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- PDB-1c9m: BACILLUS LENTUS SUBTILSIN (SER 87) N76D/S103A/V104I -

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Basic information

Entry
Database: PDB / ID: 1c9m
TitleBACILLUS LENTUS SUBTILSIN (SER 87) N76D/S103A/V104I
ComponentsSERINE PROTEASE
KeywordsHYDROLASE / SERINE PROTEASE / SUBTILISIN / SITE-SPECIFIC VARIANT / ALTERED FLEXIBILITY
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 / Serine proteases, subtilase domain profile. / 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 / Serine proteases, subtilase domain profile. / Peptidase S8, subtilisin-related / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesBacillus lentus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.67 Å
AuthorsBott, R.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: Engineered Bacillus lentus subtilisins having altered flexibility.
Authors: Graycar, T. / Knapp, M. / Ganshaw, G. / Dauberman, J. / Bott, R.
History
DepositionAug 2, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SERINE PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0484
Polymers26,8721
Non-polymers1763
Water1,874104
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.250, 61.250, 75.050
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 SERINE PROTEASE /


Mass: 26871.576 Da / Num. of mol.: 1 / Mutation: N76D, S103A, V104I FROM NATIVE (SER 87)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus lentus (bacteria) / Production host: Bacillus subtilis (bacteria) / References: UniProt: P29600, subtilisin
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 2.28 Å3/Da / Density % sol: 45.96 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 5.9
Details: SODIUM ACTETATE, CALCIUM CHLORIDE, AMMONIUM SULFATE ,PHENYLMETHYLSULFANYL- FLOURIDE, pH 5.9, VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
13 mg/mlenzyme1drop
225 mMsodium acetate1drop
35 mM1dropCaCl2
414.5 %(w/v)satammonium sulfate1drop
529 %(w/v)satammonium sulfate1reservoir

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Sep 10, 1993
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.67→10 Å / Num. all: 26797 / Num. obs: 26797 / % possible obs: 91 % / Observed criterion σ(F): 2 / Redundancy: 2.5 % / Rmerge(I) obs: 0.04
Reflection shellResolution: 1.67→10 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.04 / % possible all: 91
Reflection
*PLUS
Rmerge(I) obs: 0.04

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.67→10 Å / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.168 --
all0.168 26797 -
obs0.168 26797 91 %
Refinement stepCycle: LAST / Resolution: 1.67→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1890 0 7 104 2001
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.013
X-RAY DIFFRACTIONp_angle_d2.8
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d2.8
X-RAY DIFFRACTIONp_plane_restr0.02

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