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- PDB-9g5j: Structure of the PRO-PRO endopeptidase (PPEP-3) E153A Y189F in co... -

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Basic information

Entry
Database: PDB / ID: 9g5j
TitleStructure of the PRO-PRO endopeptidase (PPEP-3) E153A Y189F in complex with substrate peptide Ac-EPLPPPP-NH2 from Geobacillus thermodenitrificans
Components
  • ACE-GLU-PRO-LEU-PRO-PRO-PRO-PRO-NH2
  • ATLF-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 / TRIETHYLENE GLYCOL / ATLF-like domain-containing protein
Function and homology information
Biological speciesGeobacillus thermodenitrificans NG80-2 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 in complex with substrate peptide Ac-EPLPPPP-NH2 from Geobacillus thermodenitrificans
Authors: Claushuis, B. / Wojtalla, F. / van Leeuwen, H. / Corver, J. / Baumann, U. / Hensbergen, P.
History
DepositionJul 17, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 30, 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
C: ATLF-like domain-containing protein
D: ATLF-like domain-containing protein
E: ACE-GLU-PRO-LEU-PRO-PRO-PRO-PRO-NH2
F: ACE-GLU-PRO-LEU-PRO-PRO-PRO-PRO-NH2
G: ACE-GLU-PRO-LEU-PRO-PRO-PRO-PRO-NH2
H: ACE-GLU-PRO-LEU-PRO-PRO-PRO-PRO-NH2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,91614
Polymers108,3108
Non-polymers6066
Water8,449469
1
A: ATLF-like domain-containing protein
E: ACE-GLU-PRO-LEU-PRO-PRO-PRO-PRO-NH2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3374
Polymers27,0772
Non-polymers2602
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-52 kcal/mol
Surface area9950 Å2
MethodPISA
2
B: ATLF-like domain-containing protein
F: ACE-GLU-PRO-LEU-PRO-PRO-PRO-PRO-NH2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1433
Polymers27,0772
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1380 Å2
ΔGint-51 kcal/mol
Surface area10010 Å2
MethodPISA
3
C: ATLF-like domain-containing protein
G: ACE-GLU-PRO-LEU-PRO-PRO-PRO-PRO-NH2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1433
Polymers27,0772
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1700 Å2
ΔGint-49 kcal/mol
Surface area9940 Å2
MethodPISA
4
D: ATLF-like domain-containing protein
H: ACE-GLU-PRO-LEU-PRO-PRO-PRO-PRO-NH2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2934
Polymers27,0772
Non-polymers2162
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-51 kcal/mol
Surface area10320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.430, 95.410, 126.810
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Protein/peptide , 2 types, 8 molecules ABCDEFGH

#1: Protein
ATLF-like domain-containing protein


Mass: 26307.477 Da / Num. of mol.: 4
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
#2: Protein/peptide
ACE-GLU-PRO-LEU-PRO-PRO-PRO-PRO-NH2


Mass: 769.906 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 475 molecules

#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 469 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.08 Å3/Da / Density % sol: 40.72 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: Morpheus E9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.967697 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Apr 30, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.967697 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 60314 / % possible obs: 98.9 % / Redundancy: 4.95 % / CC1/2: 0.992 / Rmerge(I) obs: 0.184 / Rrim(I) all: 0.187 / Net I/σ(I): 7.65
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2-2.055.141.2831.3444250.3621.43999.8
2.05-2.115.111.1421.5843440.4881.24499.8
2.11-2.175.120.8652.1941920.6180.92499.6
2.17-2.240.9140900.8460.984
2.24-2.310.6222.6239700.6940.62299.6
6.32-8.940.0524.0112850.9980.05497.2
8.94-704.50.04228.167940.9980.04693.3

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Processing

Software
NameVersionClassification
PHENIX(2.0rc1_5617: ???)refinement
XDSJun 30, 2023 BUILT=20230630data scaling
XDSJun 30, 2023 BUILT=20230630data reduction
PHASER1.21_5207phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→47.71 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2284 2602 4.32 %Random selection
Rwork0.1904 ---
obs0.192 60271 98.97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→47.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6970 0 27 469 7466
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037220
X-RAY DIFFRACTIONf_angle_d0.6099836
X-RAY DIFFRACTIONf_dihedral_angle_d15.8832644
X-RAY DIFFRACTIONf_chiral_restr0.0441063
X-RAY DIFFRACTIONf_plane_restr0.0061289
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.040.29991400.29283042X-RAY DIFFRACTION99
2.04-2.080.32091340.27312993X-RAY DIFFRACTION100
2.08-2.120.31121370.25343000X-RAY DIFFRACTION100
2.12-2.160.26161370.2473036X-RAY DIFFRACTION100
2.16-2.210.3021350.23512994X-RAY DIFFRACTION100
2.21-2.270.24281350.23363053X-RAY DIFFRACTION100
2.27-2.330.2541370.22373016X-RAY DIFFRACTION100
2.33-2.40.28461370.21153037X-RAY DIFFRACTION100
2.4-2.480.26011360.20992998X-RAY DIFFRACTION100
2.48-2.570.24371350.20223044X-RAY DIFFRACTION99
2.57-2.670.24731370.19843004X-RAY DIFFRACTION99
2.67-2.790.24461320.19643024X-RAY DIFFRACTION99
2.79-2.940.25561410.19843061X-RAY DIFFRACTION99
2.94-3.120.24041300.18792958X-RAY DIFFRACTION97
3.12-3.360.23731390.1753037X-RAY DIFFRACTION99
3.36-3.70.21091380.15893054X-RAY DIFFRACTION99
3.7-4.230.17391400.14293052X-RAY DIFFRACTION98
4.24-5.330.1791390.14593089X-RAY DIFFRACTION98
5.33-47.710.19311430.20023177X-RAY DIFFRACTION97
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)
11.5429-0.0522-0.20571.4197-0.64141.66830.00830.09150.0744-0.0654-0.00280.07180.0233-0.038-0.00410.1476-0.0097-0.01640.16540.01420.19131.651424.0935.9084
21.0322-0.04360.20691.2736-0.00751.9391-0.01280.04440.0271-0.0032-0.00330.0948-0.0030.0080.02350.1344-0.0070.00540.1591-0.00380.182620.329247.694526.6312
31.80410.16350.72722.0364-0.06241.67960.0629-0.0233-0.22870.0785-0.095-0.07730.14640.01730.01730.16650.02220.01260.1573-0.00430.189214.5348-2.785217.8152
42.418-0.8248-0.04681.7488-0.661.4-0.1195-0.2072-0.0120.16010.17020.1364-0.0285-0.0585-0.05230.24150.03360.0080.1930.01790.18724.189920.718944.8143
52.8406-2.44021.76229.4676-5.37725.1514-0.1927-0.33340.25820.34860.2055-0.25610.0318-0.20230.01430.18670.00380.01080.25950.02830.26319.394124.566312.2957
66.51012.9915-7.15751.6957-3.40317.90870.7865-0.69071.0257-0.6525-0.1263-1.0846-1.36420.8215-0.52050.4904-0.01970.15840.3201-0.04390.491129.451742.112829.6517
72.0017-1.96030.07985.3563-5.87217.0817-0.23220.8549-0.9793-0.698-0.2678-0.98980.46561.02440.19560.1694-0.0229-0.00160.4061-0.10250.498917.77762.17438.3783
84.7032-4.112-0.59535.68431.01565.6436-0.32440.2457-0.7465-0.3950.09891.6892-0.239-0.45860.23510.20570.0359-0.04570.2984-0.0050.453721.943620.5935.0123
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 28 through 235)
2X-RAY DIFFRACTION2(chain 'B' and resid 27 through 233)
3X-RAY DIFFRACTION3(chain 'C' and resid 28 through 234)
4X-RAY DIFFRACTION4(chain 'D' and resid 19 through 233)
5X-RAY DIFFRACTION5(chain 'E' and resid 0 through 7)
6X-RAY DIFFRACTION6(chain 'F' and resid 1 through 7)
7X-RAY DIFFRACTION7(chain 'G' and resid 1 through 7)
8X-RAY DIFFRACTION8(chain 'H' and resid 0 through 7)

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