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- PDB-9g3t: Structure of the PRO-PRO endopeptidase (PPEP-3) E153A Y189F from ... -

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Basic information

Entry
Database: PDB / ID: 9g3t
TitleStructure of the PRO-PRO endopeptidase (PPEP-3) E153A Y189F 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: 1.6 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) E153A Y189F from Geobacillus thermodenitrificans
Authors: Claushuis, B. / Wojtalla, F. / van Leeuwen, H. / Corver, J. / Baumann, U. / Hensbergen, P.
History
DepositionJul 12, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 23, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)53,58510
Polymers52,6152
Non-polymers9708
Water4,576254
1
A: ATLF-like domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7304
Polymers26,3071
Non-polymers4233
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ATLF-like domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8546
Polymers26,3071
Non-polymers5475
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)125.622, 125.622, 63.483
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
11B-503-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein ATLF-like domain-containing protein


Mass: 26307.477 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(DE3) (bacteria) / References: UniProt: A4INY2

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Non-polymers , 5 types, 262 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: obtained synthetically / Formula: C6H13NO4 / Comment: pH buffer*YM
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / 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: 2.42 Å3/Da / Density % sol: 49.16 %
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: ID30B / Wavelength: 0.87313 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 17, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87313 Å / Relative weight: 1
ReflectionResolution: 1.6→70 Å / Num. obs: 128364 / % possible obs: 99.9 % / Redundancy: 13.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.134 / Rrim(I) all: 0.14 / Net I/σ(I): 12.08
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.6-1.6491.7651.5493390.2841.83598.3
1.64-1.681.6011.9892640.4791.686100
1.68-1.7312.21.13912.5390110.6391.441100
1.73-1.7914.21.1843.387610.7691.229100
5.05-7.1514.20.07432.9726390.9980.081100
7.15-7013.440.0733.6914510.9980.0899.7

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Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→62.81 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1774 4438 3.46 %Random
Rwork0.1565 ---
obs0.1572 128292 99.87 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→62.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3422 0 58 254 3734
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093607
X-RAY DIFFRACTIONf_angle_d1.0164893
X-RAY DIFFRACTIONf_dihedral_angle_d14.7711340
X-RAY DIFFRACTIONf_chiral_restr0.058523
X-RAY DIFFRACTIONf_plane_restr0.01639
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.620.30541550.31223983X-RAY DIFFRACTION96
1.62-1.640.3391430.30514087X-RAY DIFFRACTION100
1.64-1.660.26371610.28494188X-RAY DIFFRACTION100
1.66-1.680.29341400.26334130X-RAY DIFFRACTION100
1.68-1.70.24481450.24784109X-RAY DIFFRACTION100
1.7-1.720.30561470.23994132X-RAY DIFFRACTION100
1.72-1.750.27021420.22644133X-RAY DIFFRACTION100
1.75-1.770.22811520.21474121X-RAY DIFFRACTION100
1.77-1.80.21591510.20174134X-RAY DIFFRACTION100
1.8-1.830.20411490.18234102X-RAY DIFFRACTION100
1.83-1.860.19751480.16414145X-RAY DIFFRACTION100
1.86-1.90.20251370.16474125X-RAY DIFFRACTION100
1.9-1.930.1441550.15934190X-RAY DIFFRACTION100
1.93-1.970.17981490.14754108X-RAY DIFFRACTION100
1.97-2.010.1721490.14474149X-RAY DIFFRACTION100
2.01-2.060.19461480.15234118X-RAY DIFFRACTION100
2.06-2.110.1641490.14224122X-RAY DIFFRACTION100
2.11-2.170.15751530.13684142X-RAY DIFFRACTION100
2.17-2.230.16431490.12674160X-RAY DIFFRACTION100
2.23-2.310.16451480.12664105X-RAY DIFFRACTION100
2.31-2.390.15711370.12524141X-RAY DIFFRACTION100
2.39-2.480.13281520.13064159X-RAY DIFFRACTION100
2.48-2.60.17391480.12854110X-RAY DIFFRACTION100
2.6-2.730.18141490.13624155X-RAY DIFFRACTION100
2.73-2.90.15351550.14634119X-RAY DIFFRACTION100
2.9-3.130.16251480.14654140X-RAY DIFFRACTION100
3.13-3.440.17331460.15624112X-RAY DIFFRACTION100
3.44-3.940.18021460.13724154X-RAY DIFFRACTION100
3.94-4.970.13081460.1324149X-RAY DIFFRACTION100
4.97-62.810.19231410.18414132X-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)
11.0019-0.014-0.04650.5856-0.16621.0109-0.00270.05590.0169-0.03550.0019-0.0190.0105-0.06340.0030.197-0.0113-0.00920.1414-0.020.1711-34.149817.75035.5813
21.68830.62940.19191.4457-0.13840.92250.0476-0.0782-0.01180.0993-0.0497-0.1023-0.03930.00260.00370.18950.0181-0.03330.1138-0.00710.1317-33.5098-11.971618.5745
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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