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- PDB-3a3n: Crystal structure of complex between SA-subtilisin and Tk-propept... -

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Basic information

Entry
Database: PDB / ID: 3a3n
TitleCrystal structure of complex between SA-subtilisin and Tk-propeptide with deletion of the two C-terminal residues
Components(Tk-subtilisin) x 2
KeywordsHYDROLASE / subtilisin / propeptide / Thermococcus kodakaraensis / Protease / Secreted / Serine protease / Zymogen
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: 2.2 Å
AuthorsTanaka, S. / Matsumura, H. / Koga, Y. / Takano, K. / Kanaya, S.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Identification of the interactions critical for propeptide-catalyzed folding of Tk-subtilisin
Authors: Tanaka, S. / Matsumura, H. / Koga, Y. / Takano, K. / Kanaya, S.
History
DepositionJun 15, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 18, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 22, 2014Group: Database references
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 30, 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)41,66112
Polymers41,1842
Non-polymers47710
Water3,603200
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2760 Å2
ΔGint-160 kcal/mol
Surface area14190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.732, 68.468, 73.704
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: 33897.562 Da / Num. of mol.: 1 / Fragment: Residue in UNP 94-422 / Mutation: S324A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis (archaea) / Plasmid: pET25b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P58502, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Protein Tk-subtilisin


Mass: 7286.513 Da / Num. of mol.: 1 / Fragment: Tk-propeptide, Residue in UNP 25-91
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis (archaea) / Plasmid: pET25b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P58502
#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.: 3 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / 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: 2.01 Å3/Da / Density % sol: 38.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M Sodium Cacodylate, 0.2M Zinc Acetate, 2%(w/v) PEG4000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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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: Apr 17, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 17483 / % possible obs: 96.3 % / Rmerge(I) obs: 0.125 / Net I/σ(I): 18.3
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.384 / Mean I/σ(I) obs: 2.5 / % possible all: 80.7

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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: 2Z30

2z30


Resolution: 2.2→36.86 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.923 / SU B: 5.985 / SU ML: 0.152 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / ESU R: 0.339 / ESU R Free: 0.227 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23074 843 5 %RANDOM
Rwork0.16974 ---
obs0.1727 15948 96.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.458 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20 Å2
2---0.04 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.2→36.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2805 0 10 200 3015
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0222863
X-RAY DIFFRACTIONr_angle_refined_deg1.8431.9583919
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9925380
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.04925.446112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.18315421
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.665159
X-RAY DIFFRACTIONr_chiral_restr0.1140.2458
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022192
X-RAY DIFFRACTIONr_nbd_refined0.2310.21460
X-RAY DIFFRACTIONr_nbtor_refined0.3080.21983
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2490.2169
X-RAY DIFFRACTIONr_metal_ion_refined0.3310.230
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3390.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.190.29
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.2470.22
X-RAY DIFFRACTIONr_mcbond_it1.2081.51941
X-RAY DIFFRACTIONr_mcangle_it1.70623050
X-RAY DIFFRACTIONr_scbond_it2.84331059
X-RAY DIFFRACTIONr_scangle_it4.114.5869
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 56 -
Rwork0.192 934 -
obs--78.82 %

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