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- PDB-2z2n: Crystal Structure of selenomethionine substituted virginiamycin B... -

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Basic information

Entry
Database: PDB / ID: 2z2n
TitleCrystal Structure of selenomethionine substituted virginiamycin B lyase from Staphylococcus aureus
Componentsvirginiamycin B lyase
KeywordsLYASE / seven-bladed beta-propeller / antibiotic resistance / enzyme mechanism / virginiamycin B lyase / virginiamycin B hydrolase / streptogramin
Function / homology
Function and homology information


carbon-oxygen lyase activity / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / antibiotic catabolic process / outer membrane-bounded periplasmic space / response to antibiotic / magnesium ion binding
Similarity search - Function
Streptogramin lyase / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
Virginiamycin B lyase / Virginiamycin B lyase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.65 Å
AuthorsKorczynska, M. / Berghuis, A.M.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Structural basis for streptogramin B resistance in Staphylococcus aureus by virginiamycin B lyase
Authors: Korczynska, M. / Mukhtar, T.A. / Wright, G.D. / Berghuis, A.M.
History
DepositionMay 25, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 19, 2007Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: virginiamycin B lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3992
Polymers33,3641
Non-polymers351
Water3,783210
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.970, 34.752, 86.601
Angle α, β, γ (deg.)90.00, 117.86, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-416-

HOH

21A-418-

HOH

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Components

#1: Protein virginiamycin B lyase / Vgh protein / Hydrolase VgB


Mass: 33363.652 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: BM30002/pIP524 / Gene: vgb, vgh / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q53744, UniProt: P17978*PLUS, Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases, Isomerases; Intramolecular lyases
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS SEQUENCE DERIVES FROM THE ORIGINAL GENE.

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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: 1.85 Å3/Da / Density % sol: 33.6 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100mM phosphate citrate buffer (pH 4.2), 15%(w/v) PEG 8000, 10-17%(v/v) PEG 500MME, 175mM NaCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.9000, 0.9798, 1.0600
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 1, 2004
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.91
20.97981
31.061
ReflectionResolution: 1.65→50 Å / Num. obs: 29320 / % possible obs: 96.7 % / Redundancy: 7.5 % / Rsym value: 0.038 / Net I/σ(I): 18.5
Reflection shellResolution: 1.65→1.75 Å / Redundancy: 6 % / Mean I/σ(I) obs: 3.7 / Rsym value: 0.383 / % possible all: 78.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SnBphasing
BEASTphasing
RefinementMethod to determine structure: MAD / Resolution: 1.65→20 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.953 / SU B: 4.765 / SU ML: 0.08 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.112 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: The structure was refined also with CNS.
RfactorNum. reflection% reflectionSelection details
Rfree0.20309 2747 9.9 %RANDOM
Rwork0.15604 ---
obs0.16092 25084 93.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 20.205 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å20 Å2-1.77 Å2
2---1.43 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.65→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2272 0 1 210 2483
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0222376
X-RAY DIFFRACTIONr_bond_other_d0.0020.022118
X-RAY DIFFRACTIONr_angle_refined_deg2.2711.9523248
X-RAY DIFFRACTIONr_angle_other_deg1.12534985
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.1095312
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.67125.588102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.13215404
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.475158
X-RAY DIFFRACTIONr_chiral_restr0.1650.2363
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022663
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02445
X-RAY DIFFRACTIONr_nbd_refined0.2540.2509
X-RAY DIFFRACTIONr_nbd_other0.2160.22343
X-RAY DIFFRACTIONr_nbtor_refined0.1920.21139
X-RAY DIFFRACTIONr_nbtor_other0.0950.21448
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2520.2157
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2070.230
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2550.253
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.380.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6561.51598
X-RAY DIFFRACTIONr_mcbond_other0.4491.5610
X-RAY DIFFRACTIONr_mcangle_it2.122423
X-RAY DIFFRACTIONr_scbond_it3.29131008
X-RAY DIFFRACTIONr_scangle_it4.2394.5815
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.739 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.237 265 -
Rwork0.195 2930 -
obs--74.56 %
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)
118.50460.2294-23.43917.14296.478158.0334-0.16220.9529-0.3165-0.222-0.0971-1.12030.405-0.34920.2594-0.13950.1012-0.09720.10920.14150.176333.38022.02716.9445
26.83670.14370.49893.47212.01126.72370.1276-0.1311-0.16050.6317-0.073-0.65720.2530.3406-0.05470.1057-0.1071-0.2532-0.26250.1313-0.41220.159710.102631.1317
35.33261.17682.09345.22740.68383.44580.1001-0.74850.26231.1615-0.2888-0.1916-0.2248-0.31550.18870.1491-0.10180.0165-0.0628-0.0423-0.35619.071116.086130.7058
42.86941.33731.06634.49090.41742.4480.0987-0.46150.27090.5327-0.19580.4821-0.124-0.39470.0971-0.06270.0060.12240.0449-0.0441-0.06720.856715.920521.2423
50.70180.52380.48594.02640.25251.45540.0226-0.06290.06570.0578-0.04050.3576-0.0706-0.140.0179-0.08260.00530.0133-0.01170.00480.01192.705811.34529.882
60.99390.27860.01354.8808-0.95010.67550.03750.074-0.0687-0.2337-0.01560.03480.07570.051-0.0219-0.04420.00180.024-0.0151-0.0122-0.025811.82944.44925.695
72.77050.77-0.11926.70150.10083.29350.0857-0.0524-0.3450.1174-0.1098-0.67010.21310.27220.0241-0.10520.0230.0195-0.01150.02380.044322.27851.357610.3151
82.24523.1295-0.81124.7678-1.91019.07160.08510.1366-0.15310.2749-0.1628-0.90760.28060.92530.0777-0.0671-0.0048-0.1237-0.02250.070.03826.67695.657818.5274
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 82 - 8
2X-RAY DIFFRACTION2AA17 - 5917 - 59
3X-RAY DIFFRACTION3AA60 - 10160 - 101
4X-RAY DIFFRACTION4AA102 - 143102 - 143
5X-RAY DIFFRACTION5AA144 - 185144 - 185
6X-RAY DIFFRACTION6AA186 - 227186 - 227
7X-RAY DIFFRACTION7AA228 - 269228 - 269
8X-RAY DIFFRACTION8AA270 - 294270 - 294

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