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- PDB-2zf4: Crystal Structure of VioE complexed with phenylpyruvic acid -

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Basic information

Entry
Database: PDB / ID: 2zf4
TitleCrystal Structure of VioE complexed with phenylpyruvic acid
ComponentsHypothetical protein VioE
KeywordsANTIBIOTIC / putative isomerase / BETA protein / Protein-ligand analogue complex
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
3-PHENYLPYRUVIC ACID / VioE domain-containing protein
Similarity search - Component
Biological speciesChromobacterium violaceum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 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 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,49618
Polymers132,5276
Non-polymers1,97012
Water5,765320
1
A: Hypothetical protein VioE
B: Hypothetical protein VioE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8326
Polymers44,1762
Non-polymers6574
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3420 Å2
MethodPISA
2
C: Hypothetical protein VioE
D: Hypothetical protein VioE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8326
Polymers44,1762
Non-polymers6574
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3420 Å2
MethodPISA
3
E: Hypothetical protein VioE
F: Hypothetical protein VioE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8326
Polymers44,1762
Non-polymers6574
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.415, 91.030, 158.999
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


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: Chemical
ChemComp-PPY / 3-PHENYLPYRUVIC ACID


Mass: 164.158 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C9H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 320 / 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: 2.28 Å3/Da / Density % sol: 45.99 %
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: Sep 24, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.18→30 Å / Num. obs: 63652 / % possible obs: 97.1 % / Redundancy: 6.7 % / Biso Wilson estimate: 36.6 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 15.6
Reflection shellResolution: 2.18→2.26 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.265 / Mean I/σ(I) obs: 4 / Rsym value: 0.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZF3

2zf3


Resolution: 2.18→29.93 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.923 / SU B: 14.734 / SU ML: 0.192 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.302 / ESU R Free: 0.227 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25432 3115 5 %RANDOM
Rwork0.20567 ---
obs0.20817 58569 96.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.795 Å2
Baniso -1Baniso -2Baniso -3
1--0.83 Å20 Å20 Å2
2--0.29 Å20 Å2
3---0.54 Å2
Refinement stepCycle: LAST / Resolution: 2.18→29.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8733 0 144 320 9197
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0229167
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.371.97212441
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.39551087
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.921.565460
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.532151402
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.39315128
X-RAY DIFFRACTIONr_chiral_restr0.0920.21233
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027368
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.20.23683
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.25818
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2517
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1750.2101
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1410.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5761.55603
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.97128711
X-RAY DIFFRACTIONr_scbond_it1.41734219
X-RAY DIFFRACTIONr_scangle_it2.2284.53725
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.183→2.239 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 188 -
Rwork0.237 3485 -
obs--79.02 %
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)
12.1173-0.8885-0.19121.9309-0.85412.1650.37160.01780.4631-0.204-0.1152-0.2667-0.01350.0299-0.2564-0.3830.00370.1303-0.11180.00980.0645-17.34525.481-12.905
24.741-1.4001-0.3132.50090.16842.72670.1073-0.97830.21980.25610.2115-0.03160.25790.1252-0.3187-0.4232-0.0863-0.01440.1609-0.057-0.0265-21.17517.3717.26
32.97670.24030.50581.2689-0.51713.18380.11370.0867-0.251-0.1788-0.0257-0.08440.30650.1144-0.088-0.34250.00810.0379-0.06170.0075-0.1274-31.42762.527-12.437
43.67240.17020.57861.63070.26232.44530.1387-0.70110.16990.2214-0.0447-0.0148-0.0077-0.0688-0.0941-0.3534-0.10060.04440.21-0.0147-0.1613-35.39168.8478.48
52.75060.0472-0.42732.2220.45622.3451-0.0750.12490.1324-0.59320.2648-0.2586-0.36220.1088-0.18990.0722-0.03720.1852-0.03210.0504-0.11963.713.231-43.352
63.01121.19290.09842.46780.41582.0505-0.05890.02940.0771-0.240.0370.1853-0.1634-0.2990.022-0.14350.10780.0831-0.04480.1072-0.1756-13.28-4.079-31.384
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA5 - 1918 - 194
2X-RAY DIFFRACTION1AG - H192 - 1931
3X-RAY DIFFRACTION2BB6 - 1889 - 191
4X-RAY DIFFRACTION2BI - J192 - 1931
5X-RAY DIFFRACTION3CC5 - 1918 - 194
6X-RAY DIFFRACTION3CK - L192 - 1931
7X-RAY DIFFRACTION4DD7 - 18910 - 192
8X-RAY DIFFRACTION4DM - N192 - 1931
9X-RAY DIFFRACTION5EE5 - 1908 - 193
10X-RAY DIFFRACTION5EO - P192 - 1931
11X-RAY DIFFRACTION6FF5 - 1898 - 192
12X-RAY DIFFRACTION6FQ - R192 - 1931

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