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- PDB-3c4a: Crystal structure of vioD hydroxylase in complex with FAD from Ch... -

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Basic information

Entry
Database: PDB / ID: 3c4a
TitleCrystal structure of vioD hydroxylase in complex with FAD from Chromobacterium violaceum. Northeast Structural Genomics Consortium Target CvR158
ComponentsProbable tryptophan hydroxylase vioD
KeywordsOXIDOREDUCTASE / alpha-beta protein / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / Antibiotic biosynthesis / FAD / Flavoprotein
Function / homology
Function and homology information


protodeoxyviolaceinate monooxygenase / antibiotic biosynthetic process / monooxygenase activity
Similarity search - Function
D-Amino Acid Oxidase; Chain A, domain 2 - #20 / D-Amino Acid Oxidase; Chain A, domain 2 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Protodeoxyviolaceinate monooxygenase
Similarity search - Component
Biological speciesChromobacterium violaceum ATCC 12472 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsForouhar, F. / Neely, H. / Seetharaman, J. / Janjua, H. / Xiao, R. / Maglaqui, M. / Wang, H. / Baran, M.C. / Acton, T.B. / Montelione, G.T. ...Forouhar, F. / Neely, H. / Seetharaman, J. / Janjua, H. / Xiao, R. / Maglaqui, M. / Wang, H. / Baran, M.C. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of vioD hydroxylase in complex with FAD from Chromobacterium violaceum.
Authors: Forouhar, F. / Neely, H. / Seetharaman, J. / Janjua, H. / Xiao, R. / Maglaqui, M. / Wang, H. / Baran, M.C. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionJan 29, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable tryptophan hydroxylase vioD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9542
Polymers43,1691
Non-polymers7861
Water1,54986
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.179, 97.725, 40.605
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Probable tryptophan hydroxylase vioD


Mass: 43168.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chromobacterium violaceum ATCC 12472 (bacteria)
Species: Chromobacterium violaceum / Strain: DSM 30191 / IFO 12614 / JCM 1249 / NCIB 9131 / Gene: vioD, CV_3271 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q9S3U8, Oxidoreductases
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 2.05 Å3/Da / Density % sol: 39.98 %
Description: The structure factor file contains Friedel pairs
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Protein solution: 10 mM Tris-HCl, 100 mM NaCl, 3 mM FAD, 5 mM DTT. Reservoir solution: 100 mM Bis-Tris pH 6.5, 25% PEG 3350, 200 mM MgCl2, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.979 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jan 18, 2008 / Details: Mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. all: 30479 / Num. obs: 30479 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Biso Wilson estimate: 18.4 Å2 / Rmerge(I) obs: 0.105 / Rsym value: 0.082 / Net I/σ(I): 20.58
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.473 / Mean I/σ(I) obs: 3.32 / Num. unique all: 3061 / Rsym value: 0.422 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.2refinement
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
SnBphasing
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→19.88 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 345893.74 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: The Friedel pairs were used in phasing
RfactorNum. reflection% reflectionSelection details
Rfree0.262 2522 9.7 %RANDOM
Rwork0.202 ---
all0.205 25909 --
obs0.202 25883 84.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 28.3601 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 31.9 Å2
Baniso -1Baniso -2Baniso -3
1--7.78 Å20 Å20 Å2
2--5.55 Å20 Å2
3---2.23 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.4 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2.3→19.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2870 0 53 86 3009
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONc_improper_angle_d1.37
LS refinement shellResolution: 2.3→2.38 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.325 201 10.2 %
Rwork0.24 1777 -
obs-1777 64.7 %

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