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- PDB-3vv2: Crystal structure of complex form between S324A-subtilisin and mu... -

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Basic information

Entry
Database: PDB / ID: 3vv2
TitleCrystal structure of complex form between S324A-subtilisin and mutant Tkpro
Components
  • PROPEPTIDE from Tk-subtilisinProtein precursor
  • Tk-subtilisin
KeywordsHYDROLASE / Proteolysis
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type endopeptidase activity / proteolysis / extracellular region / identical protein binding
Similarity search - Function
Peptidase S8 propeptide/proteinase inhibitor I9 / Subtilisin Carlsberg-like catalytic domain / Peptidase S8/S53 domain / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily / Serine proteases, subtilase family, aspartic acid active site. / Peptidase S8, subtilisin, Asp-active site / Serine proteases, subtilase family, serine active site. / Peptidase S8, subtilisin, Ser-active site / Serine proteases, subtilase domain profile. / Peptidase S8, subtilisin-related ...Peptidase S8 propeptide/proteinase inhibitor I9 / Subtilisin Carlsberg-like catalytic domain / Peptidase S8/S53 domain / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily / Serine proteases, subtilase family, aspartic acid active site. / Peptidase S8, subtilisin, Asp-active site / Serine proteases, subtilase family, serine active site. / Peptidase S8, subtilisin, Ser-active site / Serine proteases, subtilase domain profile. / Peptidase S8, subtilisin-related / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain / Alpha-Beta Plaits / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesThermococcus kodakarensis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsUehara, R. / Ueda, Y. / You, D.J. / Takano, K. / Koga, Y. / Kanaya, S.
CitationJournal: Febs J. / Year: 2013
Title: Accelerated maturation of Tk-subtilisin by a Leu Pro mutation at the C-terminus of the propeptide, which reduces the binding of the propeptide to Tk-subtilisin
Authors: Uehara, R. / Ueda, Y. / You, D.J. / Koga, Y. / Kanaya, S.
History
DepositionJul 12, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 6, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_conn.pdbx_dist_value / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tk-subtilisin
B: PROPEPTIDE from Tk-subtilisin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,77611
Polymers41,3942
Non-polymers3819
Water1,964109
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2860 Å2
ΔGint-91 kcal/mol
Surface area13860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.051, 68.583, 74.054
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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Protein , 2 types, 2 molecules AB

#1: Protein Tk-subtilisin


Mass: 33897.562 Da / Num. of mol.: 1 / Fragment: UNP residues 94-422 / Mutation: S324A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis (archaea) / Strain: KOD1 / Gene: TK1675 / Production host: Escherichia coli (E. coli) / Strain (production host): bl21(de3)codon plus-ril
References: UniProt: P58502, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Protein PROPEPTIDE from Tk-subtilisin / Protein precursor


Mass: 7496.786 Da / Num. of mol.: 1 / Fragment: UNP residues 25-93 / Mutation: L69P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis (archaea) / Strain: KOD1 / Gene: TK1675 / Production host: Escherichia coli (E. coli) / Strain (production host): bl21(de3)codon plus-ril / References: UniProt: P58502

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Non-polymers , 4 types, 118 molecules

#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 38.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M Sodium cacodylate, 0.2M Zinc acetate, 2% PEG4000, pH6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 2, 2011
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.83→50 Å / Num. obs: 28926 / % possible obs: 96.7 % / Observed criterion σ(F): 5 / Observed criterion σ(I): 5
Reflection shellResolution: 1.83→1.86 Å / % possible all: 93.7

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Processing

Software
NameVersionClassification
BL44BSSdata collection
MOLREPphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Z30

2z30


Resolution: 1.83→31.12 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.896 / SU B: 3.768 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.18 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26806 1476 5.1 %RANDOM
Rwork0.21847 ---
obs0.22103 27383 96.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2---0.04 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.83→31.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2826 0 9 109 2944
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0222905
X-RAY DIFFRACTIONr_angle_refined_deg1.8231.9613984
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7645391
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.3925.487113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.8915429
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.098159
X-RAY DIFFRACTIONr_chiral_restr0.1280.2467
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212228
X-RAY DIFFRACTIONr_mcbond_it1.1651.51920
X-RAY DIFFRACTIONr_mcangle_it1.85623102
X-RAY DIFFRACTIONr_scbond_it2.8663985
X-RAY DIFFRACTIONr_scangle_it4.2474.5878
LS refinement shellResolution: 1.83→1.878 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 111 -
Rwork0.246 1978 -
obs--97.34 %

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