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- PDB-6y5t: Crystal structure of savinase at room temperature -

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Basic information

Entry
Database: PDB / ID: 6y5t
TitleCrystal structure of savinase at room temperature
ComponentsSubtilisin Savinase
KeywordsHYDROLASE / SUBTILISIN SAVINASE / Protein dynamics / alternative conformations
Function / homology
Function and homology information


subtilisin / sporulation resulting in formation of a cellular spore / serine-type endopeptidase activity / proteolysis / extracellular region / metal ion binding
Similarity search - Function
Subtilisin Carlsberg-like catalytic domain / Peptidase S8/S53 domain / 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 ...Subtilisin Carlsberg-like catalytic domain / Peptidase S8/S53 domain / 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 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesBacillus lentus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsWu, S. / Moroz, O. / Turkenburg, J. / Nielsen, J.E. / Wilson, K.S. / Teilum, K.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Danish Council for Independent Research1335-00317B Denmark
CitationJournal: Peerj / Year: 2020
Title: Conformational heterogeneity of Savinase from NMR, HDX-MS and X-ray diffraction analysis.
Authors: Wu, S. / Nguyen, T.T.T.N. / Moroz, O.V. / Turkenburg, J.P. / Nielsen, J.E. / Wilson, K.S. / Rand, K.D. / Teilum, K.
History
DepositionFeb 25, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 17, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 24, 2024Group: 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 / struct_conn
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Subtilisin Savinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7813
Polymers26,7181
Non-polymers632
Water3,135174
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-12 kcal/mol
Surface area9390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.704, 62.205, 75.766
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Subtilisin Savinase / Alkaline protease


Mass: 26718.381 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus lentus (bacteria) / Production host: Bacillus licheniformis (bacteria) / References: UniProt: P29600, subtilisin
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 174 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.1 Å3/Da / Density % sol: 41.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5 / Details: 0.2 M NaBr, 0.1 M Bis Tris propane, 20% PEG3350

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Data collection

DiffractionMean temperature: 297 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.8856 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 31, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.1→48.08 Å / Num. obs: 91686 / % possible obs: 99.7 % / Redundancy: 4.9 % / Biso Wilson estimate: 11.23 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.07 / Net I/σ(I): 19.8
Reflection shellResolution: 1.1→1.11 Å / Rmerge(I) obs: 1.341 / Num. unique obs: 4525 / CC1/2: 0.502

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4cfy

4cfy


Resolution: 1.1→40.37 Å / SU ML: 0.1049 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 14.1402
RfactorNum. reflection% reflection
Rfree0.1498 4510 4.92 %
Rwork0.1304 --
obs0.1314 91615 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 16.37 Å2
Refinement stepCycle: LAST / Resolution: 1.1→40.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1880 0 2 174 2056
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00562158
X-RAY DIFFRACTIONf_angle_d0.84823000
X-RAY DIFFRACTIONf_chiral_restr0.0814344
X-RAY DIFFRACTIONf_plane_restr0.0059414
X-RAY DIFFRACTIONf_dihedral_angle_d5.4537347
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1-1.110.31031450.28812918X-RAY DIFFRACTION99.77
1.11-1.130.24171530.25522842X-RAY DIFFRACTION99.97
1.13-1.140.25321490.24612903X-RAY DIFFRACTION99.71
1.14-1.150.24051480.23342858X-RAY DIFFRACTION99.67
1.15-1.170.2331330.21492897X-RAY DIFFRACTION99.54
1.17-1.180.2151500.19952879X-RAY DIFFRACTION99.64
1.18-1.20.22011580.19272852X-RAY DIFFRACTION99.67
1.2-1.220.20971480.18282881X-RAY DIFFRACTION99.67
1.22-1.240.19081500.17582895X-RAY DIFFRACTION99.77
1.24-1.260.21531370.18042880X-RAY DIFFRACTION99.7
1.26-1.280.19821620.16392865X-RAY DIFFRACTION99.51
1.28-1.30.19551600.14432864X-RAY DIFFRACTION99.74
1.3-1.330.15761460.14072904X-RAY DIFFRACTION99.8
1.33-1.360.17291460.13092908X-RAY DIFFRACTION99.71
1.36-1.390.14751410.12452880X-RAY DIFFRACTION99.87
1.39-1.420.14711660.1152892X-RAY DIFFRACTION99.8
1.42-1.450.14511460.10482908X-RAY DIFFRACTION99.71
1.45-1.490.14951560.1042874X-RAY DIFFRACTION99.61
1.49-1.540.14681500.0982909X-RAY DIFFRACTION99.84
1.54-1.590.161510.09242888X-RAY DIFFRACTION99.57
1.59-1.640.10871640.09592888X-RAY DIFFRACTION99.38
1.64-1.710.12461380.09392924X-RAY DIFFRACTION99.84
1.71-1.790.11941670.09492907X-RAY DIFFRACTION99.71
1.79-1.880.11381520.09962911X-RAY DIFFRACTION99.45
1.88-20.13131520.1042933X-RAY DIFFRACTION99.55
2-2.150.12311560.10082908X-RAY DIFFRACTION99.38
2.15-2.370.12481400.11872958X-RAY DIFFRACTION99.1
2.37-2.710.13961370.13152977X-RAY DIFFRACTION99.14
2.71-3.420.15311570.14012953X-RAY DIFFRACTION98.39
3.42-40.370.14221520.13543049X-RAY DIFFRACTION96.85

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