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- PDB-1bh6: SUBTILISIN DY IN COMPLEX WITH THE SYNTHETIC INHIBITOR N-BENZYLOXY... -

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Basic information

Entry
Database: PDB / ID: 1bh6
TitleSUBTILISIN DY IN COMPLEX WITH THE SYNTHETIC INHIBITOR N-BENZYLOXYCARBONYL-ALA-PRO-PHE-CHLOROMETHYL KETONE
ComponentsSUBTILISIN DY
KeywordsHYDROLASE / SUBTILISIN / PROTEIN DEGRADATION
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
Chem-1BH / Subtilisin DY
Similarity search - Component
Biological speciesBacillus licheniformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsEschenburg, S. / Genov, N. / Wilson, K.S. / Betzel, C.
Citation
Journal: Eur.J.Biochem. / Year: 1998
Title: Crystal structure of subtilisin DY, a random mutant of subtilisin Carlsberg.
Authors: Eschenburg, S. / Genov, N. / Peters, K. / Fittkau, S. / Stoeva, S. / Wilson, K.S. / Betzel, C.
#1: Journal: Arch.Biochem.Biophys. / Year: 1993
Title: Crystallization and Preliminary X-Ray Analysis of Subtilisin Dy, a Natural Mutant of Subtilisin Carlsberg
Authors: Betzel, C. / Visanji, M. / Eschenburg, S. / Wilson, K.S. / Peters, K. / Fittkau, S. / Singh, T.P. / Genov, N.
History
DepositionJun 15, 1998Processing site: BNL
Revision 1.0Nov 4, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: database_2 / diffrn_source ...database_2 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_conn_angle / 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 / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_asym_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.pdbx_leaving_atom_flag / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SUBTILISIN DY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0304
Polymers27,4991
Non-polymers5313
Water4,071226
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.830, 72.750, 59.890
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 DY


Mass: 27499.416 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: X-IRRADIATED JAPANESE STRAIN OF BACILLUS LICHENIFORMIS
Source: (natural) Bacillus licheniformis (bacteria) / Variant: DY / References: UniProt: P00781, 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: Chemical ChemComp-1BH / N-BENZYLOXYCARBONYL-ALA-PRO-3-AMINO-4-PHENYL-BUTAN-2-OL


Mass: 467.557 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H33N3O5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / 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: 2.1 Å3/Da / Density % sol: 41 %
Crystal growpH: 6 / Details: AS GIVEN IN REFERENCE 1, pH 6.0
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 16 ℃ / 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 mMsodium citrate1drop
610 %PEG40001reservoir
71 M1reservoirNaCl
85 mM1reservoirCaCl2
950 mMsodium citrate1reservoir

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Data collection

DiffractionMean temperature: 278 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.92
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 1, 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.75→10 Å / Num. obs: 22887 / % possible obs: 96.7 % / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Rmerge(I) obs: 0.03 / Rsym value: 0.03 / Net I/σ(I): 23
Reflection shellResolution: 1.75→1.79 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.052 / Mean I/σ(I) obs: 14 / Rsym value: 0.052 / % possible all: 92.2
Reflection
*PLUS
Num. measured all: 101587
Reflection shell
*PLUS
% possible obs: 92.2 %

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Processing

Software
NameClassification
AMoREphasing
CCP4refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CSE

1cse


Resolution: 1.75→10 Å / σ(F): 0 /
RfactorNum. reflection% reflection
obs0.14 22887 96.7 %
Refine analyzeLuzzati sigma a obs: 0.12 Å
Refinement stepCycle: LAST / Resolution: 1.75→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1948 0 36 226 2210
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0220.02
X-RAY DIFFRACTIONp_angle_d0.0410.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0480.04
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.22.5
X-RAY DIFFRACTIONp_mcangle_it2.93
X-RAY DIFFRACTIONp_scbond_it3.32.5
X-RAY DIFFRACTIONp_scangle_it4.93
X-RAY DIFFRACTIONp_plane_restr0.0190.02
X-RAY DIFFRACTIONp_chiral_restr0.0180.015
X-RAY DIFFRACTIONp_singtor_nbd0.120.3
X-RAY DIFFRACTIONp_multtor_nbd0.290.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor3.610
X-RAY DIFFRACTIONp_staggered_tor13.615
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor18.445
X-RAY DIFFRACTIONp_special_tor

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