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- PDB-7c4x: Crystal structure of germination protease from the spore-forming ... -

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Basic information

Entry
Database: PDB / ID: 7c4x
TitleCrystal structure of germination protease from the spore-forming bacterium Paenisporosarcina sp. TG-20 in its inactive form
Componentsgermination protease
KeywordsPROTEASE / germination protease / zymogen / HYDROLASE
Biological speciesPaenisporosarcina sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsLee, J.H. / Lee, C.W.
CitationJournal: J.Microbiol / Year: 2020
Title: Structural insights into the psychrophilic germinal protease PaGPR and its autoinhibitory loop.
Authors: Lee, C.W. / Lee, S. / Jeong, C.S. / Hwang, J. / Chang, J.H. / Choi, I.G. / Kim, T.D. / Park, H. / Kim, H.Y. / Lee, J.H.
History
DepositionMay 18, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 31, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: germination protease
B: germination protease


Theoretical massNumber of molelcules
Total (without water)80,4972
Polymers80,4972
Non-polymers00
Water81145
1
A: germination protease
B: germination protease

A: germination protease
B: germination protease


Theoretical massNumber of molelcules
Total (without water)160,9954
Polymers160,9954
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area13260 Å2
ΔGint-75 kcal/mol
Surface area50780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.617, 156.617, 95.497
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

#1: Protein germination protease


Mass: 40248.629 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: WP_019415885.1 / Source: (gene. exp.) Paenisporosarcina sp. (bacteria) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 4.41 Å3/Da / Density % sol: 72.09 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop
Details: 3.5 M sodium formate and 0.1 M Bis-Tris propane pH 7.0 with 2.8 M sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9796 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 46339 / % possible obs: 98.9 % / Redundancy: 13.2 % / Biso Wilson estimate: 53.66 Å2 / CC1/2: 0.779 / CC star: 0.936 / Net I/σ(I): 29.4
Reflection shellResolution: 2.5→2.54 Å / Num. unique obs: 2020 / CC1/2: 0.779

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1C8B

1c8b


Resolution: 2.5→45.21 Å / SU ML: 0.361 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 25.1767 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2392 2256 4.87 %
Rwork0.2009 44040 -
obs0.2027 46296 98.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.9 Å2
Refinement stepCycle: LAST / Resolution: 2.5→45.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5146 0 0 45 5191
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00855245
X-RAY DIFFRACTIONf_angle_d0.99447124
X-RAY DIFFRACTIONf_chiral_restr0.0627837
X-RAY DIFFRACTIONf_plane_restr0.006921
X-RAY DIFFRACTIONf_dihedral_angle_d22.39871933
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.560.35181340.33112321X-RAY DIFFRACTION84.71
2.56-2.610.32751320.32042678X-RAY DIFFRACTION96.56
2.61-2.680.36921410.30462720X-RAY DIFFRACTION99.34
2.68-2.750.32471250.27212782X-RAY DIFFRACTION99.76
2.75-2.830.27321620.26732736X-RAY DIFFRACTION99.83
2.83-2.930.26081360.25062765X-RAY DIFFRACTION99.86
2.93-3.030.29651770.23532728X-RAY DIFFRACTION99.93
3.03-3.150.29151190.24372784X-RAY DIFFRACTION99.73
3.15-3.290.27981570.23142770X-RAY DIFFRACTION99.93
3.29-3.470.28521430.22342772X-RAY DIFFRACTION99.93
3.47-3.690.24881310.19422807X-RAY DIFFRACTION100
3.69-3.970.23231470.18382773X-RAY DIFFRACTION100
3.97-4.370.19131570.16652804X-RAY DIFFRACTION100
4.37-50.17371200.14972805X-RAY DIFFRACTION100
5-6.30.241410.18342850X-RAY DIFFRACTION99.97
6.3-100.19251340.1742945X-RAY DIFFRACTION99.81

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