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- PDB-3pss: Crystal Structure of AhQnr, the Qnr protein from Aeromonas hydrop... -

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Basic information

Entry
Database: PDB / ID: 3pss
TitleCrystal Structure of AhQnr, the Qnr protein from Aeromonas hydrophila (P21 crystal form)
ComponentsQnr
KeywordsCELL CYCLE / pentapeptide repeat / antibiotic resistance / DNA topoisomerase II
Function / homologyPentapeptide repeats (8 copies) / E3 ubiquitin-protein ligase SopA / Pentapeptide repeats (9 copies) / Pentapeptide repeat / Pectate Lyase C-like / 3 Solenoid / Mainly Beta / Qnr
Function and homology information
Biological speciesAeromonas hydrophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsXiong, X. / Spencer, J.
CitationJournal: Nucleic Acids Res. / Year: 2011
Title: Structural insights into quinolone antibiotic resistance mediated by pentapeptide repeat proteins: conserved surface loops direct the activity of a Qnr protein from a Gram-negative bacterium
Authors: Xiong, X. / Bromley, E.H.C. / Oelschlaeger, P. / Woolfson, D.N. / Spencer, J.
History
DepositionDec 2, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 26, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Qnr
B: Qnr


Theoretical massNumber of molelcules
Total (without water)48,6692
Polymers48,6692
Non-polymers00
Water5,441302
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2040 Å2
ΔGint-10 kcal/mol
Surface area19790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.230, 57.710, 85.120
Angle α, β, γ (deg.)90.00, 106.96, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1116A1 - 216
2116B1 - 216

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Components

#1: Protein Qnr


Mass: 24334.252 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeromonas hydrophila (bacteria) / Strain: hydrophila ATCC 7966 / Gene: AHA_0291 / Plasmid: pET-26b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: A0KF03
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 302 / 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: 2.52 Å3/Da / Density % sol: 51.21 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M bis-tris propane, 0.2M potassium thiocyanate, 20% PEG 3350, 16% glycerol, 40mM DTT, 18mM spermine-HCl Reductively methylated protein, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 18, 2009
RadiationMonochromator: SI (111) DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2→49.96 Å / Num. all: 32803 / Num. obs: 32765 / % possible obs: 99.9 % / Redundancy: 7.3 % / Biso Wilson estimate: 23.6 Å2 / Rmerge(I) obs: 0.101 / Net I/σ(I): 12.8
Reflection shellResolution: 2→2.11 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.562 / Mean I/σ(I) obs: 3.5 / Num. unique all: 4744 / % possible all: 99.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2→49.5 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.936 / SU B: 9.545 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.23277 1662 5.1 %RANDOM
Rwork0.17867 ---
obs0.18137 31090 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.142 Å2
Baniso -1Baniso -2Baniso -3
1--1.78 Å20 Å2-2.09 Å2
2--0.07 Å20 Å2
3---0.49 Å2
Refinement stepCycle: LAST / Resolution: 2→49.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3382 0 0 302 3684
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0213482
X-RAY DIFFRACTIONr_bond_other_d0.0010.022354
X-RAY DIFFRACTIONr_angle_refined_deg1.2111.9574699
X-RAY DIFFRACTIONr_angle_other_deg1.03335701
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2065443
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.44825.127197
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.17415566
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2361525
X-RAY DIFFRACTIONr_chiral_restr0.0750.2493
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024068
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02751
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2971.52149
X-RAY DIFFRACTIONr_mcbond_other0.091.5903
X-RAY DIFFRACTIONr_mcangle_it0.5223403
X-RAY DIFFRACTIONr_scbond_it1.02931333
X-RAY DIFFRACTIONr_scangle_it1.6164.51290
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2767 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
loose positional0.635
loose thermal0.8210
LS refinement shellResolution: 2.003→2.055 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 123 -
Rwork0.277 2286 -
obs--99.67 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
14.4722-5.5380.24458.11970.10484.13050.03011.143-0.0593-0.57230.12731.16940.2579-1.9979-0.15740.4314-0.1621-0.35051.77180.19530.5638-27.20814.196-6.471
28.1455.58430.674412.8608-7.101522.80770.40130.4535-0.5801-0.3354-0.3682-0.11810.4018-0.5114-0.03310.50350.181-0.37110.6518-0.12110.4197-22.10810.445-5.669
35.6082-1.48042.15867.26821.05336.082-0.08280.26240.1072-0.53180.1840.1456-0.15060.0379-0.10120.2335-0.0199-0.10280.48830.00870.2374-18.19815.711-3.509
44.3089-0.23030.32915.71810.85414.6668-0.01770.35340.0683-0.2826-0.01750.1271-0.1405-0.42920.03530.16480.0251-0.0870.42680.01060.188-16.33216.1832.324
54.0236-0.6622-0.96724.44430.83027.89150.05440.35330.132-0.00660.02970.0463-0.3712-0.1724-0.08410.12920.0293-0.06750.31630.01450.211-12.78117.6067.311
62.1436-3.7444-3.97066.15836.28779.7320.12190.2544-0.006-0.1734-0.37120.019-0.3046-0.31180.24930.19980.05-0.00480.14310.0130.208-13.94421.7522.405
73.10180.250.59961.8421-0.27594.0772-0.04110.51560.0905-0.2266-0.0624-0.2493-0.10490.18430.10350.15950.0233-0.0280.27040.01820.2588-1.86815.110.662
89.03590.31650.89421.512-0.04513.110.07340.40820.25050.0528-0.0156-0.0862-0.20420.1151-0.05780.18050.0249-0.04180.16680.07470.26096.7513.44518.642
911.6622-0.94481.26981.8983-0.10091.86520.0060.4057-0.6017-0.06890.11710.01340.17730.0945-0.12310.19370.014-0.0510.1364-0.01570.197814.7386.73121.397
102.7762-0.4365-0.84363.5948-1.52046.23520.0049-0.1581-0.0940.708-0.051-0.58450.03810.20230.04610.267-0.0254-0.19070.15640.00280.331955.7818.54157.903
1115.65916.443827.796636.550722.909840.8354-0.20341.285-0.3344-0.39031.2508-1.9278-0.48292.075-1.04740.3243-0.1483-0.04920.40060.01370.663261.56411.93251.1
122.75890.2446-0.05958.1345-0.93445.35510.0166-0.0138-0.0510.1876-0.0225-0.32040.1050.08550.00590.0782-0.0204-0.12360.04370.01140.248252.3910.72551.794
132.5422-0.73450.7755.1316-0.14664.2950.0922-0.406-0.03130.6498-0.05930.1484-0.1616-0.3836-0.03290.1656-0.0336-0.06240.07930.00690.200245.18611.87654.826
142.02170.45721.70916.5139-0.00953.0236-0.02050.08160.12940.0834-0.0298-0.0955-0.10270.00050.05020.0984-0.0229-0.05730.01410.01260.174345.15712.34747.259
159.17938.6829-5.36212.3309-7.45087.612-0.07270.2755-0.0942-0.20930.1223-0.05970.0526-0.0704-0.04960.10090.0044-0.08140.0115-0.00020.181744.6269.39341.943
161.35080.08141.00243.9702-1.04324.526-0.02580.04250.1893-0.0961-0.0554-0.1107-0.27730.0840.08120.107-0.0157-0.0430.0104-0.01360.204240.79116.60538.874
173.92510.39230.31544.93190.04994.4978-0.0037-0.16940.14670.093-0.05610.1854-0.0423-0.37530.05980.1035-0.0015-0.07470.0301-0.00660.185930.70212.95737.299
1810.1435-0.22771.77480.5738-0.29272.73510.0067-0.1619-0.0070.09830.11560.111-0.0579-0.3668-0.12230.17040.0117-0.03270.06340.010.208318.8519.09729.193
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 19
2X-RAY DIFFRACTION2A20 - 30
3X-RAY DIFFRACTION3A31 - 56
4X-RAY DIFFRACTION4A57 - 79
5X-RAY DIFFRACTION5A80 - 105
6X-RAY DIFFRACTION6A106 - 117
7X-RAY DIFFRACTION7A118 - 171
8X-RAY DIFFRACTION8A172 - 193
9X-RAY DIFFRACTION9A194 - 216
10X-RAY DIFFRACTION10B1 - 14
11X-RAY DIFFRACTION11B15 - 20
12X-RAY DIFFRACTION12B21 - 41
13X-RAY DIFFRACTION13B42 - 63
14X-RAY DIFFRACTION14B64 - 81
15X-RAY DIFFRACTION15B82 - 92
16X-RAY DIFFRACTION16B93 - 131
17X-RAY DIFFRACTION17B132 - 172
18X-RAY DIFFRACTION18B173 - 216

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