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- PDB-9g0j: Structure of the PRO-PRO endopeptidase (PPEP-3) from Geobacillus ... -

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Basic information

Entry
Database: PDB / ID: 9g0j
TitleStructure of the PRO-PRO endopeptidase (PPEP-3) from Geobacillus thermodenitrificans
ComponentsATLF-like domain-containing protein
KeywordsHYDROLASE / Endopeptidase / Metalloprotease / Zinc
Function / homologyAnthrax toxin, lethal/endema factor, N-/C-terminal / : / Anthrax toxin lethal factor, N- and C-terminal domain / Anthrax toxin lethal factor (ATLF)-like domain profile. / Metallopeptidase, catalytic domain superfamily / metallopeptidase activity / extracellular region / DI(HYDROXYETHYL)ETHER / ATLF-like domain-containing protein
Function and homology information
Biological speciesGeobacillus thermodenitrificans NG80-2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsClaushuis, B. / Wojtalla, F. / van Leeuwen, H. / Corver, J. / Baumann, U. / Hensbergen, P.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO)OCENW.KLEIN.103 Netherlands
CitationJournal: To Be Published
Title: Structure of the PRO-PRO endopeptidase (PPEP-3) from Geobacillus thermodenitrificans
Authors: Claushuis, B. / Wojtalla, F. / van Leeuwen, H. / Corver, J. / Baumann, U. / Hensbergen, P.
History
DepositionJul 8, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATLF-like domain-containing protein
B: ATLF-like domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,60110
Polymers52,7632
Non-polymers8388
Water4,360242
1
A: ATLF-like domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7785
Polymers26,3821
Non-polymers3974
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ATLF-like domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8225
Polymers26,3821
Non-polymers4414
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)126.247, 126.247, 64.043
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-926-

HOH

21B-830-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein ATLF-like domain-containing protein


Mass: 26381.512 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus thermodenitrificans NG80-2 (bacteria)
Gene: GTNG_1672 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A4INY2

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Non-polymers , 5 types, 250 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-BCN / BICINE


Mass: 163.172 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C6H13NO4 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.43 Å3/Da / Density % sol: 49.4 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.12 M Ethylene Glycols 0.1 M Tris-Bicine pH 8.5 30 % P550MME_P20K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jul 21, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.55→44.64 Å / Num. obs: 143852 / % possible obs: 100 % / Redundancy: 14.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.232 / Rrim(I) all: 0.234 / Net I/σ(I): 9.25
Reflection shellResolution: 1.55→1.59 Å / Rmerge(I) obs: 3.79 / Num. unique obs: 10626 / CC1/2: 0.24 / Rrim(I) all: 4

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Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
XSCALEJun 30, 2023 BUILT=20230630data scaling
XDSJun 30, 2023 BUILT=20230630data reduction
PHASER1.21_5207phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→44.64 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1982 4974 3.46 %
Rwork0.1729 --
obs0.1738 143703 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.55→44.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3432 0 49 242 3723
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013578
X-RAY DIFFRACTIONf_angle_d0.9744850
X-RAY DIFFRACTIONf_dihedral_angle_d14.2951324
X-RAY DIFFRACTIONf_chiral_restr0.057517
X-RAY DIFFRACTIONf_plane_restr0.01632
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.570.36951610.35524559X-RAY DIFFRACTION98
1.57-1.590.39061680.33114593X-RAY DIFFRACTION100
1.59-1.60.39131660.33574684X-RAY DIFFRACTION100
1.6-1.620.31241740.32554600X-RAY DIFFRACTION100
1.62-1.650.34361650.31354614X-RAY DIFFRACTION100
1.65-1.670.30521710.30074606X-RAY DIFFRACTION100
1.67-1.690.30261610.29024648X-RAY DIFFRACTION100
1.69-1.720.28391700.27074595X-RAY DIFFRACTION100
1.72-1.740.33181670.27214684X-RAY DIFFRACTION100
1.74-1.770.29211580.26724631X-RAY DIFFRACTION100
1.77-1.80.28581700.24764589X-RAY DIFFRACTION100
1.8-1.840.26791700.22984617X-RAY DIFFRACTION100
1.84-1.870.20121610.22154646X-RAY DIFFRACTION100
1.87-1.910.29471610.22024606X-RAY DIFFRACTION100
1.91-1.950.2331720.19574633X-RAY DIFFRACTION100
1.95-20.18711670.17624670X-RAY DIFFRACTION100
2-2.050.18561620.1674591X-RAY DIFFRACTION100
2.05-2.10.1961670.15814619X-RAY DIFFRACTION100
2.1-2.160.17021690.14414611X-RAY DIFFRACTION100
2.16-2.230.14441690.14114630X-RAY DIFFRACTION100
2.23-2.310.16721610.14214642X-RAY DIFFRACTION100
2.31-2.410.18481610.13574627X-RAY DIFFRACTION100
2.41-2.520.14941670.13624616X-RAY DIFFRACTION100
2.52-2.650.16521700.13314659X-RAY DIFFRACTION100
2.65-2.810.18331670.13964603X-RAY DIFFRACTION100
2.81-3.030.16521680.14554621X-RAY DIFFRACTION100
3.03-3.340.15571650.14774644X-RAY DIFFRACTION100
3.34-3.820.18361670.14774637X-RAY DIFFRACTION100
3.82-4.810.15621570.13354619X-RAY DIFFRACTION100
4.81-44.640.19051620.17494635X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.7213-0.0547-0.01480.6271-0.10581.01340.00510.03630.0115-0.03580.00060.0480.0239-0.1055-0.00830.1557-0.0147-0.01170.1195-0.01120.1466-34.542717.93985.6911
21.22030.43310.18191.4876-0.07270.81720.0471-0.03280.00840.029-0.0544-0.025-0.0423-0.00180.00470.16530.014-0.02070.1073-0.00250.1152-33.6833-12.055118.7585
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 21 through 235)
2X-RAY DIFFRACTION2(chain 'B' and resid 29 through 234)

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