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- PDB-2z2z: Crystal structure of unautoprocessed form of Tk-subtilisin soaked... -

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Basic information

Entry
Database: PDB / ID: 2z2z
TitleCrystal structure of unautoprocessed form of Tk-subtilisin soaked by 10mM CaCl2
ComponentsTk-subtilisin precursor
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 propeptide/proteinase inhibitor I9 superfamily / Peptidase S8/S53 domain / 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 propeptide/proteinase inhibitor I9 superfamily / Peptidase S8/S53 domain / 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 / 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: 1.87 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
Revision 1.4Oct 9, 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 precursor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3598
Polymers41,0781
Non-polymers2817
Water7,386410
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.658, 124.173, 72.314
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Tk-subtilisin precursor


Mass: 41078.031 Da / Num. of mol.: 1 / Fragment: UNP residues 28-422 / Mutation: S324A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis (archaea) / Strain: KOD1 / Plasmid: pET25b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: P58502, subtilisin
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 410 / 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: 2.53 Å3/Da / Density % sol: 51.39 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 4.0M Sodium Formate, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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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: Oct 20, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.87→50 Å / Num. obs: 34961 / % possible obs: 99.9 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 45
Reflection shellResolution: 1.87→1.93 Å / Rmerge(I) obs: 0.188 / Mean I/σ(I) obs: 7.4 / % possible all: 99.9

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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: 1.87→46.33 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.941 / SU B: 3.821 / SU ML: 0.118 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21191 1752 5 %RANDOM
Rwork0.16941 ---
obs0.17155 33178 99.6 %-
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: 19.491 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.87→46.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2861 0 7 410 3278
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0212922
X-RAY DIFFRACTIONr_bond_other_d0.0010.022654
X-RAY DIFFRACTIONr_angle_refined_deg2.2791.9523998
X-RAY DIFFRACTIONr_angle_other_deg1.05736174
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3513387
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.84715472
X-RAY DIFFRACTIONr_chiral_restr0.2410.2465
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023326
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02530
X-RAY DIFFRACTIONr_nbd_refined0.2470.3755
X-RAY DIFFRACTIONr_nbd_other0.2270.32853
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2190.5374
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0020.51
X-RAY DIFFRACTIONr_metal_ion_refined0.2130.535
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.250.318
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3320.346
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4770.527
X-RAY DIFFRACTIONr_mcbond_it1.4291.51926
X-RAY DIFFRACTIONr_mcangle_it2.36623102
X-RAY DIFFRACTIONr_scbond_it3.5853996
X-RAY DIFFRACTIONr_scangle_it5.4374.5896
LS refinement shellResolution: 1.866→1.914 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.248 106
Rwork0.19 2309

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