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- PDB-4dgk: Crystal structure of Phytoene desaturase CRTI from Pantoea ananatis -

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Basic information

Entry
Database: PDB / ID: 4dgk
TitleCrystal structure of Phytoene desaturase CRTI from Pantoea ananatis
ComponentsPhytoene dehydrogenase
KeywordsOXIDOREDUCTASE / the FAD/NAD(P)-binding Rossmann fold
Function / homology
Function and homology information


phytoene desaturase (lycopene-forming) / carotene biosynthetic process / carotenoid biosynthetic process / oxidoreductase activity, acting on the CH-CH group of donors / FAD binding / plasma membrane
Similarity search - Function
Phytoene dehydrogenase, bacterial-type, conserved site / Bacterial-type phytoene dehydrogenase signature. / Carotenoid/retinoid oxidoreductase / Amine oxidase / Flavin containing amine oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha Beta
Similarity search - Domain/homology
Phytoene desaturase (lycopene-forming)
Similarity search - Component
Biological speciesPantoea ananatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.35 Å
AuthorsSchaub, P. / Yu, Q. / Gemmecker, S. / Poussin-Courmontagne, P. / Mailliot, J. / McEwen, A.G. / Ghisla, S. / Beyer, P. / Cavarelli, J.
CitationJournal: Plos One / Year: 2012
Title: On the structure and function of the phytoene desaturase CRTI from Pantoea ananatis, a membrane-peripheral and FAD-dependent oxidase/isomerase.
Authors: Schaub, P. / Yu, Q. / Gemmecker, S. / Poussin-Courmontagne, P. / Mailliot, J. / McEwen, A.G. / Ghisla, S. / Al-Babili, S. / Cavarelli, J. / Beyer, P.
History
DepositionJan 26, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.2Feb 28, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phytoene dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4487
Polymers56,1021
Non-polymers3466
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.690, 90.690, 130.030
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Phytoene dehydrogenase / Phytoene desaturase


Mass: 56102.391 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pantoea ananatis (bacteria) / Gene: crtI / Production host: Escherichia coli (E. coli)
References: UniProt: P21685, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; Miscellaneous
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.75 Å3/Da / Density % sol: 55.3 %
Crystal growTemperature: 290 K / pH: 6.2
Details: 8% PEG 8K, 0.1 M NaCl, 0.1 M Na/K phosphate pH 6.2, VAPOR DIFFUSION, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9791, 0.9794, 0.9770
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 18, 2009
RadiationMonochromator: CHANNEL CUT CRYOGENICALLY COOLED MONOCHROMATOR CRYSTAL
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97911
20.97941
30.9771
ReflectionResolution: 2.35→27.85 Å / Num. obs: 26274 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 68.8 Å2 / Rmerge(I) obs: 0.056 / Rsym value: 0.056 / Net I/σ(I): 22.5
Reflection shellResolution: 2.35→2.39 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.353 / Mean I/σ(I) obs: 4.4 / Rsym value: 0.353 / % possible all: 99.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHARPphasing
BUSTER2.10.0refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.35→27.85 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.923 / SU R Cruickshank DPI: 0.223 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: TLS SELECTION GROUP 1 { A|1 - A|33 A|59 - A|78 A|218 - A|275 A|456 - A|492 } GROUP 2 { A|41 - A|58 A|79 - A|100 A|212 - A|217 A|303 - A|425 } GROUP 3 { A|101 - A|211 }
RfactorNum. reflection% reflectionSelection details
Rfree0.23 1299 4.94 %RANDOM
Rwork0.19 ---
obs0.192 26274 99.8 %-
all-26329 --
Displacement parametersBiso mean: 72.87 Å2
Baniso -1Baniso -2Baniso -3
1-7.0106 Å20 Å20 Å2
2--7.0106 Å20 Å2
3----14.0211 Å2
Refine analyzeLuzzati coordinate error obs: 0.39 Å
Refinement stepCycle: LAST / Resolution: 2.35→27.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3193 0 21 67 3281
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013293HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.084457HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1096SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes72HARMONIC2
X-RAY DIFFRACTIONt_gen_planes482HARMONIC5
X-RAY DIFFRACTIONt_it3293HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.02
X-RAY DIFFRACTIONt_other_torsion17.7
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion410SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3612SEMIHARMONIC4
LS refinement shellResolution: 2.35→2.45 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.2512 151 5.17 %
Rwork0.2176 2768 -
all0.2192 2919 -
obs--99.79 %
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)
12.19610.54241.32984.39372.05062.9871-0.0724-0.26330.3339-0.2722-0.11350.38470.0091-0.45570.1859-0.0344-0.14940.0001-0.0846-0.0149-0.105418.384149.853627.8911
22.81490.11581.5462.6042-0.68033.8001-0.0449-0.30420.04840.24970.002-0.054-0.27440.0050.0429-0.07510.0079-0.0506-0.2375-0.0127-0.063513.850619.185933.6752
34.4104-0.14781.52760.4759-0.52291.9603-0.045-0.01810.13790.12890.0229-0.031-0.0839-0.1390.02210.02290.0572-0.0747-0.207-0.02810.0247-4.442619.614518.1643
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|1 - A|33 A|59 - A|78 A|218 - A|275 A|456 - A|492 }A1 - 33
2X-RAY DIFFRACTION1{ A|1 - A|33 A|59 - A|78 A|218 - A|275 A|456 - A|492 }A59 - 78
3X-RAY DIFFRACTION1{ A|1 - A|33 A|59 - A|78 A|218 - A|275 A|456 - A|492 }A218 - 275
4X-RAY DIFFRACTION1{ A|1 - A|33 A|59 - A|78 A|218 - A|275 A|456 - A|492 }A456 - 492
5X-RAY DIFFRACTION2{ A|41 - A|58 A|79 - A|100 A|212 - A|217 A|303 - A|425 }A41 - 58
6X-RAY DIFFRACTION2{ A|41 - A|58 A|79 - A|100 A|212 - A|217 A|303 - A|425 }A79 - 100
7X-RAY DIFFRACTION2{ A|41 - A|58 A|79 - A|100 A|212 - A|217 A|303 - A|425 }A212 - 217
8X-RAY DIFFRACTION2{ A|41 - A|58 A|79 - A|100 A|212 - A|217 A|303 - A|425 }A303 - 425
9X-RAY DIFFRACTION3{ A|101 - A|211 }A101 - 211

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