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- PDB-4jp8: Crystal structure of Pro-F17H/S324A -

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Basic information

Entry
Database: PDB / ID: 4jp8
TitleCrystal structure of Pro-F17H/S324A
ComponentsTk-subtilisin
KeywordsHYDROLASE / subtilisin-like serine protease / subtillisin / Thermococcus kodakarensis
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, 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 / 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 / molecular replacement / Resolution: 2.21 Å
AuthorsYuzaki, K. / You, D.J. / Uehara, R. / Koga, Y. / Kanaya, S.
CitationJournal: Protein Sci. / Year: 2013
Title: Increase in activation rate of Pro-Tk-subtilisin by a single nonpolar-to-polar amino acid substitution at the hydrophobic core of the propeptide domain
Authors: Yuzaki, K. / Sanda, Y. / You, D.J. / Uehara, R. / Koga, Y. / Kanaya, S.
History
DepositionMar 19, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 29, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tk-subtilisin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6247
Polymers41,3831
Non-polymers2406
Water1,42379
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.323, 92.498, 122.222
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-813-

HOH

DetailsThe matthews coefficient and the solvent content: SOLVENT CONTENT, VS (%): 53.91 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.67

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Components

#1: Protein Tk-subtilisin


Mass: 41383.293 Da / Num. of mol.: 1 / Fragment: UNP residues 25-422 / Mutation: F17H, S324A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis (archaea) / Strain: ATCC BAA-918 / JCM 12380 / KOD1 / Gene: TK1675 / Plasmid: pET25b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P58502, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 2.64 Å3/Da / Density % sol: 53.42 % / Mosaicity: 0.948 °
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20mM Tris-HCl pH7.0, 4M Sodium Formate , VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: BRUKER SMART 6500 / Detector: CCD / Date: Jul 4, 2012
RadiationMonochromator: horizontal focusing mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 22172 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 17.7 % / Rmerge(I) obs: 0.097 / Rsym value: 0.097 / Χ2: 1.054 / Net I/σ(I): 37.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.2-2.2415.70.48910730.773199.5
2.24-2.2816.40.49811090.78199.8
2.28-2.32170.47311140.8011100
2.32-2.3717.90.45610930.81100
2.37-2.4218.30.4110850.81100
2.42-2.4818.50.36111000.8131100
2.48-2.5418.80.34911030.7991100
2.54-2.6118.80.28511090.7951100
2.61-2.6918.80.25210840.8091100
2.69-2.7718.60.20211150.8191100
2.77-2.8718.70.1711080.836199.9
2.87-2.9918.70.14110980.8941100
2.99-3.1218.60.11911051.0231100
3.12-3.2918.50.11411271.394199.9
3.29-3.4917.80.09910981.68199.8
3.49-3.7617.30.08711041.914198.8
3.76-4.1416.70.07911122.057198.6
4.14-4.7416.40.06111161.543197.9
4.74-5.9717.40.04311400.943199.1
5.97-50160.03511790.916197.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.42 Å46.25 Å
Translation2.42 Å46.25 Å
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 13712
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
7.53-10045.90.46507
5.97-7.5348.80.813506
5.16-5.9752.70.84503
4.67-5.1653.70.851501
4.3-4.6751.10.854509
4.01-4.3560.82509
3.8-4.0159.80.82509
3.61-3.862.40.802508
3.44-3.6166.60.803511
3.31-3.4473.40.783508
3.19-3.3169.10.778513
3.08-3.1971.10.762519
2.98-3.0874.30.77513
2.89-2.9874.80.744527
2.81-2.8979.70.728545
2.74-2.8177.10.71510
2.67-2.7476.10.684531
2.61-2.6780.10.646530
2.55-2.6178.70.642570
2.49-2.5579.90.679549
2.44-2.49780.667530
2.39-2.4480.80.636532
2.34-2.3980.50.645523
2.3-2.34830.595562
2.26-2.382.70.592514
2.21-2.2680.10.577673

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
DM6.1phasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2E1P

2e1p


Resolution: 2.21→50 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.921 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 8.423 / SU ML: 0.207 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.298 / ESU R Free: 0.238 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2799 1129 5.1 %RANDOM
Rwork0.2298 ---
obs0.2324 22103 98.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 77.81 Å2 / Biso mean: 44.6305 Å2 / Biso min: 2.95 Å2
Baniso -1Baniso -2Baniso -3
1-8.43 Å20 Å2-0 Å2
2---4.42 Å20 Å2
3----4 Å2
Refinement stepCycle: LAST / Resolution: 2.21→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2893 0 6 79 2978
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222955
X-RAY DIFFRACTIONr_angle_refined_deg0.981.9584045
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.6125394
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.00125.439114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.33715435
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.916159
X-RAY DIFFRACTIONr_chiral_restr0.0790.2470
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0212261
X-RAY DIFFRACTIONr_mcbond_it1.2381.51954
X-RAY DIFFRACTIONr_mcangle_it2.20323146
X-RAY DIFFRACTIONr_scbond_it3.76831001
X-RAY DIFFRACTIONr_scangle_it5.2834.5899
LS refinement shellResolution: 2.21→2.267 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 83 -
Rwork0.332 1463 -
all-1546 -
obs--94.61 %

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