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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 / homologyPeptidase S8, subtilisin, Asp-active site / Peptidase S8/S53 domain superfamily / 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, subtilisin-related / Peptidase S8, subtilisin, His-active site / Subtilase family / Peptidase S8, subtilisin, Ser-active site ...Peptidase S8, subtilisin, Asp-active site / Peptidase S8/S53 domain superfamily / 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, subtilisin-related / Peptidase S8, subtilisin, His-active site / Subtilase family / Peptidase S8, subtilisin, Ser-active site / Subtilisin Carlsberg-like catalytic domain / subtilisin / sporulation resulting in formation of a cellular spore / serine-type endopeptidase activity / extracellular region / metal ion binding / Subtilisin DY
Function and homology information
Specimen sourceBacillus licheniformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 1.75 Å resolution
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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jun 15, 1998 / Release: Nov 4, 1998
RevisionDateData content typeGroupProviderType
1.0Nov 4, 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 DY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0304
Polyers27,4991
Non-polymers5313
Water4,071226
1


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

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Components

#1: Protein/peptide SUBTILISIN DY


Mass: 27499.416 Da / Num. of mol.: 1 / Source: (natural) Bacillus licheniformis (bacteria)
Details: X-IRRADIATED JAPANESE STRAIN OF BACILLUS LICHENIFORMIS
Genus: Bacillus / Variant: DY / References: UniProt: P00781, subtilisin
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Formula: Ca / Calcium
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Formula: Na / Sodium
#4: Chemical ChemComp-1BH / N-BENZYLOXYCARBONYL-ALA-PRO-3-AMINO-4-PHENYL-BUTAN-2-OL


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


Mass: 18.015 Da / Num. of mol.: 226 / Formula: H2O / Water

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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 / Density percent sol: 41 %
Crystal growpH: 6 / Details: AS GIVEN IN REFERENCE 1, pH 6.0
Crystal grow
*PLUS
Temp: 16 ℃ / Method: vapor diffusion, hanging drop
components of the solutions
*PLUS
IDConcCommon 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 kelvins
SourceSource: SYNCHROTRON / Site: EMBL/DESY, Hamburg / Beamline: X11 / Wavelength: 0.92
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Collection date: Feb 1, 1993
RadiationMonochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionD resolution high: 1.75 Å / D resolution low: 1 Å / Number obs: 22887 / Observed criterion sigma I: 0 / Rmerge I obs: 0.03 / Rsym value: 0.03 / NetI over sigmaI: 23 / Redundancy: 4.4 % / Percent possible obs: 96.7
Reflection shellRmerge I obs: 0.052 / Highest resolution: 1.75 Å / Lowest resolution: 1.79 Å / MeanI over sigI obs: 14 / Rsym value: 0.052 / Redundancy: 3.1 % / Percent possible all: 92.2
Reflection
*PLUS
Number measured all: 101587
Reflection shell
*PLUS
Percent possible obs: 92.2

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Processing

Software
NameClassification
AMoREphasing
CCP4refinement
DENZOdata reduction
SCALEPACKdata scaling
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CSE
Sigma F: 0
Least-squares processR factor obs: 0.14 / Highest resolution: 1.75 Å / Lowest resolution: 1 Å / Number reflection obs: 22887 / Percent reflection obs: 96.7
Refine analyzeLuzzati sigma a obs: 0.12 Å
Refine hist #LASTHighest resolution: 1.75 Å / Lowest resolution: 1 Å
Number of atoms included #LASTProtein: 1948 / Nucleic acid: 0 / Ligand: 36 / Solvent: 226 / Total: 2210
Refine LS restraints
Refine IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0220.020
X-RAY DIFFRACTIONp_angle_d0.0410.030
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0480.040
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.22.5
X-RAY DIFFRACTIONp_mcangle_it2.93.0
X-RAY DIFFRACTIONp_scbond_it3.32.5
X-RAY DIFFRACTIONp_scangle_it4.93.0
X-RAY DIFFRACTIONp_plane_restr0.0190.020
X-RAY DIFFRACTIONp_chiral_restr0.0180.015
X-RAY DIFFRACTIONp_singtor_nbd0.120.30
X-RAY DIFFRACTIONp_multtor_nbd0.290.30
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor3.610.0
X-RAY DIFFRACTIONp_staggered_tor13.615.0
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor18.445.0
X-RAY DIFFRACTIONp_special_tor

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