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- PDB-1svn: SAVINASE -

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Basic information

Entry
Database: PDB / ID: 1svn
TitleSAVINASE
ComponentsSAVINASE (TM)
KeywordsSERINE PROTEASE / HYDROLASE / SPORULATION / CALCIUM-BINDING
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 / 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 / Peptidase S8, subtilisin-related / Serine proteases, subtilase domain profile. / 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 / Resolution: 1.4 Å
AuthorsBetzel, C. / Klupsch, S. / Papendorf, G. / Hastrup, S. / Branner, S. / Wilson, K.S.
Citation
Journal: J.Mol.Biol. / Year: 1992
Title: Crystal structure of the alkaline proteinase Savinase from Bacillus lentus at 1.4 A resolution.
Authors: Betzel, C. / Klupsch, S. / Papendorf, G. / Hastrup, S. / Branner, S. / Wilson, K.S.
#1: Journal: J.Mol.Biol. / Year: 1988
Title: Crystallization and Preliminary X-Ray Diffraction Studies of an Alkaline Protease from Bacillus Lentu
Authors: Betzel, C. / Dauter, Z. / Dauter, M. / Ingelman, M. / Papendorf, G. / Wilson, K.S. / Branner, S.
History
DepositionSep 1, 1995Processing site: BNL
Revision 1.0Oct 14, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_database_status.process_site / _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.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_conn.ptnr2_label_seq_id / _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

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Assembly

Deposited unit
A: SAVINASE (TM)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7993
Polymers26,7181
Non-polymers802
Water2,882160
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.470, 64.240, 42.890
Angle α, β, γ (deg.)90.00, 118.80, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein SAVINASE (TM) / PEPTIDYL PEPTIDE HYDROLASE


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


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.83 Å3/Da / Density % sol: 32 %
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 18 K / pH: 6.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
24 %PEG40001drop
30.33 M1dropNaCl
41.5 mM1dropCaCl2
518 mMcitrate1drop
610 %(w/v)PEG40001reservoir
71 M1reservoirNaCl
85 mM1reservoirCaCl2
950 mMcitrate1reservoir

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 1.009, 1.5418
DetectorType: CEA FILM / Detector: FILM / Date: 1991
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.0091
21.54181
ReflectionRedundancy: 5.2 % / Rmerge(I) obs: 0.083
Reflection
*PLUS
Highest resolution: 1.4 Å / Lowest resolution: 2.5 Å / Num. obs: 29065 / % possible obs: 77 % / Observed criterion σ(I): 3

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Processing

Software
NameClassification
PROLSQrefinement
MOSFLMdata reduction
RefinementResolution: 1.4→10 Å / σ(F): 0 /
Num. reflection% reflection
obs29046 77 %
Refine analyzeLuzzati sigma a obs: 0.13 Å
Refinement stepCycle: LAST / Resolution: 1.4→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1880 0 2 160 2042
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0240.02
X-RAY DIFFRACTIONp_angle_d0.0510.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0540.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.72
X-RAY DIFFRACTIONp_mcangle_it2.23
X-RAY DIFFRACTIONp_scbond_it3.94
X-RAY DIFFRACTIONp_scangle_it5.25
X-RAY DIFFRACTIONp_plane_restr0.0180.02
X-RAY DIFFRACTIONp_chiral_restr0.1870.15
X-RAY DIFFRACTIONp_singtor_nbd0.1750.3
X-RAY DIFFRACTIONp_multtor_nbd0.310.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.2050.3
X-RAY DIFFRACTIONp_planar_tor33
X-RAY DIFFRACTIONp_staggered_tor16.315
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor3020
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.174
Solvent computation
*PLUS
Displacement parameters
*PLUS

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