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- PDB-2z2y: Crystal structure of autoprocessed form of Tk-subtilisin -

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Basic information

Entry
Database: PDB / ID: 2z2y
TitleCrystal structure of autoprocessed form of Tk-subtilisin
Components(Tk-subtilisin) x 2
KeywordsHYDROLASE / subtilisin / Thermococcus kodakaraensis / autoprocessed
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 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: 1.89 Å
AuthorsTanaka, S. / Matsumura, H. / Koga, Y. / Takano, K. / Kanaya, S.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Four new crystal structures of Tk-subtilisin in unautoprocessed, autoprocessed and mature forms: insight into structural changes during maturation
Authors: Tanaka, S. / Matsumura, H. / Koga, Y. / Takano, K. / Kanaya, S.
History
DepositionMay 29, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 1, 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

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Assembly

Deposited unit
A: Tk-subtilisin
B: Tk-subtilisin
C: Tk-subtilisin
D: Tk-subtilisin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,92324
Polymers79,9704
Non-polymers95420
Water11,313628
1
A: Tk-subtilisin
B: Tk-subtilisin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,46212
Polymers39,9852
Non-polymers47710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Tk-subtilisin
D: Tk-subtilisin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,46212
Polymers39,9852
Non-polymers47710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.908, 65.365, 70.385
Angle α, β, γ (deg.)87.59, 67.44, 69.76
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Tk-subtilisin


Mass: 32900.500 Da / Num. of mol.: 2 / Mutation: S324C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis (archaea) / Strain: KOD1 / Plasmid: pET25b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: P58502, subtilisin
#2: Protein Tk-subtilisin


Mass: 7084.432 Da / Num. of mol.: 2 / Fragment: propeptide domain, UNP Residues 29-93
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis (archaea) / Strain: KOD1 / Plasmid: pET25b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: P58502, subtilisin
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 628 / 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: 2.67 Å3/Da / Density % sol: 53.95 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Sodium Cacodylate, 0.2M Zinc Acetate, 2% (w/v) PEG 4000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 283K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Mar 15, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.89→50 Å / Num. obs: 65891 / % possible obs: 96.4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 17
Reflection shellResolution: 1.89→1.96 Å / Rmerge(I) obs: 0.282 / Mean I/σ(I) obs: 2.2 / % possible all: 85.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2E1P

2e1p


Resolution: 1.89→46.88 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.719 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.134 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19778 3226 5.1 %RANDOM
Rwork0.16291 ---
obs0.16472 60274 96.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.071 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.89→46.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5630 0 20 628 6278
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0225746
X-RAY DIFFRACTIONr_angle_refined_deg1.4671.9617864
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1775762
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.0325.446224
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.01315850
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2721518
X-RAY DIFFRACTIONr_chiral_restr0.1050.2920
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024392
X-RAY DIFFRACTIONr_nbd_refined0.2120.23048
X-RAY DIFFRACTIONr_nbtor_refined0.3070.24007
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2490.2519
X-RAY DIFFRACTIONr_metal_ion_refined0.2220.270
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3440.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2140.218
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.4730.23
X-RAY DIFFRACTIONr_mcbond_it0.8511.53871
X-RAY DIFFRACTIONr_mcangle_it1.37826116
X-RAY DIFFRACTIONr_scbond_it2.28832118
X-RAY DIFFRACTIONr_scangle_it3.554.51748
LS refinement shellResolution: 1.892→1.942 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 195 -
Rwork0.214 3708 -
obs--79.83 %

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