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- PDB-3s9a: Russell's viper venom serine proteinase, RVV-V (closed-form) -

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Basic information

Entry
Database: PDB / ID: 3s9a
TitleRussell's viper venom serine proteinase, RVV-V (closed-form)
ComponentsVipera russelli proteinase RVV-V gamma
KeywordsHYDROLASE / serine proteinase / double six-stranded beta-barrels / glycosylation
Function / homology
Function and homology information


snake venom factor V activator / secretory granule / toxin activity / serine-type endopeptidase activity / proteolysis / extracellular region
Similarity search - Function
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 ...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
Factor V activator RVV-V gamma
Similarity search - Component
Biological speciesDaboia russellii siamensis (Siamese Russell's viper)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsNakayama, D. / Ben Ammar, Y. / Takeda, S.
Citation
Journal: Febs Lett. / Year: 2011
Title: Structural basis of coagulation factor V recognition for cleavage by RVV-V
Authors: Nakayama, D. / Ben Ammar, Y. / Miyata, T. / Takeda, S.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2009
Title: Crystallization and preliminary X-ray crystallographic analysis of blood coagulation factor V-activating proteinase (RVV-V) from Russell's viper venom
Authors: Nakayama, D. / Ben Ammar, Y. / Takeda, S.
History
DepositionJun 1, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 7, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2013Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / 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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Vipera russelli proteinase RVV-V gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1822
Polymers25,9611
Non-polymers2211
Water3,063170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.928, 78.928, 157.370
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Vipera russelli proteinase RVV-V gamma / Factor V-activating proteinase gamma / Snake venom factor V activator gamma


Mass: 25960.971 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Daboia russellii siamensis (Siamese Russell's viper)
Tissue: venom / References: UniProt: P18965, snake venom factor V activator
#2: 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE RESIDUE NUMBERING IS NOT SEQUENTIAL. THE RESIDUE NUMBERING IS BASED ON THE TOPOLOGICAL ...THE RESIDUE NUMBERING IS NOT SEQUENTIAL. THE RESIDUE NUMBERING IS BASED ON THE TOPOLOGICAL EQUIVALENCE TO CHYMOTRYPSINOGEN.

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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: 2.73 Å3/Da / Density % sol: 54.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 16% PEG 3350, 50mM sodium citrate, 50mM bis-tris propane , pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Apr 21, 2009 / Details: mirrors
RadiationMonochromator: Rotated-inclined double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 23594 / Num. obs: 23547 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 18.3 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 22.8
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.255 / Mean I/σ(I) obs: 8.6 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.3refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2AIQ

2aiq


Resolution: 1.9→35.28 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 2221293.05 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.2555 1149 4.9 %RANDOM
Rwork0.219 ---
obs0.22 23544 99.6 %-
all-23594 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.4674 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 29.6516 Å2
Baniso -1Baniso -2Baniso -3
1--1.253 Å20 Å20 Å2
2---1.253 Å20 Å2
3---2.506 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.9→35.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1817 0 14 170 2001
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d24.7
X-RAY DIFFRACTIONc_improper_angle_d2.61
X-RAY DIFFRACTIONc_mcbond_it1.2761.5
X-RAY DIFFRACTIONc_scbond_it1.8932
X-RAY DIFFRACTIONc_mcangle_it1.9282
X-RAY DIFFRACTIONc_scangle_it2.8432.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.269 196 5.1 %
Rwork0.242 3618 -
obs--99.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4carbohydrate.paramcarbohydrate.top

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