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- PDB-2p7k: Crystal structure of genomically encoded fosfomycin resistance pr... -

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Basic information

Entry
Database: PDB / ID: 2p7k
TitleCrystal structure of genomically encoded fosfomycin resistance protein, FosX, from Listeria monocytogenes (hexagonal form)
ComponentsGlyoxalase family protein
KeywordsMETAL BINDING PROTEIN / hydrolase / FOSFOMYCIN RESISTANCE PROTEIN / MN BINDING / ANTIBIOTIC RESISTANCE
Function / homology
Function and homology information


response to antibiotic / metal ion binding / cytoplasm
Similarity search - Function
Fosfomycin resistance protein FosX / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 / 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 / Roll / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / : / Fosfomycin resistance protein FosX
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsFillgrove, K.L. / Pakhomova, S. / Schaab, M. / Newcomer, M.E. / Armstrong, R.N.
CitationJournal: Biochemistry / Year: 2007
Title: Structure and Mechanism of the Genomically Encoded Fosfomycin Resistance Protein, FosX, from Listeria monocytogenes.
Authors: Fillgrove, K.L. / Pakhomova, S. / Schaab, M.R. / Newcomer, M.E. / Armstrong, R.N.
History
DepositionMar 20, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glyoxalase family protein
B: Glyoxalase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5654
Polymers31,1812
Non-polymers3842
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4490 Å2
ΔGint-20 kcal/mol
Surface area11300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.524, 83.524, 114.446
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B

NCS domain segments:

Component-ID: 1 / Refine code: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETSERSERAA1 - 331 - 33
21METMETSERSERBB1 - 331 - 33
12LEULEULEULEUAA41 - 12841 - 128
22LEULEULEULEUBB41 - 12841 - 128

NCS ensembles :
ID
1
2

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Components

#1: Protein Glyoxalase family protein


Mass: 15590.603 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria) / Strain: EGD-e / Plasmid: pET20b(+) / Production host: Escherichia coli (E. coli) / References: UniProt: Q71YW5, UniProt: Q8Y6I2*PLUS
#2: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O

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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: 3.7 Å3/Da / Density % sol: 66.71 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 15% PEG 8000, 20 mM Na acetate, 0.1 M Na citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CAMD / Beamline: GCPCC / Wavelength: 1.069 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jan 13, 2002 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.069 Å / Relative weight: 1
ReflectionResolution: 3.3→30 Å / Num. all: 6831 / Num. obs: 6831 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Rsym value: 0.099 / Net I/σ(I): 6.83
Reflection shellResolution: 3.3→3.42 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 1.3 / Num. unique all: 666 / Rsym value: 0.44 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1R9C

1r9c


Resolution: 3.3→15 Å / Cor.coef. Fo:Fc: 0.897 / Cor.coef. Fo:Fc free: 0.867 / SU ML: 0.371 / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.555 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.277 293 4.8 %RANDOM
Rwork0.228 ---
all0.23 5815 --
obs0.23 5815 90.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.51 Å21.26 Å20 Å2
2--2.51 Å20 Å2
3----3.77 Å2
Refinement stepCycle: LAST / Resolution: 3.3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1904 0 26 6 1936
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221968
X-RAY DIFFRACTIONr_angle_refined_deg1.2441.9612664
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8195238
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.27924.37596
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.32815322
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.271510
X-RAY DIFFRACTIONr_chiral_restr0.0730.2296
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021510
X-RAY DIFFRACTIONr_nbd_refined0.2360.2978
X-RAY DIFFRACTIONr_nbtor_refined0.3270.21342
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.285
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1990.214
X-RAY DIFFRACTIONr_mcbond_it0.2721.51226
X-RAY DIFFRACTIONr_mcangle_it0.5121912
X-RAY DIFFRACTIONr_scbond_it0.6843824
X-RAY DIFFRACTIONr_scangle_it1.1834.5752
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
1247tight positional0.010.05
2691tight positional0.010.05
1247tight thermal0.020.5
2691tight thermal0.020.5
LS refinement shellResolution: 3.3→3.382 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.511 15 -
Rwork0.31 370 -
obs-370 80.88 %
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)
16.7273-2.40430.13678.19270.59096.1108-0.017-0.34520.0426-0.24030.0163-0.27130.39690.31580.0007-0.0148-0.0463-0.009-0.0568-0.0144-0.02135.568710.073-1.6623
25.7121-1.8394-0.81769.12370.31746.3743-0.1953-0.02380.2393-0.19430.1543-0.1234-0.4048-0.18160.041-0.06340.00240.00830.0129-0.0037-0.025826.49225.81922.4511
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 331 - 33
2X-RAY DIFFRACTION1AA42 - 12842 - 128
3X-RAY DIFFRACTION2BB1 - 331 - 33
4X-RAY DIFFRACTION2BB42 - 12842 - 128

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