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- PDB-1dbi: CRYSTAL STRUCTURE OF A THERMOSTABLE SERINE PROTEASE -

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Basic information

Entry
Database: PDB / ID: 1dbi
TitleCRYSTAL STRUCTURE OF A THERMOSTABLE SERINE PROTEASE
ComponentsAK.1 SERINE PROTEASE
KeywordsHYDROLASE
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type endopeptidase activity / extracellular region / metal ion binding
Similarity search - Function
Thermitase-like, 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 ...Thermitase-like, 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
Thermophilic serine proteinase
Similarity search - Component
Biological speciesBacillus sp. AK1 (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsSmith, C.A. / Toogood, H.S. / Baker, H.M. / Daniel, R.M. / Baker, E.N.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: Calcium-mediated thermostability in the subtilisin superfamily: the crystal structure of Bacillus Ak.1 protease at 1.8 A resolution.
Authors: Smith, C.A. / Toogood, H.S. / Baker, H.M. / Daniel, R.M. / Baker, E.N.
History
DepositionNov 2, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 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 / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AK.1 SERINE PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9335
Polymers29,7891
Non-polymers1434
Water4,432246
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.050, 51.680, 52.780
Angle α, β, γ (deg.)90.00, 96.10, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein AK.1 SERINE PROTEASE


Mass: 29789.393 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus sp. AK1 (bacteria) / Strain: AK.1 / References: UniProt: Q45670
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 246 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 38.65 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.9
Details: PEG 4000, acetate, calcium chloride, pH 4.9, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlenzyme1drop
210 mMTES1drop
35 mM1dropCaCl2
40.01 %Triton X-1001drop
514 %PEG40001reservoir
6100 mMacetate1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Mar 19, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. all: 20847 / Num. obs: 20847 / % possible obs: 87.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 8.5
Reflection shellResolution: 1.8→20 Å / Rmerge(I) obs: 0.372 / % possible all: 47
Reflection
*PLUS
Num. measured all: 97032
Reflection shell
*PLUS
% possible obs: 47 % / Mean I/σ(I) obs: 1.9

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Processing

Software
NameVersionClassification
DENZOdata reduction
ROTAVATAdata reduction
AMoREphasing
TNTrefinement
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
RefinementResolution: 1.8→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.247 1028 RANDOM
Rwork0.182 --
all-19473 -
obs-19473 -
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2031 0 4 246 2281
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.012
X-RAY DIFFRACTIONt_angle_deg1.49

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