracellular space ...coagulation factor XIa / serine-type aminopeptidase activity / Defective F9 activation / positive regulation of fibrinolysis / plasminogen activation / Intrinsic Pathway of Fibrin Clot Formation / blood coagulation / heparin binding / serine-type endopeptidase activity / extracellular space / extracellular exosome / extracellular region / membrane / identical protein binding / plasma membrane
Similarity search - Function
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. ...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 / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-367 / Coagulation factor XI
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.3 Å
AuthorsGuo, Z. / Bannister, T. / Noll, R. / Jin, L. / Rynkiewicz, M.J. / Bibbins, F. / Magee, S. / Gorga, J. / Babine, R. / Strickler, J.
CitationJournal: To be Published
Title: Synthesis and Optimization of Potent and Selective Inhibitors for Human Factor XIa: Substituted Naphthamidine Series
Authors: Guo, Z. / Bannister, T. / Noll, R. / Jin, L. / Rynkiewicz, M.J. / Bibbins, F. / Magee, S. / Gorga, J. / Babine, R. / Strickler, J.
History
DepositionMay 19, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.4Aug 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

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Assembly

Deposited unit
A: Coagulation factor XI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5145
Polymers26,7981
Non-polymers7164
Water2,522140
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)120.899, 120.899, 120.899
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

#1: Protein Coagulation factor XI / Factor XI / Plasma thromboplastin antecedent / PTA / FXI


Mass: 26798.395 Da / Num. of mol.: 1 / Fragment: catalytic domain / Mutation: S434A,T475A,C482S,K437A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F11 / Plasmid: pPICZa A / Production host: Pichia pastoris (fungus) / Strain (production host): X-33 / References: UniProt: P03951, coagulation factor XIa
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-367 / 3-HYDROXYPROPYL 3-[({7-[AMINO(IMINO)METHYL]-1-NAPHTHYL}AMINO)CARBONYL]BENZENESULFONATE


Mass: 427.474 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H21N3O5S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 2.76 Å3/Da / Density % sol: 55.11 %
Crystal growTemperature: 283 K / Method: vapor diffusion / pH: 8.5
Details: 2 M ammonium sulfate, 0.1 M tris, pH 8.5, VAPOR DIFFUSION, temperature 283K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 26, 2002 / Details: Osmic mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. all: 13237 / Num. obs: 13237 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 18.5 Å2 / Rmerge(I) obs: 0.127
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.342 / % possible all: 100

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Processing

Software
NameVersionClassification
CNX2002refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: pdb code 1ZHR

1zhr


Resolution: 2.3→28.5 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 2811512.53 / 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
Rfree0.235 698 5.3 %RANDOM
Rwork0.192 ---
all-13237 --
obs-13237 100 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 28.9284 Å2 / ksol: 0.380303 e/Å3
Displacement parametersBiso mean: 22 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2.3→28.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1877 0 41 140 2058
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d24.4
X-RAY DIFFRACTIONc_improper_angle_d0.72
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.256 112 5.1 %
Rwork0.213 2083 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.pprotein.top
X-RAY DIFFRACTION2ion.paramion.top
X-RAY DIFFRACTION3water_rep.parwater_rep.top
X-RAY DIFFRACTION4carbohydrate.carbohydrate.
X-RAY DIFFRACTION5368.par368.top

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