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- PDB-1nnr: Crystal structure of a probable fosfomycin resistance protein (PA... -

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Basic information

Entry
Database: PDB / ID: 1nnr
TitleCrystal structure of a probable fosfomycin resistance protein (PA1129) from Pseudomonas aeruginosa with sulfate present in the active site
Componentsprobable fosfomycin resistance protein
KeywordsTRANSFERASE / POTASSIUM BINDING LOOP / MANGANESE BINDING
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
: / Glutathione transferase FosA
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsRife, C.L. / Pharris, R.E. / Newcomer, M.E. / Armstrong, R.N.
CitationJournal: Biochemistry / Year: 2004
Title: Phosphonoformate: a minimal transition state analogue inhibitor of the fosfomycin resistance protein, FosA.
Authors: Rigsby, R.E. / Rife, C.L. / Fillgrove, K.L. / Newcomer, M.E. / Armstrong, R.N.
History
DepositionJan 14, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Aug 16, 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: probable fosfomycin resistance protein
B: probable fosfomycin resistance protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5886
Polymers30,2862
Non-polymers3024
Water1,62190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6000 Å2
ΔGint-88 kcal/mol
Surface area12160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.930, 64.524, 78.825
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 of chains A and B.

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Components

#1: Protein probable fosfomycin resistance protein


Mass: 15143.006 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: PA1129 / 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-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 1.83 Å3/Da / Density % sol: 32.38 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: ammonium sulfate, MES, cobaltous (II) chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Method: unknown / Details: Rife, C.L., (2002) J.Am.Chem.Soc., 124, 11001.

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 26, 2002 / Details: mirrors
RadiationMonochromator: Yale mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.25→20 Å / Num. all: 11408 / Num. obs: 10221 / % possible obs: 89.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 12.5
Reflection shellResolution: 2.25→2.33 Å / Rmerge(I) obs: 0.316 / Mean I/σ(I) obs: 3.1 / Num. unique all: 663 / % possible all: 60.3
Reflection shell
*PLUS
% possible obs: 60.3 % / Rmerge(I) obs: 0.32

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Processing

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

1lqp


Resolution: 2.25→20 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.893 / SU B: 9.119 / SU ML: 0.223 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.8 / ESU R Free: 0.305 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2675 540 5.3 %RANDOM
Rwork0.1927 ---
all0.19688 10221 --
obs0.19688 9642 89.77 %-
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: 30.781 Å2
Baniso -1Baniso -2Baniso -3
1--2.63 Å20 Å20 Å2
2--2.89 Å20 Å2
3----0.26 Å2
Refinement stepCycle: LAST / Resolution: 2.25→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2124 0 12 90 2226
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0212194
X-RAY DIFFRACTIONr_bond_other_d0.0020.021944
X-RAY DIFFRACTIONr_angle_refined_deg1.8051.9372972
X-RAY DIFFRACTIONr_angle_other_deg1.56734452
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7455266
X-RAY DIFFRACTIONr_chiral_restr0.1040.2296
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022522
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02546
X-RAY DIFFRACTIONr_nbd_refined0.2090.2457
X-RAY DIFFRACTIONr_nbd_other0.2550.22301
X-RAY DIFFRACTIONr_nbtor_other0.0880.21290
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2010.2113
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3110.221
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2870.297
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2630.211
X-RAY DIFFRACTIONr_mcbond_it0.9321.51324
X-RAY DIFFRACTIONr_mcangle_it1.64922070
X-RAY DIFFRACTIONr_scbond_it2.7073870
X-RAY DIFFRACTIONr_scangle_it4.3254.5902
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.343 28
Rwork0.244 402
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor Rfree: 0.268 / Rfactor Rwork: 0.193
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.022
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.81

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