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- PDB-7s0p: Crystal structure of Porcine Factor VIII C2 Domain Bound to Phosp... -

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Basic information

Entry
Database: PDB / ID: 7s0p
TitleCrystal structure of Porcine Factor VIII C2 Domain Bound to Phosphatidylserine
ComponentsCoagulation factor VIII
KeywordsLIPID BINDING PROTEIN / factor VIII / lipid / hemostasis
Function / homology
Function and homology information


blood coagulation, intrinsic pathway / acute-phase response / signaling receptor activity / oxidoreductase activity / copper ion binding / extracellular space
Similarity search - Function
Coagulation factor 5/8-like / Coagulation factors 5/8 type C domain (FA58C) signature 2. / Multicopper oxidases, conserved site / Multicopper oxidases signature 1. / Coagulation factors 5/8 type C domain (FA58C) signature 1. / Coagulation factor 5/8 C-terminal domain, discoidin domain / Coagulation factors 5/8 type C domain (FA58C) profile. / Multicopper oxidase, C-terminal / Multicopper oxidase / F5/8 type C domain ...Coagulation factor 5/8-like / Coagulation factors 5/8 type C domain (FA58C) signature 2. / Multicopper oxidases, conserved site / Multicopper oxidases signature 1. / Coagulation factors 5/8 type C domain (FA58C) signature 1. / Coagulation factor 5/8 C-terminal domain, discoidin domain / Coagulation factors 5/8 type C domain (FA58C) profile. / Multicopper oxidase, C-terminal / Multicopper oxidase / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Multicopper oxidase, type 1 / Multicopper oxidase / Multicopper oxidase, N-terminal / Multicopper oxidase / Cupredoxin / Galactose-binding-like domain superfamily
Similarity search - Domain/homology
PHOSPHOSERINE / Coagulation factor VIII
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.3 Å
AuthorsPeters, S.C. / Childers, K.C. / Wo, S.W. / Brison, C.M. / Swanson, C.D. / Spiegel, P.C.
Funding support United States, 6items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MRI 1429164 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R15HL103518 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)U54HL141981 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R44HL117511 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R44HL110448 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)U54HL112309 United States
CitationJournal: Front Mol Biosci / Year: 2022
Title: Stable binding to phosphatidylserine-containing membranes requires conserved arginine residues in tandem C domains of blood coagulation factor VIII.
Authors: Peters, S.C. / Childers, K.C. / Mitchell, C.E. / Avery, N.G. / Reese Jr., S.S. / Mitchell, C. / Wo, S.W. / Swanson, C.D. / Brison, C.M. / Spiegel Jr., P.C.
History
DepositionAug 30, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 30, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Oct 25, 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
M: Coagulation factor VIII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6872
Polymers17,5021
Non-polymers1851
Water3,099172
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.072, 68.323, 105.987
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Coagulation factor VIII / Procoagulant component


Mass: 17501.822 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: F8, CF8 / Production host: Escherichia coli B (bacteria) / References: UniProt: P12263
#2: Chemical ChemComp-SEP / PHOSPHOSERINE / PHOSPHONOSERINE


Type: L-peptide linking / Mass: 185.072 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8NO6P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.54 Å3/Da / Density % sol: 51.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 2:1 drop ratio 0.1 M CHES (pH 7.4) 0.1M magnesium acetate 10% ethanol (v/v) Crystal soaked with 5 mM OPLS

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1.1158 Å
DetectorType: ADSC QUANTUM 1 / Detector: CCD / Date: Feb 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1158 Å / Relative weight: 1
ReflectionResolution: 1.3→44.531 Å / Num. obs: 42676 / % possible obs: 96.5 % / Redundancy: 13.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.029 / Rrim(I) all: 0.078 / Net I/σ(I): 18.3
Reflection shellResolution: 1.3→1.32 Å / Rmerge(I) obs: 0.764 / Num. unique obs: 1614 / CC1/2: 0.832 / Rpim(I) all: 0.44 / Rrim(I) all: 0.892

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
Adxvdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MO3

4mo3


Resolution: 1.3→44.531 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1559 2000 4.69 %
Rwork0.1365 40666 -
obs0.1374 42666 96.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 314.6 Å2 / Biso mean: 22.1641 Å2 / Biso min: 9.18 Å2
Refinement stepCycle: final / Resolution: 1.3→44.531 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1230 0 11 172 1413
Biso mean--132.43 30.79 -
Num. residues----157
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071404
X-RAY DIFFRACTIONf_angle_d1.0711928
X-RAY DIFFRACTIONf_chiral_restr0.123220
X-RAY DIFFRACTIONf_plane_restr0.006246
X-RAY DIFFRACTIONf_dihedral_angle_d22.907520
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.3-1.33250.2191080.221218274
1.3325-1.36850.26931210.1798247383
1.3685-1.40880.18511390.1618280794
1.4088-1.45430.18351440.13982960100
1.4543-1.50630.17251470.12472980100
1.5063-1.56660.16781470.11362982100
1.5666-1.63790.14871470.10752983100
1.6379-1.72420.13511470.11332985100
1.7242-1.83230.12271470.11583016100
1.8323-1.97370.1611490.12122997100
1.9737-2.17240.13281470.11983020100
2.1724-2.48670.15191500.12733025100
2.4867-3.13280.15991500.14563065100
3.1328-44.530.15631570.15463191100

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