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- PDB-1avt: SUBTILISIN CARLSBERG D-PARA-CHLOROPHENYL-1-ACETAMIDO BORONIC ACID... -

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Basic information

Entry
Database: PDB / ID: 1avt
TitleSUBTILISIN CARLSBERG D-PARA-CHLOROPHENYL-1-ACETAMIDO BORONIC ACID INHIBITOR COMPLEX
ComponentsSUBTILISIN CARLSBERG, TYPE VIII
KeywordsSERINE PROTEASE / HYDROLASE / BORONIC ACID INHIBITORS
Function / homologyPeptidase S8, subtilisin, Ser-active site / Subtilase family / Serine proteases, subtilase family, serine active site. / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, aspartic acid active site. / Peptidase S8/S53 domain / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase S8, subtilisin-related / Peptidase S8, subtilisin, His-active site / Peptidase S8, subtilisin, Asp-active site ...Peptidase S8, subtilisin, Ser-active site / Subtilase family / Serine proteases, subtilase family, serine active site. / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, aspartic acid active site. / Peptidase S8/S53 domain / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase S8, subtilisin-related / Peptidase S8, subtilisin, His-active site / Peptidase S8, subtilisin, Asp-active site / Peptidase inhibitor I9 / Subtilisin Carlsberg-like catalytic domain / Peptidase S8/S53 domain superfamily / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily / subtilisin / sporulation resulting in formation of a cellular spore / serine-type endopeptidase activity / extracellular region / metal ion binding / Subtilisin Carlsberg
Function and homology information
Specimen sourceBacillus licheniformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / ISOSTRUCTURAL TO 1SCA / 2 Å resolution
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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Sep 19, 1997 / Release: Mar 25, 1998
RevisionDateData content typeGroupProviderType
1.0Mar 25, 1998Structure modelrepositoryInitial release
1.1Mar 24, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SUBTILISIN CARLSBERG, TYPE VIII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5933
Polyers27,5471
Non-polymers462
Water2,738152
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
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-MP 21 21 21

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Components

#1: Protein/peptide SUBTILISIN CARLSBERG, TYPE VIII / SUBTILOPEPTIDASE A


Mass: 27546.670 Da / Num. of mol.: 1 / Fragment: FULL PROTEIN / Source: (natural) Bacillus licheniformis (bacteria) / Details: PURCHASED FROM SIGMA / Genus: Bacillus / References: UniProt: P00780, subtilisin
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Formula: Na / Sodium
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / Formula: H2O / Water

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 7

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Sample preparation

CrystalDensity Matthews: 2.2 / Density percent sol: 41.5 %
Description: THE COORDINATES OF THE STARTING MODEL WERE 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
IDConcCommon nameCrystal IDSol ID
10.5 %protein11
217 %aqueous sodium sulfate11

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Data collection

DiffractionMean temperature: 287 kelvins
SourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.918
DetectorType: FUJI / Details: MIRRORS / Detector: IMAGE PLATE / Collection date: Nov 1, 1993
RadiationMonochromator: SI(111) / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionD resolution high: 2 Å / D resolution low: 2 Å / Number obs: 15092 / Rmerge I obs: 0.082 / Rsym value: 0.082 / NetI over sigmaI: 14 / Redundancy: 1.7 % / Percent possible obs: 96
Reflection shellRmerge I obs: 0.083 / Highest resolution: 2 Å / Lowest resolution: 2.09 Å / MeanI over sigI obs: 7 / Rsym value: 0.083 / Redundancy: 1.4 % / Percent possible all: 94.3

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
XSCALEdata scaling
X-PLOR3.1phasing
RefineMethod to determine structure: ISOSTRUCTURAL TO 1SCA
Starting model: PDB ENTRY 1SCA
R Free selection details: RANDOM / Data cutoff high absF: 1 / Data cutoff low absF: 0.1 / Isotropic thermal model: INDIVIDUAL / Cross valid method: THROUGHOUT / Sigma F: 1
Displacement parametersB iso mean: 12 Å2
Least-squares processR factor R free: 0.226 / R factor R free error: 0.005 / R factor R work: 0.157 / R factor obs: 0.157 / Highest resolution: 2 Å / Lowest resolution: 8 Å / Number reflection R free: 1452 / Number reflection obs: 14776 / Percent reflection R free: 1 / Percent reflection obs: 95.6
Refine analyzeLuzzati d res low obs: 8 Å
Refine hist #LASTHighest resolution: 2 Å / Lowest resolution: 8 Å
Number of atoms included #LASTProtein: 1920 / Nucleic acid: 0 / Ligand: 16 / Solvent: 153 / Total: 2089
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
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_deg1.48
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.34
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
Refine LS shellHighest resolution: 2 Å / R factor R free: 0.227 / R factor R free error: 0.016 / R factor R work: 0.1808 / Lowest resolution: 2.09 Å / Number reflection R free: 189 / Number reflection R work: 1572 / Total number of bins used: 8 / Percent reflection R free: 9.92 / Percent reflection obs: 91.9
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_deg24.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.34
Refine LS shell
*PLUS
R factor R free: 0.227

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