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- PDB-3sk2: Crystal structure of phenazine resistance protein EhpR from Enter... -

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Basic information

Entry
Database: PDB / ID: 3sk2
TitleCrystal structure of phenazine resistance protein EhpR from Enterobacter agglomerans (Erwinia herbicola, Pantoea agglomerans) Eh1087 in complex with griseoluteic acid
ComponentsEhpR
KeywordsGRISEOLUTEATE-BINDING PROTEIN / antibiotic resistance
Function / homology
Function and homology information


organic acid binding / response to antibiotic / protein homodimerization activity
Similarity search - Function
Glyoxalase/dioxygenase/EhpR / 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
6-formyl-9-methoxyphenazine-1-carboxylic acid / Phenazine antibiotic resistance protein EhpR
Similarity search - Component
Biological speciesPantoea agglomerans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.01 Å
AuthorsBlankenfeldt, W. / Yu, S.
CitationJournal: Bmc Struct.Biol. / Year: 2011
Title: Atomic resolution structure of EhpR: phenazine resistance in Enterobacter agglomerans Eh1087 follows principles of bleomycin / mitomycin C resistance in other bacteria.
Authors: Yu, S. / Vit, A. / Devenish, S. / Mahanty, H.K. / Itzen, A. / Goody, R.S. / Blankenfeldt, W.
History
DepositionJun 22, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: EhpR
B: EhpR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1263
Polymers29,8442
Non-polymers2821
Water8,773487
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4320 Å2
ΔGint-30 kcal/mol
Surface area13530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.500, 79.770, 82.850
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein EhpR


Mass: 14921.942 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pantoea agglomerans (bacteria) / Strain: Eh1087 / Gene: ehpR / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta pLys(S) / References: UniProt: Q8GPH6
#2: Chemical ChemComp-GRI / 6-formyl-9-methoxyphenazine-1-carboxylic acid


Mass: 282.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H10N2O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 487 / 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: 2.02 Å3/Da / Density % sol: 39.13 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1 M Na-citrate, 0.2 M ammonium acetate, 27-30% (w/v) PEG 4000, pre-incubation with 2.5 mM griseoluteic acid on ice for 1 hour, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 26, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.01→20 Å / Num. all: 125504 / Num. obs: 125504 / % possible obs: 98.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 12 Å2 / Rsym value: 0.04 / Net I/σ(I): 19
Reflection shellResolution: 1.01→1.11 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 4 / Num. unique all: 29661 / Rsym value: 0.359 / % possible all: 95.5

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
PHENIX(phenix.refine: 1.7_650)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: dimer of the apo structure

Resolution: 1.01→19.389 Å / SU ML: 0.09 / σ(F): 2 / Phase error: 11.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1459 6275 5 %
Rwork0.1257 --
obs0.1267 125498 98.56 %
Solvent computationShrinkage radii: 0.17 Å / VDW probe radii: 0.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.803 Å2 / ksol: 0.38 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.9007 Å2-0 Å2-0 Å2
2---2.1023 Å2-0 Å2
3----0.7984 Å2
Refinement stepCycle: LAST / Resolution: 1.01→19.389 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2110 0 21 487 2618
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0222498
X-RAY DIFFRACTIONf_angle_d2.0853478
X-RAY DIFFRACTIONf_dihedral_angle_d13.311995
X-RAY DIFFRACTIONf_chiral_restr0.131385
X-RAY DIFFRACTIONf_plane_restr0.014456
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.01-1.02150.24341830.23743480X-RAY DIFFRACTION88
1.0215-1.03350.24391910.21983629X-RAY DIFFRACTION91
1.0335-1.04610.22271950.19643721X-RAY DIFFRACTION94
1.0461-1.05930.22282010.18363872X-RAY DIFFRACTION97
1.0593-1.07330.18552100.18773949X-RAY DIFFRACTION98
1.0733-1.0880.21372050.18153947X-RAY DIFFRACTION99
1.088-1.10350.17752120.14614010X-RAY DIFFRACTION100
1.1035-1.120.16172080.15123959X-RAY DIFFRACTION100
1.12-1.13750.1592120.14274025X-RAY DIFFRACTION100
1.1375-1.15610.13852110.11643947X-RAY DIFFRACTION100
1.1561-1.17610.13252120.11064033X-RAY DIFFRACTION100
1.1761-1.19750.13852100.11613956X-RAY DIFFRACTION100
1.1975-1.22050.12942100.10254045X-RAY DIFFRACTION100
1.2205-1.24540.13892100.11293971X-RAY DIFFRACTION100
1.2454-1.27250.10942120.09074016X-RAY DIFFRACTION100
1.2725-1.30210.1352120.1084027X-RAY DIFFRACTION100
1.3021-1.33460.11542090.09853995X-RAY DIFFRACTION100
1.3346-1.37070.14172140.10064012X-RAY DIFFRACTION100
1.3707-1.4110.12632090.09364015X-RAY DIFFRACTION100
1.411-1.45650.12262140.0934042X-RAY DIFFRACTION100
1.4565-1.50860.10882110.0924025X-RAY DIFFRACTION100
1.5086-1.5690.12732110.09044014X-RAY DIFFRACTION100
1.569-1.64030.13342110.0994025X-RAY DIFFRACTION100
1.6403-1.72680.12252150.10214071X-RAY DIFFRACTION100
1.7268-1.83490.12192140.10464050X-RAY DIFFRACTION100
1.8349-1.97640.15152120.11734038X-RAY DIFFRACTION99
1.9764-2.17510.11442150.11474089X-RAY DIFFRACTION100
2.1751-2.48920.14612120.12594043X-RAY DIFFRACTION98
2.4892-3.1340.16792130.154044X-RAY DIFFRACTION97
3.134-19.39230.15972210.1444173X-RAY DIFFRACTION96

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