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- PDB-1r9c: Crystal Structure of Fosfomycin Resistance Protein FosX from Meso... -

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Basic information

Entry
Database: PDB / ID: 1r9c
TitleCrystal Structure of Fosfomycin Resistance Protein FosX from Mesorhizobium Loti
Componentsglutathione transferaseGlutathione S-transferase
KeywordsTRANSFERASE / 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
: / Fosfomycin resistance protein FosX
Similarity search - Component
Biological speciesMesorhizobium loti (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsFillgrove, K.L. / Pakhomova, S. / Newcomer, M.E. / Armstrong, R.N.
CitationJournal: J.Am.Chem.Soc. / Year: 2003
Title: Mechanistic diversity of fosfomycin resistance in pathogenic microorganisms.
Authors: Fillgrove, K.L. / Pakhomova, S. / Newcomer, M.E. / Armstrong, R.N.
History
DepositionOct 28, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 23, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_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

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Assembly

Deposited unit
A: glutathione transferase
B: glutathione transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5214
Polymers32,4112
Non-polymers1102
Water2,180121
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4030 Å2
ΔGint-36 kcal/mol
Surface area12080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.034, 84.024, 66.861
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe biological assembly is a dimer.

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Components

#1: Protein glutathione transferase / Glutathione S-transferase


Mass: 16205.359 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mesorhizobium loti (bacteria) / Gene: fosfomycin resistance protein / Plasmid: pET20-b(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q98GG1, dimethylallyltranstransferase
#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 / Water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 1.95 Å3/Da / Density % sol: 36.96 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG8000, Tris, Li2SO4, MnCl2, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
132 %PEG80001drop
2100 mMTris1droppH8.5
350 mM1dropLi2SO4
41 mM1reservoirMnCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 19, 2002 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.83→30 Å / Num. obs: 21017 / % possible obs: 91.1 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Rsym value: 0.077 / Net I/σ(I): 17.9
Reflection shellResolution: 1.83→1.9 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 1.9 / Num. unique all: 1263 / Rsym value: 0.414 / % possible all: 55.8

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1LQP

1lqp


Resolution: 1.83→30 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.929 / SU B: 3.676 / SU ML: 0.109 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.175 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24307 1391 6.9 %RANDOM
Rwork0.20179 ---
all0.2046 21034 --
obs0.2046 18860 87.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 26.16 Å2
Baniso -1Baniso -2Baniso -3
1--1.94 Å20 Å20 Å2
2--3.23 Å20 Å2
3----1.29 Å2
Refinement stepCycle: LAST / Resolution: 1.83→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1950 0 2 121 2073
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0211999
X-RAY DIFFRACTIONr_angle_refined_deg1.3631.9422682
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2935238
X-RAY DIFFRACTIONr_chiral_restr0.1010.2287
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021552
X-RAY DIFFRACTIONr_nbd_refined0.1970.2767
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2145
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2330.256
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1080.28
X-RAY DIFFRACTIONr_mcbond_it0.7881.51203
X-RAY DIFFRACTIONr_mcangle_it1.42621908
X-RAY DIFFRACTIONr_scbond_it2.5373796
X-RAY DIFFRACTIONr_scangle_it3.7694.5774
LS refinement shellResolution: 1.83→1.877 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.318 53
Rwork0.352 702
obs-702
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)
12.6192-0.02290.71851.57950.07952.81720.0011-0.0182-0.1043-0.03390.0915-0.09910.040.1373-0.09260.0406-0.00050.02410.0030.0050.032921.236914.988445.001
22.51410.0571-0.39721.4795-0.23.43450.047-0.21230.1720.0948-0.02770.0578-0.1243-0.158-0.01930.050.035-0.00210.0247-0.00520.05116.341920.072753.826
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1301 - 130
2X-RAY DIFFRACTION2BB1 - 1291 - 129
Refinement
*PLUS
Rfactor Rfree: 0.243 / Rfactor Rwork: 0.201
Solvent computation
*PLUS
Displacement parameters
*PLUS

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