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- PDB-9g1k: Fragment screening of FosAKP, cryo structure in complex with frag... -

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Basic information

Entry
Database: PDB / ID: 9g1k
TitleFragment screening of FosAKP, cryo structure in complex with fragment F2X-entry A09
ComponentsFosfomycin resistance protein
KeywordsTRANSFERASE / antibiotic resistance / fosfomycin / fragment screening
Function / homology
Function and homology information


: / Glyoxalase/fosfomycin resistance/dioxygenase domain / Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily / Vicinal oxygen chelate (VOC) domain / Vicinal oxygen chelate (VOC) domain profile. / Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase
Similarity search - Domain/homology
: / : / Fosfomycin resistance protein
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.14 Å
AuthorsGuenther, S. / Galchenkova, M. / Fischer, P. / Reinke, P.Y.A. / Falke, S. / Thekku Veedu, S. / Rodrigues, A.C. / Senst, J. / Meents, A.
Funding support Germany, 5items
OrganizationGrant numberCountry
German Federal Ministry for Education and Research16GW0277 Germany
German Federal Ministry for Education and Research13K22CHB Germany
Helmholtz AssociationFISCOV Germany
Helmholtz AssociationSFragX Germany
Helmholtz AssociationHIR3X Germany
CitationJournal: Nat Commun / Year: 2025
Title: Room-temperature X-ray fragment screening with serial crystallography.
Authors: Gunther, S. / Fischer, P. / Galchenkova, M. / Falke, S. / Reinke, P.Y.A. / Thekku Veedu, S. / Rodrigues, A.C. / Senst, J. / Elinjikkal, D. / Gumprecht, L. / Meyer, J. / Chapman, H.N. / ...Authors: Gunther, S. / Fischer, P. / Galchenkova, M. / Falke, S. / Reinke, P.Y.A. / Thekku Veedu, S. / Rodrigues, A.C. / Senst, J. / Elinjikkal, D. / Gumprecht, L. / Meyer, J. / Chapman, H.N. / Barthelmess, M. / Meents, A.
History
DepositionJul 10, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 23, 2025Provider: repository / Type: Initial release
Revision 1.1Oct 22, 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.journal_volume / _citation.page_first / _citation.page_last / _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: Fosfomycin resistance protein
B: Fosfomycin resistance protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0067
Polymers32,6192
Non-polymers3875
Water8,071448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5930 Å2
ΔGint-36 kcal/mol
Surface area12480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.728, 89.608, 44.930
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

#1: Protein Fosfomycin resistance protein


Mass: 16309.347 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: KPNJ1_04856 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0E1CQ35
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-A1IHZ / 2-sulfanylpyridine-3-carboximidamide


Mass: 153.205 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H7N3S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 448 / Source method: isolated from a natural source / Formula: H2O
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: 2.09 Å3/Da / Density % sol: 41.15 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: The protein was crystallized by mixing 0.45 uL of 12 mg/mL protein solution in 10 mM Hepes, pH 7.5, 50 mM NaCl, with 0.45 uL 16% (w/v) PEG3350, 0.25 M MgCl2, 0.2 M KBr, 0.1 M BisTris, pH 5.5 ...Details: The protein was crystallized by mixing 0.45 uL of 12 mg/mL protein solution in 10 mM Hepes, pH 7.5, 50 mM NaCl, with 0.45 uL 16% (w/v) PEG3350, 0.25 M MgCl2, 0.2 M KBr, 0.1 M BisTris, pH 5.5 and 0.1 uL crystal microseeds in 26% (w/v) PEG3350, 0.25 M MgCl2, 0.2 M KBr, 0.1 M BisTris, pH 5.5. After at least 4 days of crystal growth, 40 nL of 100 mM compound, solubilized in 100% DMSO, was added using an acoustic droplet dispensing system.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 7, 2023 / Details: KB mirrors
RadiationMonochromator: Si111 DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.14→54.031 Å / Num. obs: 89917 / % possible obs: 89.7 % / Redundancy: 11.9 % / Biso Wilson estimate: 12.26 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.017 / Rrim(I) all: 0.063 / Net I/σ(I): 20.3
Reflection shellResolution: 1.14→1.16 Å / Redundancy: 4.9 % / Rmerge(I) obs: 1.046 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2102 / CC1/2: 0.562 / Rpim(I) all: 0.518 / Rrim(I) all: 1.175 / % possible all: 42.2

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Processing

Software
NameVersionClassification
PHENIX1.20-4459_9999phasing
PHENIX1.20-4459_9999refinement
autoPROC1.0.5data processing
Coot0.9.8.92model building
XDSJan 10, 2022data reduction
Aimless0.7.4data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.14→54.03 Å / SU ML: 0.0987 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.5697
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1609 4438 4.94 %
Rwork0.1403 85461 -
obs0.1413 89899 89.7 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.43 Å2
Refinement stepCycle: LAST / Resolution: 1.14→54.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2144 0 20 448 2612
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00652403
X-RAY DIFFRACTIONf_angle_d1.03263290
X-RAY DIFFRACTIONf_chiral_restr0.0803344
X-RAY DIFFRACTIONf_plane_restr0.0179442
X-RAY DIFFRACTIONf_dihedral_angle_d6.6873350
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.14-1.150.3862670.341282X-RAY DIFFRACTION40.69
1.15-1.170.2986800.29061411X-RAY DIFFRACTION45.75
1.17-1.180.2657850.24581633X-RAY DIFFRACTION51.48
1.18-1.20.3105950.21131865X-RAY DIFFRACTION59.45
1.2-1.210.23041190.19882064X-RAY DIFFRACTION65.91
1.21-1.230.21481380.17382269X-RAY DIFFRACTION73.77
1.23-1.250.20221470.16562512X-RAY DIFFRACTION79.85
1.25-1.260.17451240.15272745X-RAY DIFFRACTION87.42
1.26-1.280.18021540.15122965X-RAY DIFFRACTION93.44
1.28-1.310.15831640.14173086X-RAY DIFFRACTION99.12
1.31-1.330.17481700.13673114X-RAY DIFFRACTION98.56
1.33-1.350.16571650.13293119X-RAY DIFFRACTION99.64
1.35-1.380.16631490.1333134X-RAY DIFFRACTION99.03
1.38-1.410.17361850.13493145X-RAY DIFFRACTION99.2
1.41-1.440.1671750.13393101X-RAY DIFFRACTION99.97
1.44-1.470.15661630.13383132X-RAY DIFFRACTION99.49
1.47-1.510.17841580.13883154X-RAY DIFFRACTION99.4
1.51-1.550.14651580.12993147X-RAY DIFFRACTION99.16
1.55-1.590.13391590.12313170X-RAY DIFFRACTION99.7
1.59-1.640.14551500.11853151X-RAY DIFFRACTION99.91
1.64-1.70.14951690.12573184X-RAY DIFFRACTION99.7
1.7-1.770.14621160.12723212X-RAY DIFFRACTION99.97
1.77-1.850.13951440.13193197X-RAY DIFFRACTION100
1.85-1.950.16331890.13273184X-RAY DIFFRACTION99.85
1.95-2.070.14581620.12323171X-RAY DIFFRACTION99.64
2.07-2.230.15051670.12393194X-RAY DIFFRACTION99.44
2.23-2.460.14881730.12983201X-RAY DIFFRACTION99.82
2.46-2.810.14641580.14033281X-RAY DIFFRACTION99.83
2.81-3.540.14571860.14023237X-RAY DIFFRACTION99.97
3.54-54.030.18131690.1593401X-RAY DIFFRACTION98.84

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