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- PDB-9g58: Pseudomonas fluorescens periplasmic aspartic peptidase Pfl01_1762... -

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Basic information

Entry
Database: PDB / ID: 9g58
TitlePseudomonas fluorescens periplasmic aspartic peptidase Pfl01_1762 (RloA)
ComponentsPutative ATP-dependent zinc protease domain-containing protein
KeywordsHYDROLASE / retropepsin-like / periplasm / bacteria
Function / homologyPutative ATP-dependent zinc protease / Putative ATP-dependent zinc protease / Aspartic peptidase domain superfamily / Putative ATP-dependent zinc protease domain-containing protein
Function and homology information
Biological speciesPseudomonas fluorescens Pf0-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLormand, J.D. / Sondermann, H.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI114261 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI168017 United States
CitationJournal: Biorxiv / Year: 2025
Title: Secreted retropepsin-like enzymes are essential for stress tolerance and biofilm formation in Pseudomonas aeruginosa.
Authors: Lormand, J.D. / Savelle, C.H. / Teschler, J.K. / Lopez, E. / Little, R.H. / Malone, J. / Yildiz, F.H. / Garcia-Garcia, M.J. / Sondermann, H.
History
DepositionJul 16, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 9, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 16, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative ATP-dependent zinc protease domain-containing protein
B: Putative ATP-dependent zinc protease domain-containing protein


Theoretical massNumber of molelcules
Total (without water)34,7922
Polymers34,7922
Non-polymers00
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1350 Å2
ΔGint-7 kcal/mol
Surface area12250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.042, 90.042, 37.166
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41
Space group name HallP4w
Symmetry operation#1: x,y,z
#2: -y,x,z+1/4
#3: y,-x,z+3/4
#4: -x,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 23 through 37 or (resid 38...
d_2ens_1(chain "B" and (resid 23 through 60 or (resid 61...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11GLUGLUALAALAAA23 - 904 - 71
d_12ALAALASERSERAA112 - 14793 - 128
d_13ALAALACYSCYSAA149 - 170130 - 151
d_21GLUGLUALAALABB23 - 904 - 71
d_22ALAALASERSERBB112 - 14793 - 128
d_23ALAALACYSCYSBB149 - 170130 - 151

NCS oper: (Code: givenMatrix: (-0.936714235549, -0.0673599407506, 0.343553604699), (-0.0283467356777, -0.963500777858, -0.266200513979), (0.348945416213, -0.259092434178, 0.900615460147)Vector: -27. ...NCS oper: (Code: given
Matrix: (-0.936714235549, -0.0673599407506, 0.343553604699), (-0.0283467356777, -0.963500777858, -0.266200513979), (0.348945416213, -0.259092434178, 0.900615460147)
Vector: -27.9655161285, 56.7397287001, 13.1013480297)

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Components

#1: Protein Putative ATP-dependent zinc protease domain-containing protein


Mass: 17395.867 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens Pf0-1 (bacteria)
Gene: Pfl01_1762 / Production host: Escherichia coli (E. coli) / References: UniProt: Q3KFF1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O
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: 2.17 Å3/Da / Density % sol: 43.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2M ammonium acetate, 20% PEG 3350 and 0.1 M HEPES pH 8.0 (soak with condition incl. 20% xylitol)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.28→45.02 Å / Num. obs: 26253 / % possible obs: 98.91 % / Redundancy: 5.7 % / Biso Wilson estimate: 57.22 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.09684 / Net I/σ(I): 8.91
Reflection shellResolution: 2.28→2.36 Å / Redundancy: 5.4 % / Rmerge(I) obs: 1.069 / Mean I/σ(I) obs: 1.42 / Num. unique obs: 2402 / CC1/2: 0.837 / % possible all: 91.98

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
pointlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→45.02 Å / SU ML: 0.3804 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.9271
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2447 1363 9.94 %
Rwork0.2113 10759 -
obs0.2147 13726 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 71.48 Å2
Refinement stepCycle: LAST / Resolution: 2.4→45.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1945 0 0 27 1972
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00261985
X-RAY DIFFRACTIONf_angle_d0.60932689
X-RAY DIFFRACTIONf_chiral_restr0.0431309
X-RAY DIFFRACTIONf_plane_restr0.0048347
X-RAY DIFFRACTIONf_dihedral_angle_d20.1189724
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.17553061568 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.510.411470.33121331X-RAY DIFFRACTION99.53
2.51-2.640.37681490.27351338X-RAY DIFFRACTION99.6
2.64-2.810.34381470.27311320X-RAY DIFFRACTION99.53
2.81-3.020.35481450.29021326X-RAY DIFFRACTION99.59
3.02-3.330.3021440.23791344X-RAY DIFFRACTION99.87
3.33-3.810.23611480.22521333X-RAY DIFFRACTION99.87
3.81-4.80.19791520.16851359X-RAY DIFFRACTION99.8
4.8-45.020.19251550.17871408X-RAY DIFFRACTION99.74
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)
18.34683308987-0.07896119781752.793676586795.741184276130.2494660575795.44209219743-0.120315313888-0.1354719759320.0811489611754-0.622911449851-0.1523683864590.658646212731-0.236717107087-1.061801378630.2208088568780.5321939756160.0424646630675-0.1187377596180.592155405386-0.04821403436920.42097392415-33.67140496128.09198811572.91574738868
27.68923404255-1.795299900860.3106521904989.349878780061.225811852843.55051755830.1698951860330.0637580152136-0.553309138258-0.5397204965990.0814763023070.391266393963-0.0755492059165-0.437393998615-0.2555862075080.489151402027-0.0792147851344-0.08154299380820.4070909844490.07671757158170.469632221742-22.606585888224.57683622956.96202795211
34.192885995071.19202293661-4.093120649014.829732564360.7105117205434.770705872970.171194474105-0.1475137318980.06501622599140.09870214533330.102316494103-0.54180164756-0.4296921622510.485704944637-0.3912692919790.4787046011230.023978521593-0.06647621432380.36451423974-0.004909506023970.502268784169-3.788375044531.93382400975.14232113989
45.791855187450.443856866344-4.455927995892.594381568540.8021419987516.86570933468-0.009761725064230.2313898277930.189704789632-0.400308116711-0.05861595896580.00481950205140.1457744650980.3347396228650.03260178266540.493747567490.113479721403-0.08946014924520.510453080597-0.01190776514950.5160798600356.0062281716729.240298871-6.8825776285
59.195216509830.82066895593-4.472248152065.481785228353.106065202876.37392766676-0.100554219160.1995611501890.318350956173-0.4247790451360.292349858492-0.133357276569-0.27189005066-0.201280453436-0.1607103707580.484286453228-0.00150891291219-0.1440065836650.39576121812-0.005049731281280.471985865166-5.8234201182632.05104778395.31673378994
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain A and resid 23:135)AA23 - 1351 - 96
22(chain A and resid 136:170)AA136 - 17097 - 131
33(chain B and resid 23:54)BB23 - 541 - 32
44(chain B and resid 55:134)BB55 - 13433 - 92
55(chain B and resid 135:170)BB135 - 17093 - 128

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