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- PDB-1bfu: SUBTILISIN CARLSBERG IN 20% DIOXANE -

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Basic information

Entry
Database: PDB / ID: 1bfu
TitleSUBTILISIN CARLSBERG IN 20% DIOXANE
ComponentsSUBTILISIN CARLSBERG
KeywordsSERINE PROTEASE / ORGANIC SOLVENT / MIXTURES
Function / homology
Function and homology information


subtilisin / serine-type endopeptidase activity / proteolysis / extracellular region / metal ion binding
Similarity search - Function
Subtilisin Carlsberg-like catalytic domain / Peptidase S8/S53 domain / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase inhibitor I9 / : / 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 ...Subtilisin Carlsberg-like catalytic domain / Peptidase S8/S53 domain / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase inhibitor I9 / : / 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 / 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
1,4-DIETHYLENE DIOXIDE / Subtilisin Carlsberg
Similarity search - Component
Biological speciesBacillus licheniformis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSchmitke, J.L. / Stern, L.J. / Klibanov, A.M.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 1998
Title: Organic solvent binding to crystalline subtilisin1 in mostly aqueous media and in the neat solvents.
Authors: Schmitke, J.L. / Stern, L.J. / Klibanov, A.M.
History
DepositionMay 22, 1998Processing site: BNL
Revision 1.0Oct 28, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Aug 2, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / 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 / _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
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SUBTILISIN CARLSBERG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4343
Polymers27,3061
Non-polymers1282
Water1,62190
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.555, 55.173, 53.862
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 CARLSBERG


Mass: 27306.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus licheniformis (bacteria) / References: UniProt: P00780, subtilisin
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE


Mass: 88.105 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 42 %
Crystal growpH: 5.6
Details: PROTEIN WAS CRYSTALLIZED FROM 13% SODIUM SULFATE, 30 MM CACODYLATE, PH 5.6; THEN CROSS-LINKED WITH 10% GLUTARALDEHYDE IN 13% SODIUM SULFATE, 30 MM CACODYLATE, PH 7.5, WASHED WITH DISTILLED ...Details: PROTEIN WAS CRYSTALLIZED FROM 13% SODIUM SULFATE, 30 MM CACODYLATE, PH 5.6; THEN CROSS-LINKED WITH 10% GLUTARALDEHYDE IN 13% SODIUM SULFATE, 30 MM CACODYLATE, PH 7.5, WASHED WITH DISTILLED WATER, AND TRANSFERRED TO 20% DIOXANE.
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
1330 mMcacodylate11
213 %satsodium sulfate11

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Data collection

DiffractionMean temperature: 296 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jan 17, 1998 / Details: MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 11408 / % possible obs: 93.8 % / Redundancy: 3.9 % / Biso Wilson estimate: 27 Å2 / Rsym value: 0.129 / Net I/σ(I): 9.9
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 3.9 / Rsym value: 0.36 / % possible all: 85
Reflection
*PLUS
Num. measured all: 44882 / Rmerge(I) obs: 0.129
Reflection shell
*PLUS
% possible obs: 85 % / Num. unique obs: 1195 / Num. measured obs: 3478 / Rmerge(I) obs: 0.357

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Processing

Software
NameVersionClassification
X-PLOR3.8model building
X-PLOR3.8refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.8phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AF4

1af4


Resolution: 2.2→20 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.245 -10 %RANDOM
Rwork0.187 ---
obs0.187 11000 --
Displacement parametersBiso mean: 23 Å2
Refine analyzeLuzzati coordinate error obs: 0.31 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.28 Å
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1920 0 1 96 2017
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.689
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.2→2.3 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.338 -9.4 %
Rwork0.262 1031 -
obs--85 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1TOPPAR:PROTEIN_REP.PARAMTOPPAR:TOPHCSDX.PRO
X-RAY DIFFRACTION2DIO.PARDIO.TOP
X-RAY DIFFRACTION3TOPPAR:PARAMETER.ELEMENTSTOPPAR:TOPH19.SOL
X-RAY DIFFRACTION4TOPPAR:TOPOLOGY.ELEMENTS
LS refinement shell
*PLUS
Rfactor obs: 0.262

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