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- PDB-1sdd: Crystal Structure of Bovine Factor Vai -

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Basic information

Entry
Database: PDB / ID: 1sdd
TitleCrystal Structure of Bovine Factor Vai
Components(Coagulation factor ...) x 2
KeywordsBLOOD CLOTTING / COAGULATION / COPPER-BINDING PROTEIN / COFACTOR
Function / homology
Function and homology information


platelet alpha granule / blood circulation / blood coagulation / copper ion binding / extracellular region
Similarity search - Function
Coagulation factor V, LSPD / Coagulation Factor V LSPD Repeat / 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. / F5/8 type C domain ...Coagulation factor V, LSPD / Coagulation Factor V LSPD Repeat / 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. / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Multicopper oxidase, N-terminal / Multicopper oxidase / Galactose-binding domain-like / Cupredoxins - blue copper proteins / Cupredoxin / Galactose-binding-like domain superfamily / Jelly Rolls / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / Coagulation factor V
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR, MAD / Resolution: 2.8 Å
AuthorsAdams, T.E. / Hockin, M.F. / Mann, K.G. / Everse, S.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2004
Title: The crystal structure of activated protein C-inactivated bovine factor Va: Implications for cofactor function.
Authors: Adams, T.E. / Hockin, M.F. / Mann, K.G. / Everse, S.J.
History
DepositionFeb 13, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2004Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_validate_chiral / struct_asym / struct_conn / struct_conn_type / 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_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_asym.entity_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.ptnr1_label_seq_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 / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.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: Coagulation factor V
B: Coagulation factor V
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,6519
Polymers109,4422
Non-polymers1,2107
Water3,405189
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4750 Å2
ΔGint-25 kcal/mol
Surface area37640 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)63.370, 86.560, 229.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Coagulation factor ... , 2 types, 2 molecules AB

#1: Protein Coagulation factor V / Activated protein C cofactor


Mass: 34730.359 Da / Num. of mol.: 1 / Fragment: A1 Domain (residues 29-305) / Source method: isolated from a natural source / Details: purified from plasma / Source: (natural) Bos taurus (cattle) / References: UniProt: Q28107
#2: Protein Coagulation factor V / Activated protein C cofactor


Mass: 74711.453 Da / Num. of mol.: 1
Fragment: Light Chain (A3, C1, C2 domains, residues 1565-2211)
Source method: isolated from a natural source / Details: purified from plasma / Source: (natural) Bos taurus (cattle) / References: UniProt: Q28107

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Sugars , 1 types, 5 molecules

#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 5
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

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Non-polymers , 3 types, 191 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / 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: 4

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Sample preparation

CrystalDensity Matthews: 3.17 Å3/Da / Density % sol: 60.9 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 7
Details: PEG3350, MAGNESIUM CHLORIDE, CALCIUM CHLORIDE, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 285K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
41001
1,2,3,41
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONCHESS A110.935
SYNCHROTRONNSLS X12C20.9803, 1.0097, 1.0106
SYNCHROTRONNSLS X2531.1
SYNCHROTRONNSLS X2541.1
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDMar 20, 2002
BRANDEIS - B1.32CCDApr 12, 2001
BRANDEIS - B43CCDMar 10, 2000
BRANDEIS - B44CCDMar 9, 2000
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Rh-COATED SiSINGLE WAVELENGTHMx-ray1
2CHANNEL-CUT Si(111)MADMx-ray1
3CHANNEL-CUT Si(111)SINGLE WAVELENGTHMx-ray1
4CHANNEL-CUT Si(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9351
20.98031
31.00971
41.01061
51.11
ReflectionResolution: 2.8→30 Å / Num. all: 32016 / Num. obs: 28745 / % possible obs: 88.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.2 % / Rmerge(I) obs: 0.049 / Rsym value: 0.054 / Net I/σ(I): 7.2
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 2 % / Rmerge(I) obs: 0.206 / Mean I/σ(I) obs: 2.3 / Num. unique all: 3154 / Rsym value: 0.307 / % possible all: 80.8

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
CNSrefinement
RefinementMethod to determine structure: MIR, MAD / Resolution: 2.8→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.296 1098 -RANDOM
Rwork0.252 ---
all0.258 31911 --
obs0.262 28745 90.1 %-
Refine analyze
FreeObs
Luzzati coordinate error0.56 Å0.45 Å
Luzzati d res low-5 Å
Luzzati sigma a0.63 Å0.55 Å
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7010 0 72 189 7271
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.94
X-RAY DIFFRACTIONx_bond_d0.019
X-RAY DIFFRACTIONx_dihedral_angle_d25.56
X-RAY DIFFRACTIONx_improper_angle_d1.19
LS refinement shellResolution: 2.8→2.9 Å / Rfactor Rfree error: 0.035
RfactorNum. reflection% reflection
Rfree0.446 72 -
Rwork0.388 --
obs-2409 76.4 %

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