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- PDB-9g1a: Fragment screening of FosAKP, room-temperature structure, ground state -

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Basic information

Entry
Database: PDB / ID: 9g1a
TitleFragment screening of FosAKP, room-temperature structure, ground state
ComponentsFosfomycin resistance protein
KeywordsTRANSFERASE / antibiotic resistance / fosfomycin / fragment screening
Function / homology: / 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 / metal ion binding / : / Fosfomycin resistance protein
Function and homology information
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 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: To Be Published
Title: Room temperature X-ray fragment screening with serial crystallography
Authors: Guenther, S. / Meents, A.
History
DepositionJul 10, 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: Fosfomycin resistance protein
B: Fosfomycin resistance protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7294
Polymers32,6192
Non-polymers1102
Water3,783210
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5680 Å2
ΔGint-42 kcal/mol
Surface area12780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.620, 91.690, 45.300
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-MN / MANGANESE (II) ION


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


Mass: 18.015 Da / Num. of mol.: 210 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.28 Å3/Da / Density % sol: 46.05 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 25 mg/mL FosAKP in 10 mM Hepes, pH 7.5, 75 mM NaCl was supplemented with 6 mM MnCl2 and mixed with an equal volume of 16% (w/v) PEG3350, 0.25 M MgCl2, 0.2 M KBr, 0.1 M BisTris, pH 5.5 and ...Details: 25 mg/mL FosAKP in 10 mM Hepes, pH 7.5, 75 mM NaCl was supplemented with 6 mM MnCl2 and mixed with an equal volume of 16% (w/v) PEG3350, 0.25 M MgCl2, 0.2 M KBr, 0.1 M BisTris, pH 5.5 and 1/10 volume of seed stock in 26% (w/v) PEG3350, 0.25 M MgCl2, 0.2 M KBr, 0.1 M BisTris, pH 5.5. From this, approximately 14 uL were added per window of the fixed-target chip. The sample holder was then inserted for into a 3D-printed crystal growth chamber with 3 mL of precipitant solution in the bottom for vapor-diffusion crystallization and incubated at 20C. Before data collection sample holder was removed from the crystal growth chamber and excess precipitant was removed by blotting through the micropores of the membranes, before 10 uL of crystallization solution with 5 % DMSO were pipetted to the crystals in the individual compartments. Sample holders were then placed back into the growths vessel and incubated for 24h. Before data collection blotting was repeated for removal of excess liquid in order to minimize background scattering. Sample holders were then equipped with a protective cover to prevent them from drying-out and stored in a humid atmosphere (figure ??). Compound addition and liquid removal were conducted in a glove box with >95% rel. humidity.

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Data collection

DiffractionMean temperature: 296.15 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P09 HiPhaX / Wavelength: 0.7749 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 12, 2023 / Details: CRL
RadiationMonochromator: Si111 DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7749 Å / Relative weight: 1
ReflectionResolution: 1.3→71.43 Å / Num. obs: 74175 / % possible obs: 100 % / Redundancy: 349.1 % / Biso Wilson estimate: 16.64 Å2 / CC1/2: 0.9893 / CC star: 0.9973 / R split: 0.0837 / Net I/σ(I): 9.12
Reflection shellResolution: 1.3→1.322 Å / Redundancy: 42.9 % / Mean I/σ(I) obs: 0.78 / Num. unique obs: 3642 / CC1/2: 0.3519 / CC star: 0.7216 / R split: 1.1628 / % possible all: 99.97
Serial crystallography sample deliveryDescription: Roadrunner Goniometer / Method: fixed target
Serial crystallography sample delivery fixed targetDescription: Kapton with micropores / Motion control: Roadrunner Goniometer
Serial crystallography data reductionFrame hits: 126907 / Frames indexed: 104856 / Frames total: 310004 / Lattices indexed: 132089

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Processing

Software
NameVersionClassification
CrystFEL0.10.1data reduction
CrystFEL0.10.1data scaling
PHENIX1.20-4459_9999phasing
PHENIX1.20-4459_9999refinement
Coot0.9.8.92model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→45.85 Å / SU ML: 0.1495 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 15.592
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1569 3593 4.91 %
Rwork0.1383 69640 -
obs0.1392 73233 98.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.66 Å2
Refinement stepCycle: LAST / Resolution: 1.3→45.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2144 0 2 210 2356
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00522392
X-RAY DIFFRACTIONf_angle_d0.88583285
X-RAY DIFFRACTIONf_chiral_restr0.0765344
X-RAY DIFFRACTIONf_plane_restr0.0114441
X-RAY DIFFRACTIONf_dihedral_angle_d5.3827341
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.320.3691040.34872453X-RAY DIFFRACTION91.78
1.32-1.340.34921480.31112483X-RAY DIFFRACTION93.2
1.34-1.350.2861490.27432542X-RAY DIFFRACTION95.46
1.35-1.370.26411440.2382603X-RAY DIFFRACTION97
1.37-1.40.2681140.21722576X-RAY DIFFRACTION97.04
1.4-1.420.2321610.20782640X-RAY DIFFRACTION97.77
1.42-1.440.22841570.20632600X-RAY DIFFRACTION98.68
1.44-1.470.26931460.21752634X-RAY DIFFRACTION99.11
1.47-1.50.24421500.19622652X-RAY DIFFRACTION99.47
1.5-1.530.21461300.1582708X-RAY DIFFRACTION99.72
1.53-1.560.15931300.13592711X-RAY DIFFRACTION99.93
1.56-1.60.15561360.12072673X-RAY DIFFRACTION99.96
1.6-1.640.1661410.10822681X-RAY DIFFRACTION99.89
1.64-1.680.14871250.10422702X-RAY DIFFRACTION99.93
1.68-1.730.15811310.10662714X-RAY DIFFRACTION99.96
1.73-1.790.14421180.10862709X-RAY DIFFRACTION99.96
1.79-1.850.1371130.112715X-RAY DIFFRACTION100
1.85-1.930.14841230.11242758X-RAY DIFFRACTION99.97
1.93-2.010.13841500.09862684X-RAY DIFFRACTION100
2.01-2.120.11241460.09512712X-RAY DIFFRACTION100
2.12-2.250.11221500.10282705X-RAY DIFFRACTION100
2.25-2.430.1221460.11622746X-RAY DIFFRACTION99.93
2.43-2.670.14531300.1352756X-RAY DIFFRACTION100
2.67-3.060.16231510.15262755X-RAY DIFFRACTION100
3.06-3.850.15311570.13772791X-RAY DIFFRACTION100
3.85-45.850.14951430.15212937X-RAY DIFFRACTION99.94

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