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- PDB-1lqo: Crystal Strutcure of the Fosfomycin Resistance Protein A (FosA) C... -

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Basic information

Entry
Database: PDB / ID: 1lqo
TitleCrystal Strutcure of the Fosfomycin Resistance Protein A (FosA) Containing Bound Thallium Cations
ComponentsPROBABLE Fosfomycin Resistance Protein
KeywordsTRANSFERASE / manganese binding / thallium binding loop
Function / homology
Function and homology information


glutathione transferase / glutathione transferase activity / response to antibiotic / metal ion binding / cytoplasm
Similarity search - Function
: / 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
: / PHOSPHATE ION / THALLIUM (I) ION / Glutathione transferase FosA
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsRife, C.L. / Pharris, R.E. / Newcomer, M.E. / Armstrong, R.N.
CitationJournal: J.Am.Chem.Soc. / Year: 2002
Title: Crystal structure of a genomically encoded fosfomycin resistance protein (FosA) at 1.19 A resolution by MAD phasing off the L-III edge of Tl(+)
Authors: Rife, C.L. / Pharris, R.E. / Newcomer, M.E. / Armstrong, R.N.
History
DepositionMay 11, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_validate_close_contact / 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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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 / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _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

Downloads & links

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Assembly

Deposited unit
A: PROBABLE Fosfomycin Resistance Protein
B: PROBABLE Fosfomycin Resistance Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,00214
Polymers30,2862
Non-polymers1,71612
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6870 Å2
ΔGint-95 kcal/mol
Surface area12270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.797, 65.874, 76.958
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a dimer consisting of chains A and B.

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Components

#1: Protein PROBABLE Fosfomycin Resistance Protein / FOSA


Mass: 15143.006 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: FosA / Plasmid: pET-20 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3 / References: UniProt: Q9I4K6, glutathione transferase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Chemical
ChemComp-TL / THALLIUM (I) ION


Mass: 204.383 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Tl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 2.33 Å3/Da / Density % sol: 47.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: WELL CONTAINED 40% PENTAERYTHRITOL PROPOXYLATE 629, 0.08M K2HPO4. DROP CONTAINED 0.002 M MNCL2, 0.002M FOSFOMYCIN, 10 MG/ML FOSA, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 0.9780, 0.9789, 0.9537
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 16, 2002
RadiationMonochromator: Si(111) double-crystal monochromator, Bent cylindrical Si-mirror (Rh coating)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9781
20.97891
30.95371
ReflectionResolution: 2→30 Å / Num. all: 19809 / Num. obs: 19809 / % possible obs: 96 % / Observed criterion σ(I): -3 / Redundancy: 10.2 % / Biso Wilson estimate: 27 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 25
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 11 / % possible all: 84.9
Reflection
*PLUS
Lowest resolution: 25 Å / % possible obs: 96 % / Rmerge(I) obs: 0.07
Reflection shell
*PLUS
% possible obs: 86 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
REFMAC5refinement
RefinementMethod to determine structure: MAD / Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.907 / SU B: 5.786 / SU ML: 0.67 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.208 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25224 966 5.1 %RANDOM
Rwork0.19741 ---
all0.2001 17952 --
obs0.20014 17952 95.82 %-
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: 27.182 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å20 Å2
2--2.06 Å20 Å2
3----1.98 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2130 0 28 126 2284
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0212209
X-RAY DIFFRACTIONr_bond_other_d0.0010.021948
X-RAY DIFFRACTIONr_angle_refined_deg2.3421.9412999
X-RAY DIFFRACTIONr_angle_other_deg0.8834459
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7343270
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.74515335
X-RAY DIFFRACTIONr_chiral_restr0.1140.2297
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022544
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02548
X-RAY DIFFRACTIONr_nbd_refined0.2840.3492
X-RAY DIFFRACTIONr_nbd_other0.220.31870
X-RAY DIFFRACTIONr_nbtor_other0.4510.52
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.5173
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.2490.51
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3370.323
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3070.365
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3270.512
X-RAY DIFFRACTIONr_symmetry_hbond_other0.1610.51
X-RAY DIFFRACTIONr_mcbond_it1.1171.51332
X-RAY DIFFRACTIONr_mcangle_it1.92822085
X-RAY DIFFRACTIONr_scbond_it2.883877
X-RAY DIFFRACTIONr_scangle_it4.5454.5914
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.253 62
Rwork0.205 1077
Refinement
*PLUS
Highest resolution: 2 Å / Rfactor Rfree: 0.2522 / Rfactor Rwork: 0.1974
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.019
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg2.34

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