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- PDB-3afg: Crystal structure of ProN-Tk-SP from Thermococcus kodakaraensis -

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Basic information

Entry
Database: PDB / ID: 3afg
TitleCrystal structure of ProN-Tk-SP from Thermococcus kodakaraensis
ComponentsSubtilisin-like serine protease
KeywordsHYDROLASE / subtilisin / propeptide / Thermococcus kodakaraensis / Protease / Serine protease
Function / homology
Function and homology information


subtilisin / peptidase activity / serine-type endopeptidase activity / calcium ion binding / proteolysis
Similarity search - Function
Subtilisin-like serine protease TK1689-type / Tk-SP N-propeptide domain / Tk-SP N-propeptide domain / Jelly Rolls - #380 / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase, C-terminal, archaeal/bacterial / Bacterial pre-peptidase C-terminal domain / Peptidase S8/S53 domain / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily / Peptidase S8, subtilisin, His-active site ...Subtilisin-like serine protease TK1689-type / Tk-SP N-propeptide domain / Tk-SP N-propeptide domain / Jelly Rolls - #380 / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase, C-terminal, archaeal/bacterial / Bacterial pre-peptidase C-terminal domain / Peptidase S8/S53 domain / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily / Peptidase S8, subtilisin, His-active site / Serine proteases, subtilase family, histidine active site. / 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 / Galactose-binding-like domain superfamily / Jelly Rolls / Alpha-Beta Plaits / Sandwich / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Subtilisin-like serine protease
Similarity search - Component
Biological speciesThermococcus kodakarensis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsFoophow, T. / Tanaka, S. / Angkawidjaja, C. / Koga, Y. / Takano, K. / Kanaya, S.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Crystal structure of a subtilisin homologue, Tk-SP, from Thermococcus kodakaraensis: requirement of a C-terminal beta-jelly roll domain for hyperstability.
Authors: Foophow, T. / Tanaka, S. / Angkawidjaja, C. / Koga, Y. / Takano, K. / Kanaya, S.
History
DepositionMar 1, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 4, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_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: Subtilisin-like serine protease
B: Subtilisin-like serine protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,9716
Polymers113,8102
Non-polymers1604
Water12,196677
1
A: Subtilisin-like serine protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,9853
Polymers56,9051
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Subtilisin-like serine protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,9853
Polymers56,9051
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.009, 123.996, 141.037
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 Subtilisin-like serine protease


Mass: 56905.191 Da / Num. of mol.: 2 / Fragment: UNP Residues 24-562 / Mutation: S359A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis (archaea) / Gene: TK1689 / Plasmid: pET25b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: Q5JIZ5, subtilisin
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 677 / 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: 2.42 Å3/Da / Density % sol: 49.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M MES-NaOH (pH 6.5), 5% (w/v) PEG 1500, 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: Bruker DIP-6040 / Detector: CCD / Date: Feb 27, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 74932 / % possible obs: 99 % / Rmerge(I) obs: 0.113 / Net I/σ(I): 13.1
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.365 / Mean I/σ(I) obs: 2.6 / % possible all: 95.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SCJ

1scj


Resolution: 2→42.17 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.91 / SU B: 4.411 / SU ML: 0.121 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / ESU R: 0.173 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24007 3768 5 %RANDOM
Rwork0.18136 ---
obs0.18431 71109 98.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.631 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2→42.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7574 0 4 677 8255
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0227765
X-RAY DIFFRACTIONr_angle_refined_deg1.2271.94210577
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.41951011
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.70325.719313
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.035151197
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6261512
X-RAY DIFFRACTIONr_chiral_restr0.1110.21192
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0215896
X-RAY DIFFRACTIONr_mcbond_it1.5221.55010
X-RAY DIFFRACTIONr_mcangle_it2.33928024
X-RAY DIFFRACTIONr_scbond_it3.93932755
X-RAY DIFFRACTIONr_scangle_it5.7074.52553
LS refinement shellResolution: 1.996→2.048 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 247 -
Rwork0.262 4743 -
obs--90.15 %

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