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- PDB-3sbk: Russell's viper venom serine proteinase, RVV-V (PPACK-bound form) -

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Basic information

Entry
Database: PDB / ID: 3sbk
TitleRussell's viper venom serine proteinase, RVV-V (PPACK-bound form)
ComponentsVipera russelli proteinase RVV-V gamma
KeywordsHYDROLASE/HYDROLASE INHIBITOR / serine proteinase / glycosylation / double six-stranded beta-barrels / Hydrolase / HYDROLASE-HYDROLASE INHIBITOR complex
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
D-Phe-Pro-Arg-CH2Cl / Chem-0G6 / Factor V activator RVV-V gamma
Similarity search - Component
Biological speciesDaboia russellii siamensis (Siamese Russell's viper)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 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 5, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 7, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2012Group: Other
Revision 1.2Jul 3, 2013Group: Database references
Revision 1.3Jul 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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 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 1.5Nov 13, 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)26,6363
Polymers25,9611
Non-polymers6752
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.233, 77.233, 168.433
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: Chemical ChemComp-0G6 / D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide / PPACK


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 453.986 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H34ClN6O3 / References: D-Phe-Pro-Arg-CH2Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.79 Å3/Da / Density % sol: 55.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 9.6% PEG 3350, 0.8% tryptone, 40mM Na/HEPES , pH 7.0, 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 MX-225 / Detector: CCD / Date: Jul 14, 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: 2.55→50 Å / Num. all: 10342 / Num. obs: 10311 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 20.4 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 33.8
Reflection shellResolution: 2.55→2.64 Å / Redundancy: 21.4 % / Rmerge(I) obs: 0.267 / Mean I/σ(I) obs: 15.8 / Num. unique all: 993 / % possible all: 100

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Processing

Software
NameVersionClassification
SPACEdata collection
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3S9A

3s9a


Resolution: 2.55→28.74 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.852 / SU B: 14.957 / SU ML: 0.318 / Cross valid method: THROUGHOUT / ESU R: 0.584 / ESU R Free: 0.373 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.3276 489 4.8 %RANDOM
Rwork0.2463 ---
obs0.2501 10255 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.2571 Å2
Baniso -1Baniso -2Baniso -3
1-0.46 Å20.23 Å2-0 Å2
2--0.46 Å2-0 Å2
3----0.7 Å2
Refinement stepCycle: LAST / Resolution: 2.55→28.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1817 0 44 17 1878
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0211918
X-RAY DIFFRACTIONr_angle_refined_deg1.8951.962604
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3045234
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.48122.17978
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.05615305
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3841517
X-RAY DIFFRACTIONr_chiral_restr0.1190.2285
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211451
X-RAY DIFFRACTIONr_mcbond_it1.0881.51178
X-RAY DIFFRACTIONr_mcangle_it1.98921912
X-RAY DIFFRACTIONr_scbond_it2.4363740
X-RAY DIFFRACTIONr_scangle_it4.1674.5692
LS refinement shellResolution: 2.551→2.617 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.498 39 -
Rwork0.354 683 -
all-722 -
obs--99.72 %

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