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- PDB-1c8b: CRYSTAL STRUCTURE OF A NOVEL GERMINATION PROTEASE FROM SPORES OF ... -

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Basic information

Entry
Database: PDB / ID: 1c8b
TitleCRYSTAL STRUCTURE OF A NOVEL GERMINATION PROTEASE FROM SPORES OF BACILLUS MEGATERIUM: STRUCTURAL REARRANGEMENTS AND ZYMOGEN ACTIVATION
ComponentsSPORE PROTEASE
KeywordsHYDROLASE / NOVEL FOLD
Function / homology
Function and homology information


gpr endopeptidase / spore germination / metalloendopeptidase activity / proteolysis
Similarity search - Function
Peptidase A25, germination protease / Germination protease / HybD-like / Peptidase HybD-like domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Germination protease
Similarity search - Component
Biological speciesBacillus megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3 Å
AuthorsPonnuraj, K. / Rowland, S. / Nessi, C. / Setlow, P. / Jedrzejas, M.J.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: Crystal structure of a novel germination protease from spores of Bacillus megaterium: structural arrangement and zymogen activation.
Authors: Ponnuraj, K. / Rowland, S. / Nessi, C. / Setlow, P. / Jedrzejas, M.J.
History
DepositionMay 3, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SPORE PROTEASE
B: SPORE PROTEASE


Theoretical massNumber of molelcules
Total (without water)81,3472
Polymers81,3472
Non-polymers00
Water2,270126
1
A: SPORE PROTEASE
B: SPORE PROTEASE

A: SPORE PROTEASE
B: SPORE PROTEASE


Theoretical massNumber of molelcules
Total (without water)162,6934
Polymers162,6934
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area8430 Å2
ΔGint-80 kcal/mol
Surface area59910 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)77.41, 77.41, 313.74
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-133-

HOH

21B-1133-

HOH

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Components

#1: Protein SPORE PROTEASE / GERMINATION PROTEASE


Mass: 40673.258 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus megaterium (bacteria) / Description: ESCHERICHIA COLI / Production host: Escherichia coli (E. coli) / References: UniProt: P22321, EC: 3.4.99.-
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.89 Å3/Da / Density % sol: 57.4 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 7.4
Details: SODIUM CITRATE, SODIUM HEPES, pH 7.4, EVAPORATION, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
11.6 Msodium citrate1reservoir
20.1 Msodium HEPES1reservoirpH7.3
320 mMEDTA1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.05
DetectorType: BRANDEIS / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 3→20 Å / Num. all: 120136 / Num. obs: 18965 / % possible obs: 94.1 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.103
Reflection shellResolution: 3→3.11 Å / Rmerge(I) obs: 0.508 / % possible all: 87.7
Reflection
*PLUS
Num. measured all: 120136

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Processing

Software
NameClassification
SOLVEphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 3→15 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: 2-FOLD NCS AND GROUPED B FACTOR REFINEMENT
RfactorNum. reflection% reflection
Rfree0.33 1732 -
Rwork0.308 --
obs-18965 88 %
Refinement stepCycle: LAST / Resolution: 3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4328 0 0 126 4454
Refine LS restraintsType: x_bond_d / Dev ideal: 0.013
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 3 Å / Lowest resolution: 15 Å / σ(F): 2 / Rfactor obs: 0.308 / Rfactor Rfree: 0.33
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.81

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