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- PDB-2z30: Crystal structure of complex form between mat-Tk-subtilisin and T... -

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Basic information

Entry
Database: PDB / ID: 2z30
TitleCrystal structure of complex form between mat-Tk-subtilisin and Tk-propeptide
Components(Tk-subtilisin) x 2
KeywordsHYDROLASE / subtilisin / Thermococcus kodakaraensis
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 / 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 / Peptidase S8, subtilisin-related / Serine proteases, subtilase domain profile. / Peptidase S8/S53 domain superfamily / Peptidase S8/S53 domain / Subtilase family / 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: 1.65 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: Derived calculations / 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
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)40,48710
Polymers40,1412
Non-polymers3468
Water8,755486
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2810 Å2
ΔGint-88 kcal/mol
Surface area13670 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)64.289, 68.514, 73.627
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Tk-subtilisin


Mass: 33056.617 Da / Num. of mol.: 1 / Mutation: S324A
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.: 1 / 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.: 7 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 486 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.02 Å3/Da / Density % sol: 39.07 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M Sodium Cacodylate, 0.2M Zinc Acetate, 2% (w/v) PEG 4000, pH 6.5, VAPOR DIFFUSION, SITTING 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: Nov 21, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 39894 / % possible obs: 100 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 37.7
Reflection shellResolution: 1.65→1.71 Å / Rmerge(I) obs: 0.177 / Mean I/σ(I) obs: 6.1 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2E1P

2e1p


Resolution: 1.65→29.5 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.424 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.093 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18357 1982 5 %RANDOM
Rwork0.15133 ---
obs0.15289 37822 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 12.961 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.65→29.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2827 0 8 486 3321
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0212885
X-RAY DIFFRACTIONr_bond_other_d0.0010.022626
X-RAY DIFFRACTIONr_angle_refined_deg1.6851.9543947
X-RAY DIFFRACTIONr_angle_other_deg0.82736106
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3183383
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.75715470
X-RAY DIFFRACTIONr_chiral_restr0.1080.2463
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023287
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02522
X-RAY DIFFRACTIONr_nbd_refined0.2720.3718
X-RAY DIFFRACTIONr_nbd_other0.210.32744
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2190.5419
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.4870.52
X-RAY DIFFRACTIONr_metal_ion_refined0.2560.533
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3860.311
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1740.333
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2730.538
X-RAY DIFFRACTIONr_symmetry_hbond_other0.4370.52
X-RAY DIFFRACTIONr_mcbond_it0.9671.51907
X-RAY DIFFRACTIONr_mcangle_it1.57823072
X-RAY DIFFRACTIONr_scbond_it2.5493978
X-RAY DIFFRACTIONr_scangle_it3.8834.5875
LS refinement shellResolution: 1.649→1.692 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.225 146
Rwork0.157 2696

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