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- PDB-2zf3: Crystal Structure of VioE -

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Basic information

Entry
Database: PDB / ID: 2zf3
TitleCrystal Structure of VioE
ComponentsHypothetical protein VioEHypothesis
KeywordsANTIBIOTIC / putative isomerase / BETA protein
Function / homologyouter membrane lipoprotein receptor (LolB), chain A - #30 / Violacein biosynthesis enzyme, VioE / VioE superfamily / VioE domain / Violacein biosynthetic enzyme VioE / outer membrane lipoprotein receptor (LolB), chain A / Clam / Mainly Beta / VioE domain-containing protein
Function and homology information
Biological speciesChromobacterium violaceum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsHirano, S. / Shiro, Y. / Nagano, S.
CitationJournal: To be Published
Title: Crystal structure of VioE, a key player in the construction of the molecular skeleton of violacein
Authors: Hirano, S. / Asamizu, S. / Onaka, H. / Shiro, Y. / Nagano, S.
History
DepositionDec 20, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Mar 13, 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: Hypothetical protein VioE
B: Hypothetical protein VioE
C: Hypothetical protein VioE
D: Hypothetical protein VioE
E: Hypothetical protein VioE
F: Hypothetical protein VioE


Theoretical massNumber of molelcules
Total (without water)132,5276
Polymers132,5276
Non-polymers00
Water8,593477
1
A: Hypothetical protein VioE
B: Hypothetical protein VioE


Theoretical massNumber of molelcules
Total (without water)44,1762
Polymers44,1762
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3330 Å2
MethodPISA
2
C: Hypothetical protein VioE
D: Hypothetical protein VioE


Theoretical massNumber of molelcules
Total (without water)44,1762
Polymers44,1762
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
MethodPISA
3
E: Hypothetical protein VioE
F: Hypothetical protein VioE


Theoretical massNumber of molelcules
Total (without water)44,1762
Polymers44,1762
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.099, 88.435, 153.859
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
Hypothetical protein VioE / Hypothesis


Mass: 22087.750 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chromobacterium violaceum (bacteria) / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q7NSZ5
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 477 / 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: 2.16 Å3/Da / Density % sol: 43.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 3.5
Details: 6% PEG 4000, 0.1M Citrate, pH 3.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 5, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 77895 / % possible obs: 100 % / Redundancy: 7.3 % / Biso Wilson estimate: 28.3 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 11.9
Reflection shellResolution: 2→2.07 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.358 / Mean I/σ(I) obs: 4.67

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: SAD / Resolution: 2→39.25 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.926 / SU B: 9.046 / SU ML: 0.13 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.205 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24522 3922 5 %RANDOM
Rwork0.1992 ---
obs0.20154 73852 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.152 Å2
Baniso -1Baniso -2Baniso -3
1--0.9 Å20 Å20 Å2
2--0.99 Å20 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 2→39.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8735 0 0 477 9212
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0229082
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.361.9612352
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.351109
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.52721.54461
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.168151432
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.11115130
X-RAY DIFFRACTIONr_chiral_restr0.0930.21251
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027225
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2040.23737
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.25879
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.2612
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2160.2142
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1330.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7311.55611
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.1828774
X-RAY DIFFRACTIONr_scbond_it1.68534080
X-RAY DIFFRACTIONr_scangle_it2.6174.53560
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.002→2.054 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 265 -
Rwork0.209 5300 -
obs--98.43 %
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)
11.9202-0.30610.04050.9435-0.1731.74770.16120.34870.0014-0.1517-0.12760.0137-0.0462-0.0807-0.0337-0.16120.03450.0284-0.2085-0.0211-0.2164-18.6424.251-13.011
23.879-0.18770.94971.96910.83682.79430.1177-0.3972-0.26920.3819-0.04270.05470.3261-0.2388-0.075-0.0975-0.05120.0362-0.22230.0272-0.18-21.87418.7977.525
33.3033-0.2993-1.98381.09750.23024.1542-0.0620.9078-0.0035-0.135-0.24120.04080.3384-0.50510.3032-0.0552-0.0350.0846-0.0122-0.0391-0.0142-30.2460.439-10.912
44.3939-1.0736-1.4551.88080.46023.6689-0.0584-0.29020.33550.2867-0.09210.02620.1198-0.09650.1505-0.0543-0.08530.0931-0.2215-0.06490.0094-34.46966.7518.746
52.17480.1429-0.38421.02990.70213.179-0.07490.11530.1367-0.31860.0643-0.1446-0.4890.11280.01060.1434-0.01880.0661-0.26160.0108-0.17135.5443.472-40.165
63.23191.0752-0.40932.1635-0.77762.764-0.26070.009-0.071-0.23490.1540.07850.2981-0.49560.10660.02920.00490.0303-0.1609-0.0194-0.1772-12.333-3.268-30.364
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA4 - 1917 - 194
2X-RAY DIFFRACTION2BB5 - 1898 - 192
3X-RAY DIFFRACTION3CC5 - 1918 - 194
4X-RAY DIFFRACTION4DD5 - 1898 - 192
5X-RAY DIFFRACTION5EE4 - 1897 - 192
6X-RAY DIFFRACTION6FF5 - 1898 - 192

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