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- PDB-5pb1: Crystal Structure of Factor VIIa in complex with benzenecarboximi... -

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Basic information

Entry
Database: PDB / ID: 5pb1
TitleCrystal Structure of Factor VIIa in complex with benzenecarboximidamide
Components(Coagulation factor VII ...) x 2
KeywordsHYDROLASE/HYDROLASE INHIBITOR / GLYCOPROTEIN / HYDROLASE / SERINE PROTEASE / PLASMA / BLOOD COAGULATION FACTOR / PROTEIN INHIBITOR COMPLEX / CALCIUM-BINDING / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


coagulation factor VIIa / response to Thyroid stimulating hormone / response to astaxanthin / response to thyrotropin-releasing hormone / response to 2,3,7,8-tetrachlorodibenzodioxine / response to carbon dioxide / serine-type peptidase complex / response to genistein / response to vitamin K / positive regulation of platelet-derived growth factor receptor signaling pathway ...coagulation factor VIIa / response to Thyroid stimulating hormone / response to astaxanthin / response to thyrotropin-releasing hormone / response to 2,3,7,8-tetrachlorodibenzodioxine / response to carbon dioxide / serine-type peptidase complex / response to genistein / response to vitamin K / positive regulation of platelet-derived growth factor receptor signaling pathway / positive regulation of leukocyte chemotaxis / response to thyroxine / response to cholesterol / positive regulation of positive chemotaxis / response to growth hormone / : / positive regulation of blood coagulation / animal organ regeneration / positive regulation of TOR signaling / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Gamma-carboxylation of protein precursors / Removal of aminoterminal propeptides from gamma-carboxylated proteins / BMAL1:CLOCK,NPAS2 activates circadian expression / serine-type peptidase activity / circadian rhythm / protein processing / response to estrogen / Golgi lumen / blood coagulation / response to estradiol / extracellular matrix / vesicle / response to hypoxia / positive regulation of cell migration / endoplasmic reticulum lumen / serine-type endopeptidase activity / signaling receptor binding / calcium ion binding / : / extracellular region / plasma membrane
Similarity search - Function
Peptidase S1A, coagulation factor VII/IX/X/C/Z / : / Coagulation factor-like, Gla domain superfamily / Laminin / Laminin / Coagulation Factor Xa inhibitory site / EGF-like domain / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. ...Peptidase S1A, coagulation factor VII/IX/X/C/Z / : / Coagulation factor-like, Gla domain superfamily / Laminin / Laminin / Coagulation Factor Xa inhibitory site / EGF-like domain / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Vitamin K-dependent carboxylation/gamma-carboxyglutamic (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain superfamily / Vitamin K-dependent carboxylation domain. / Gla domain profile. / Domain containing Gla (gamma-carboxyglutamate) residues. / Epidermal growth factor-like domain. / EGF-like domain profile. / EGF-like domain signature 1. / EGF-like domain signature 2. / EGF-like domain / Ribbon / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / 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
BENZAMIDINE / Coagulation factor VII
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsStihle, M. / Mayweg, A. / Roever, S. / Rudolph, M.G.
CitationJournal: To be published
Title: Crystal Structure of a Factor VIIa complex
Authors: Mayweg, A. / Roever, S. / Rudolph, M.G.
History
DepositionNov 10, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2018Group: Structure summary / Category: pdbx_deposit_group / Item: _pdbx_deposit_group.group_type
Revision 2.0Aug 18, 2021Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_2 / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / struct_conn / struct_conn_type / struct_site
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_comp_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _pdbx_entity_nonpoly.comp_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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 / _struct_conn_type.id / _struct_site.details / _struct_site.pdbx_auth_comp_id
Revision 2.1Nov 17, 2021Group: Structure summary / Category: pdbx_deposit_group
Item: _pdbx_deposit_group.group_description / _pdbx_deposit_group.group_title
Revision 2.2Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Coagulation factor VII light chain
D: Coagulation factor VII heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,20914
Polymers35,1042
Non-polymers1,10512
Water6,810378
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.676, 95.676, 117.961
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11D-901-

HOH

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Components

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Coagulation factor VII ... , 2 types, 2 molecules AD

#1: Protein Coagulation factor VII light chain / Proconvertin / Serum prothrombin conversion accelerator / SPCA


Mass: 6984.911 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P08709, coagulation factor VIIa
#2: Protein Coagulation factor VII heavy chain / Proconvertin / Serum prothrombin conversion accelerator / SPCA


Mass: 28119.256 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P08709, coagulation factor VIIa

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Non-polymers , 5 types, 390 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-BEN / BENZAMIDINE


Mass: 120.152 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8N2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 378 / Source method: isolated from a natural source / Formula: H2O

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Details

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

CrystalMosaicity: 0.968 °
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 16 mg/ml protein in 20mM Tris/HCl pH 8.4, 5 mM benzamidine, 0.1 M NaCl, 50 mM CaCl2 mixed 1+1 with 32-35% AMMONIUM SULPHATE, 2% PEG 4000, 0.1 M Bicine-NaOH pH 8.5, 15% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 14, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 51285 / % possible obs: 99.7 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.099 / Χ2: 1.011 / Net I/av σ(I): 14.924 / Net I/σ(I): 19 / Num. measured all: 353441
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.8-1.865.60.6150220.95599.7
1.86-1.946.70.38150750.963100
1.94-2.037.10.29850441.022100
2.03-2.137.20.22350871.034100
2.13-2.277.20.1950791.062100
2.27-2.447.20.16851051.15799.9
2.44-2.697.10.13851061.101100
2.69-3.087.10.1151631.0199.9
3.08-3.8870.08552130.91899.8
3.881-506.70.05953910.86398.3

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: inhouse model

Resolution: 1.9→30.79 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.407 / SU ML: 0.072 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.115 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2105 2181 5 %RANDOM
Rwork0.1897 ---
obs0.1908 41238 98.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 80 Å2 / Biso mean: 21.492 Å2 / Biso min: 13.37 Å2
Baniso -1Baniso -2Baniso -3
1--0.96 Å20 Å20 Å2
2---0.96 Å20 Å2
3---1.91 Å2
Refinement stepCycle: final / Resolution: 1.9→30.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2364 0 64 378 2806
Biso mean--51.46 38.92 -
Num. residues----306
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222616
X-RAY DIFFRACTIONr_bond_other_d0.0020.021798
X-RAY DIFFRACTIONr_angle_refined_deg1.3181.9793591
X-RAY DIFFRACTIONr_angle_other_deg0.8713.0044376
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9785346
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.03722.752109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.5515426
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0851522
X-RAY DIFFRACTIONr_chiral_restr0.0810.2395
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022900
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02538
X-RAY DIFFRACTIONr_nbd_refined0.210.2423
X-RAY DIFFRACTIONr_nbd_other0.2050.21875
X-RAY DIFFRACTIONr_nbtor_refined0.1710.21203
X-RAY DIFFRACTIONr_nbtor_other0.0790.21419
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2303
X-RAY DIFFRACTIONr_metal_ion_refined0.10.26
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0860.22
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2280.217
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2090.223
X-RAY DIFFRACTIONr_mcbond_it0.9871.51659
X-RAY DIFFRACTIONr_mcbond_other0.1671.5651
X-RAY DIFFRACTIONr_mcangle_it1.53922590
X-RAY DIFFRACTIONr_scbond_it2.05831119
X-RAY DIFFRACTIONr_scangle_it3.0634.5980
LS refinement shellResolution: 1.897→1.946 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 168 -
Rwork0.217 3019 -
all-3187 -
obs--99.84 %

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