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- PDB-3sk1: Crystal structure of phenazine resistance protein EhpR from Enter... -

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Basic information

Entry
Database: PDB / ID: 3sk1
TitleCrystal structure of phenazine resistance protein EhpR from Enterobacter agglomerans (Erwinia herbicola, Pantoea agglomerans) Eh1087, apo form
ComponentsEhpR
KeywordsGRISEOLUTEATE-BINDING PROTEIN / antibiotic resistance
Function / homology
Function and homology information


organic acid binding / response to antibiotic / protein homodimerization activity
Similarity search - Function
Signal recognition particle alu RNA binding heterodimer, srp9/1 - #120 / Glyoxalase/dioxygenase/EhpR / Signal recognition particle alu RNA binding heterodimer, srp9/1 - #110 / Signal recognition particle alu RNA binding heterodimer, srp9/1 / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Phenazine antibiotic resistance protein EhpR
Similarity search - Component
Biological speciesPantoea agglomerans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.15 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
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: EhpR
B: EhpR
C: EhpR
D: EhpR


Theoretical massNumber of molelcules
Total (without water)59,6884
Polymers59,6884
Non-polymers00
Water1,18966
1
A: EhpR
B: EhpR


Theoretical massNumber of molelcules
Total (without water)29,8442
Polymers29,8442
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4100 Å2
ΔGint-29 kcal/mol
Surface area11020 Å2
MethodPISA
2
C: EhpR
D: EhpR


Theoretical massNumber of molelcules
Total (without water)29,8442
Polymers29,8442
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4230 Å2
ΔGint-31 kcal/mol
Surface area11560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.560, 79.340, 87.940
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.: 4
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 2.12 Å3/Da / Density % sol: 41.99 %
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, 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: ID14-3 / Wavelength: 0.934 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 19, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.15→20 Å / Num. all: 27704 / Num. obs: 27704 / % possible obs: 98.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 6.8 % / Biso Wilson estimate: 49 Å2 / Rsym value: 0.05 / Net I/σ(I): 23
Reflection shellResolution: 2.15→2.25 Å / Redundancy: 5 % / Mean I/σ(I) obs: 5.1 / Num. unique all: 3241 / Rsym value: 35.9 / % possible all: 92.5

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Processing

Software
NameVersionClassification
XDSdata scaling
SHARPphasing
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.15→19.84 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.93 / SU B: 16.436 / SU ML: 0.187 / Cross valid method: THROUGHOUT / ESU R Free: 0.222 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25876 1438 5.2 %RANDOM
Rwork0.20541 ---
obs0.20814 26266 98.23 %-
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: 72.563 Å2
Baniso -1Baniso -2Baniso -3
1--0.86 Å20 Å20 Å2
2---0.98 Å20 Å2
3---1.84 Å2
Refinement stepCycle: LAST / Resolution: 2.15→19.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3912 0 0 66 3978
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0224041
X-RAY DIFFRACTIONr_bond_other_d0.0010.022735
X-RAY DIFFRACTIONr_angle_refined_deg1.7331.9585525
X-RAY DIFFRACTIONr_angle_other_deg1.00136651
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6055490
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.17723.462182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.76515609
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.221523
X-RAY DIFFRACTIONr_chiral_restr0.1080.2615
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214479
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02864
X-RAY DIFFRACTIONr_mcbond_it0.9451.52475
X-RAY DIFFRACTIONr_mcbond_other0.2351.5971
X-RAY DIFFRACTIONr_mcangle_it1.62824072
X-RAY DIFFRACTIONr_scbond_it2.48631566
X-RAY DIFFRACTIONr_scangle_it3.794.51452
LS refinement shellResolution: 2.15→2.205 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 92 -
Rwork0.292 1708 -
obs--88.63 %
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)
16.14410.99250.277.23271.51782.69150.1271-0.8189-0.52140.9749-0.19360.04550.263-0.17170.06650.1677-0.05870.01120.21030.11990.170944.075176.264229.6353
26.6696-0.05860.65649.04110.31763.47740.14820.68070.226-1.0963-0.14830.2573-0.0793-0.22990.00020.14260.0474-0.03940.15720.04470.100542.68584.323612.8388
33.1166-0.4701-0.0187.96060.51483.73320.10220.1151-0.2241-0.1428-0.0559-0.04570.42310.193-0.04630.06190.0455-0.01230.07750.01390.11889.746968.621320.4026
44.4414-0.34681.52677.51710.16553.2393-0.03180.36350.37340.0172-0.1113-0.1055-0.5750.21840.1430.1183-0.0255-0.01050.0660.0830.11399.997287.280722.1206
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 128
2X-RAY DIFFRACTION2B8 - 129
3X-RAY DIFFRACTION3C6 - 129
4X-RAY DIFFRACTION4D6 - 129

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