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- PDB-7y6m: Intracellular Subtilisin from Bacillus sp. -

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Basic information

Entry
Database: PDB / ID: 7y6m
TitleIntracellular Subtilisin from Bacillus sp.
ComponentsIntracellular serine protease
KeywordsHYDROLASE
Function / homologyDI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesBacillus sp. (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.703 Å
AuthorsHussin, N. / Jamaluddin, H. / Jonet, M.A.
Funding support Malaysia, 1items
OrganizationGrant numberCountry
The University Grants Committee, Research Grants Council (RGC) Malaysia
CitationJournal: TO BE PUBLISHED
Title: Intracellular Subtilisin from Bacillus sp.
Authors: Hussin, N. / Jamaluddin, H. / Jonet, M.A.
History
DepositionJun 21, 2022Deposition site: PDBJ / Processing site: PDBJ
SupersessionJul 20, 2022ID: 7XAS
Revision 1.0Jul 20, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Intracellular serine protease
D: Intracellular serine protease
A: Intracellular serine protease
B: Intracellular serine protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,36910
Polymers146,9964
Non-polymers3736
Water2,108117
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Gel filtration chromatography analysis consistently shows the target protein at dimeric size
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5980 Å2
ΔGint-68 kcal/mol
Surface area20710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.057, 78.778, 113.190
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Intracellular serine protease


Mass: 36749.035 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: GenBank MN807299 / Source: (gene. exp.) Bacillus sp. (in: Bacteria) (bacteria) / Strain: B1 / Gene: intracellular serine protease / Production host: Escherichia coli BL21(DE3) (bacteria)
References: Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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

Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: PROTEIN: 25 mM Tris-HCl, 50 mM Nacl, 1 mM CaCl2 MOTHER LIQUOR: 25% PEG3350, 8% Tacsimate pH 4.5

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Data collection

DiffractionMean temperature: 200 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Mar 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5 Å / Relative weight: 1
ReflectionResolution: 2.7→40 Å / Num. obs: 16072 / % possible obs: 98.6 % / Redundancy: 3 % / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.059 / Rrim(I) all: 0.107 / Χ2: 1.264 / Net I/σ(I): 8.3 / Num. measured all: 48642
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.7-2.752.70.4217710.7240.3030.5221.23797.7
2.75-2.82.70.3527860.8380.2550.4371.08898.2
2.8-2.852.80.3137810.8580.2220.3861.00398.2
2.85-2.912.90.3027850.8890.2090.3690.91997.9
2.91-2.972.90.2447790.9240.1650.2970.93498.7
2.97-3.042.90.2098010.950.140.2530.85998.6
3.04-3.1230.1717720.960.1140.2070.8999.1
3.12-3.23.10.1598040.9750.1040.1911.00898.8
3.2-3.33.10.1338070.9830.0870.160.95299.8
3.3-3.43.20.1398050.9770.090.1661.11699.5
3.4-3.523.20.1367940.9820.0890.1641.61198.6
3.52-3.663.20.097930.9820.0580.1071.71699.4
3.66-3.833.20.0768130.9820.050.0911.78199.8
3.83-4.033.10.0977990.9630.0650.1171.9198.8
4.03-4.283.20.0658280.9920.0430.0781.42999.8
4.28-4.623.20.0558250.9920.0360.0661.93399.8
4.62-5.083.20.0468170.9960.030.0551.09899.6
5.08-5.813.10.0548180.9960.0360.0650.97698.9
5.81-7.313.10.0488400.9960.0320.0581.13998.4
7.31-402.80.0298540.9980.020.0361.37393.2

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.27data extraction
HKL-3000v714ndata reduction
HKL-3000v714nphasing
HKL-3000v714ndata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6F9M

6f9m


Resolution: 2.703→30.051 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 25.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2617 784 4.92 %RANDOM
Rwork0.1892 15158 --
obs0.1928 15942 98.12 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 82.8 Å2 / Biso mean: 31.9955 Å2 / Biso min: 9.89 Å2
Refinement stepCycle: final / Resolution: 2.703→30.051 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4418 0 18 117 4553
Biso mean--28.98 25.78 -
Num. residues----594
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.703-2.8720.35371270.2505245498
2.872-3.09350.29221330.216250399
3.0935-3.40440.26441420.2145250099
3.4044-3.89620.32571230.1876249998
3.8962-4.90530.23651040.1643257798
4.9053-30.0510.19581550.1687262598

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