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- PDB-3vsb: SUBTILISIN CARLSBERG D-NAPHTHYL-1-ACETAMIDO BORONIC ACID INHIBITO... -

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Basic information

Entry
Database: PDB / ID: 3vsb
TitleSUBTILISIN CARLSBERG D-NAPHTHYL-1-ACETAMIDO BORONIC ACID INHIBITOR COMPLEX
ComponentsSUBTILISIN CARLSBERG, TYPE VIII
KeywordsSERINE PROTEASE / HYDROLASE / BORONIC ACID INHIBITORS
Function / homology
Function and homology information


subtilisin / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding
Similarity search - Function
Subtilisin Carlsberg-like catalytic domain / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase inhibitor I9 / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily / 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 ...Subtilisin Carlsberg-like catalytic domain / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase inhibitor I9 / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily / 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
Subtilisin Carlsberg
Similarity search - Component
Biological speciesBacillus licheniformis (bacteria)
MethodX-RAY DIFFRACTION / ISOSTRUCTURAL TO 1SCA / Resolution: 2.6 Å
AuthorsStoll, V.S. / Eger, B.T. / Hynes, R.C. / Martichonok, V. / Jones, J.B. / Pai, E.F.
Citation
Journal: Biochemistry / Year: 1998
Title: Differences in binding modes of enantiomers of 1-acetamido boronic acid based protease inhibitors: crystal structures of gamma-chymotrypsin and subtilisin Carlsberg complexes.
Authors: Stoll, V.S. / Eger, B.T. / Hynes, R.C. / Martichonok, V. / Jones, J.B. / Pai, E.F.
#1: Journal: J.Am.Chem.Soc. / Year: 1996
Title: Probing the Specificity of the Serine Proteases Subtilisin Carlsberg and A-Chymotrypsin with Enantiomeric 1-Acetamido Boronic Acids. An Unexpected Reversal of the Normal "L"-Stereoselectivity Preference
Authors: Martichonok, V. / Jones, J.B.
#2: Journal: Bioorg.Med.Chem. / Year: 1994
Title: Probing the Specificity of the S1 Binding Site of Subtilisin Carlsberg with Boronic Acids
Authors: Seufer-Wasserthal, P. / Martichonok, V. / Keller, T.H. / Chin, B. / Martin, R. / Jones, J.B.
#3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1993
Title: Enzyme Crystal Structure in a Neat Organic Solvent
Authors: Fitzpatrick, P.A. / Steinmetz, A.C. / Ringe, D. / Klibanov, A.M.
#4: Journal: J.Mol.Biol. / Year: 1976
Title: The Structure of Subtilopeptidase A. I. X-Ray Crystallographic Data
Authors: Petsko, G.A. / Tsernoglou, D.
History
DepositionSep 25, 1997Processing site: BNL
Revision 1.0Mar 25, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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 / _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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SUBTILISIN CARLSBERG, TYPE VIII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6083
Polymers27,5621
Non-polymers462
Water39622
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.000, 55.400, 76.600
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, TYPE VIII / SUBTILOPEPTIDASE A


Mass: 27562.283 Da / Num. of mol.: 1 / Fragment: FULL PROTEIN / Source method: isolated from a natural source / Details: PURCHASED FROM SIGMA / Source: (natural) Bacillus licheniformis (bacteria) / References: UniProt: P00780, subtilisin
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE 274 RESIDUES ARE NUMBERED 1 - 275 WITH RESIDUE 56 DELETED TO CONFORM TO SEQUENCE NUMBERING IN ...THE 274 RESIDUES ARE NUMBERED 1 - 275 WITH RESIDUE 56 DELETED TO CONFORM TO SEQUENCE NUMBERING IN SUBTILISIN BPN'.

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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: 2.2 Å3/Da / Density % sol: 41.5 %
Description: STARTING MODEL WAS RE-INDEXED TO CONFORM TO AXIS LABELING CONVENTION A		Crystal growpH: 7 / Details: AS GIVEN IN REFERENCE 4, pH 7.0
Crystal grow
*PLUS
pH: 5.6 / Method: batch method / Details: Petsko, G.A., (1976) J.Mol.Biol., 106, 453.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.5 %protein11
217 %aqueous sodium sulfate11

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Aug 1, 1996 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. obs: 6957 / % possible obs: 77 % / Redundancy: 4 % / Rsym value: 0.091 / Net I/σ(I): 6
Reflection shellResolution: 2.6→2.71 Å / Redundancy: 3 % / Mean I/σ(I) obs: 2.5 / Rsym value: 0.15 / % possible all: 41.1
Reflection
*PLUS
Rmerge(I) obs: 0.091

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
XDSdata reduction
XSCALEdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: ISOSTRUCTURAL TO 1SCA
Starting model: PDB ENTRY 1SCA

1sca


Resolution: 2.6→8 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: GROUPED / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.299 860 15 %RANDOM
Rwork0.155 ---
obs0.155 5426 77.1 %-
Displacement parametersBiso mean: 11.2 Å2
Refine analyzeLuzzati d res low obs: 8 Å
Refinement stepCycle: LAST / Resolution: 2.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1920 0 21 22 1963
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
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_deg1.82
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2.51
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: 2.6→2.71 Å / Rfactor Rfree error: 0.046 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.352 58 6.46 %
Rwork0.219 314 -
obs--41.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
X-RAY DIFFRACTION3TOPH19.PEP
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2.51

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