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- PDB-2z56: Crystal structure of G56S-propeptide:S324A-subtilisin complex -

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Basic information

Entry
Database: PDB / ID: 2z56
TitleCrystal structure of G56S-propeptide:S324A-subtilisin complex
Components(Tk-subtilisin) x 2
KeywordsHYDROLASE / propeptide / 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: 1.9 Å
AuthorsPulido, M.A. / Tanaka, S. / Sringiew, C. / You, D.J. / Matsumura, H. / Koga, Y. / Takano, K. / Kanaya, S.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Requirement of left-handed glycine residue for high stability of the Tk-subtilisin propeptide as revealed by mutational and crystallographic analyses
Authors: Pulido, M.A. / Tanaka, S. / Sringiew, C. / You, D.J. / Matsumura, H. / Koga, Y. / Takano, K. / Kanaya, S.
History
DepositionJun 29, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 1, 2008Provider: 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 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)40,32910
Polymers39,9832
Non-polymers3468
Water2,774154
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2740 Å2
ΔGint-93 kcal/mol
Surface area13810 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)64.518, 67.463, 74.046
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: 32868.438 Da / Num. of mol.: 1 / Fragment: Mature domain, Residue 81-398 / 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: 7114.458 Da / Num. of mol.: 1 / Fragment: Propeptide domain, Residue 5-69 / Mutation: G56S
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.: 154 / 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: 38.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1M Sodium Acetate (pH 4.6), 10%(v/v) Isopropanol, 0.2M Zinc Acetate, 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 SMART 6500 / 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: 1.9→50 Å / Num. obs: 26131 / % possible obs: 99.8 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 25.3
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.561 / Mean I/σ(I) obs: 3 / % 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: 2E1P

2e1p


Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.932 / SU B: 4.44 / SU ML: 0.133 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / ESU R: 0.176 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2095 1310 5 %RANDOM
Rwork0.18851 ---
obs0.1896 24703 99.91 %-
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: 27.886 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---0.02 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2816 0 8 154 2978
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0320.0212874
X-RAY DIFFRACTIONr_bond_other_d0.0010.022617
X-RAY DIFFRACTIONr_angle_refined_deg2.2161.9543932
X-RAY DIFFRACTIONr_angle_other_deg1.02336085
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4443381
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.77215469
X-RAY DIFFRACTIONr_chiral_restr0.1520.2461
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023273
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02520
X-RAY DIFFRACTIONr_nbd_refined0.2630.3725
X-RAY DIFFRACTIONr_nbd_other0.220.32689
X-RAY DIFFRACTIONr_nbtor_other0.2290.51
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2440.5213
X-RAY DIFFRACTIONr_metal_ion_refined0.310.536
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4280.310
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2260.337
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3380.510
X-RAY DIFFRACTIONr_mcbond_it1.5631.51898
X-RAY DIFFRACTIONr_mcangle_it2.47523058
X-RAY DIFFRACTIONr_scbond_it4.0183976
X-RAY DIFFRACTIONr_scangle_it5.9034.5874
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.299 88
Rwork0.242 1768

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