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- PDB-2p7q: Crystal structure of E126Q mutant of genomically encoded fosfomyc... -

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Basic information

Entry
Database: PDB / ID: 2p7q
TitleCrystal structure of E126Q mutant of genomically encoded fosfomycin resistance protein, FosX, from Listeria monocytogenes complexed with MN(II) and 1S,2S-dihydroxypropylphosphonic acid
ComponentsGlyoxalase family protein
KeywordsMETAL BINDING PROTEIN / hydrolase / FOSFOMYCIN RESISTANCE PROTEIN / MN BINDING / ANTIBIOTIC RESISTANCE
Function / homology2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 / Roll / Alpha Beta / [(1S,2S)-1,2-DIHYDROXYPROPYL]PHOSPHONIC ACID / : / :
Function and homology information
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 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 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glyoxalase family protein
B: Glyoxalase family protein
C: Glyoxalase family protein
D: Glyoxalase family protein
E: Glyoxalase family protein
F: Glyoxalase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,80418
Polymers93,5386
Non-polymers1,26612
Water1,63991
1
A: Glyoxalase family protein
B: Glyoxalase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6016
Polymers31,1792
Non-polymers4224
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5020 Å2
ΔGint-37 kcal/mol
Surface area12010 Å2
MethodPISA
2
C: Glyoxalase family protein
D: Glyoxalase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6016
Polymers31,1792
Non-polymers4224
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5200 Å2
ΔGint-42 kcal/mol
Surface area12440 Å2
MethodPISA
3
E: Glyoxalase family protein
F: Glyoxalase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6016
Polymers31,1792
Non-polymers4224
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5140 Å2
ΔGint-39 kcal/mol
Surface area12940 Å2
MethodPISA
4
A: Glyoxalase family protein
B: Glyoxalase family protein
hetero molecules

C: Glyoxalase family protein
D: Glyoxalase family protein
hetero molecules

E: Glyoxalase family protein
F: Glyoxalase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,80418
Polymers93,5386
Non-polymers1,26612
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_546x+1/2,y-1/2,z+11
crystal symmetry operation4_546-x+1/2,y-1/2,-z+11
Buried area19040 Å2
ΔGint-137 kcal/mol
Surface area33710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.011, 69.447, 83.971
Angle α, β, γ (deg.)90.00, 113.86, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Glyoxalase family protein


Mass: 15589.618 Da / Num. of mol.: 6 / Mutation: E126Q
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
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-GG6 / [(1S,2S)-1,2-DIHYDROXYPROPYL]PHOSPHONIC ACID


Mass: 156.074 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H9O5P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 2.41 Å3/Da / Density % sol: 48.94 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 18% PEG 8000, 0.1 M Na cacodylate, 0.2 M Mg acetate, 10% glycerol , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 6, 2004 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. all: 33007 / Num. obs: 33007 / % possible obs: 72.6 % / Observed criterion σ(I): -3 / Redundancy: 2.8 % / Biso Wilson estimate: 23.2 Å2 / Rsym value: 0.088 / Net I/σ(I): 11.9
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 1.9 / Num. unique all: 1575 / Rsym value: 0.457 / % possible all: 50.6

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Processing

Software
NameVersionClassification
MAR345data collection
AMoREphasing
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2P7K

2p7k


Resolution: 2.4→28.09 Å / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.27 1627 -RANDOM
Rwork0.211 ---
all-28281 --
obs-28181 80.6 %-
Displacement parametersBiso mean: 46.3 Å2
Baniso -1Baniso -2Baniso -3
1--11.2 Å20 Å20.4 Å2
2--25.37 Å20 Å2
3----14.16 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.5 Å0.45 Å
Refinement stepCycle: LAST / Resolution: 2.4→28.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6202 0 60 91 6353
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_improper_angle_d0.65
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.035
RfactorNum. reflection% reflection
Rfree0.447 159 -
Rwork0.375 --
obs-2577 44.7 %

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