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- PDB-3bmz: Violacein biosynthetic enzyme VioE -

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Basic information

Entry
Database: PDB / ID: 3bmz
TitleViolacein biosynthetic enzyme VioE
ComponentsPutative uncharacterized protein
KeywordsBIOSYNTHETIC PROTEIN / violacein
Function / homology
Function and homology information


outer 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
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / VioE domain-containing protein
Similarity search - Component
Biological speciesChromobacterium violaceum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.21 Å
AuthorsRyan, K.S. / Drennan, C.L.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: The Violacein Biosynthetic Enzyme VioE Shares a Fold with Lipoprotein Transporter Proteins
Authors: Ryan, K.S. / Balibar, C.J. / Turo, K.E. / Walsh, C.T. / Drennan, C.L.
History
DepositionDec 13, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Feb 21, 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
Remark 650HELIX DETERMINATION METHOD: AUTHOR

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative uncharacterized protein
B: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0984
Polymers45,7532
Non-polymers3442
Water10,899605
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.527, 82.477, 90.633
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 Putative uncharacterized protein


Mass: 22876.625 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chromobacterium violaceum (bacteria) / Strain: ATCC 12472 / Gene: VioE / Plasmid: pET24b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE3) PlysS / References: UniProt: Q7NSZ5
#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 605 / 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: 2.19 Å3/Da / Density % sol: 43.74 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 25% (v/v) PEG-400, 20% (w/v) PEG-3350, 0.1 M magnesium chloride, 0.1 M Tris pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 141.6 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 21, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.21→50 Å / Num. all: 111465 / Num. obs: 111465 / % possible obs: 90.6 % / Redundancy: 13.9 % / Rsym value: 0.066 / Net I/σ(I): 35.7
Reflection shellResolution: 1.21→1.25 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 3.4 / Num. unique all: 6598 / Rsym value: 0.258 / % possible all: 54.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.21→45.31 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.088 / SU ML: 0.023 / Cross valid method: THROUGHOUT / ESU R: 0.05 / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19459 5605 5 %RANDOM
Rwork0.16781 ---
obs0.16912 105792 90.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.818 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å20 Å2
2--0.19 Å20 Å2
3----0.22 Å2
Refinement stepCycle: LAST / Resolution: 1.21→45.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2984 0 23 605 3612
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0223335
X-RAY DIFFRACTIONr_bond_other_d0.0010.022456
X-RAY DIFFRACTIONr_angle_refined_deg1.2091.9724589
X-RAY DIFFRACTIONr_angle_other_deg0.81635904
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.865444
X-RAY DIFFRACTIONr_dihedral_angle_2_deg22.46521.497167
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.19415532
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6891549
X-RAY DIFFRACTIONr_chiral_restr0.0770.2467
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023830
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02773
X-RAY DIFFRACTIONr_nbd_refined0.180.2533
X-RAY DIFFRACTIONr_nbd_other0.1960.22757
X-RAY DIFFRACTIONr_nbtor_refined0.1780.21512
X-RAY DIFFRACTIONr_nbtor_other0.080.21958
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1060.2475
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0350.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2720.283
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0880.231
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1571.52613
X-RAY DIFFRACTIONr_mcbond_other0.4031.5793
X-RAY DIFFRACTIONr_mcangle_it1.3523253
X-RAY DIFFRACTIONr_scbond_it1.82731605
X-RAY DIFFRACTIONr_scangle_it2.3944.51297
X-RAY DIFFRACTIONr_rigid_bond_restr1.72837419
X-RAY DIFFRACTIONr_sphericity_free2.5413680
X-RAY DIFFRACTIONr_sphericity_bonded2.65435662
LS refinement shellResolution: 1.21→1.241 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.211 208 -
Rwork0.181 4209 -
obs--49.02 %

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