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- PDB-4rep: Crystal Structure of gamma-carotenoid desaturase -

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Basic information

Entry
Database: PDB / ID: 4rep
TitleCrystal Structure of gamma-carotenoid desaturase
ComponentsGamma-carotene desaturase
KeywordsOXIDOREDUCTASE / FLAVOPROTEIN / Rossmann fold / FAD-binding / DESATURASE / gamma-carotenoid desaturase
Function / homology
Function and homology information


1-hydroxycarotenoid 3,4-desaturase / carotenoid biosynthetic process / oxidoreductase activity / nucleotide binding
Similarity search - Function
: / Carotenoid/retinoid oxidoreductase / Amine oxidase / Flavin containing amine oxidoreductase / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / 1-hydroxycarotenoid 3,4-desaturase
Similarity search - Component
Biological speciesNonlabens dokdonensis DSW-6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.97 Å
AuthorsAhn, J.-W. / Kim, E.-J. / Kim, S. / Kim, K.-J.
CitationJournal: Enzyme.Microb.Technol. / Year: 2015
Title: Crystal structure of 1'-OH-carotenoid 3,4-desaturase from Nonlabens dokdonensis DSW-6.
Authors: Ahn, J.W. / Kim, K.J.
History
DepositionSep 23, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
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

Downloads & links

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Assembly

Deposited unit
A: Gamma-carotene desaturase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7883
Polymers55,9101
Non-polymers8782
Water4,720262
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.369, 72.835, 68.137
Angle α, β, γ (deg.)90.00, 110.29, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Gamma-carotene desaturase


Mass: 55910.215 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nonlabens dokdonensis DSW-6 (bacteria) / Gene: DDD_2394 / Production host: Escherichia coli (E. coli)
References: UniProt: L7WC64, Oxidoreductases; Acting on the CH-CH group of donors; With unknown physiological acceptors
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 262 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.01 Å3/Da / Density % sol: 38.91 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 14% PEG3350, 0.1 M succinic acid, pH 7.0, 50 mM dimethylbenzylammonium propane sulfonate, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPAL/PLS 7A (6B, 6C1)11
SYNCHROTRONSPring-8 BL26B120.97939
Detector
TypeIDDetectorDate
ADSC QUANTUM 270r1CCDDec 14, 2011
RIGAKU JUPITER 2102CCDMar 21, 2012
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1double crystal Si(111)SINGLE WAVELENGTHMx-ray1
2double crystal Si(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.979391
ReflectionResolution: 1.97→50 Å / Num. obs: 30536 / % possible obs: 97.1 % / Redundancy: 3 % / Rmerge(I) obs: 0.067 / Χ2: 1.368 / Net I/σ(I): 11.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.97-22.10.26813250.8261,283.8
2-2.042.20.23714110.8361,291
2.04-2.082.40.22214910.8781,293.1
2.08-2.122.50.22214740.9491,296
2.12-2.172.50.2114890.871,296.2
2.17-2.222.70.19515340.9541,297.4
2.22-2.272.70.18315301.0081,297.5
2.27-2.342.80.17215121.1441,298
2.34-2.42.90.14315231.0631,298
2.4-2.482.90.13415371.0691,298
2.48-2.572.90.11915751.1571,298.4
2.57-2.6730.11115341.1481,299.3
2.67-2.83.10.09615371.2121,299
2.8-2.943.20.08715821.2611,298.9
2.94-3.133.30.06915501.2881,299.4
3.13-3.373.40.0615671.5091,299.6
3.37-3.713.50.06115732.2151,299.7
3.71-4.243.60.05515732.6671,299.9
4.24-5.353.70.03815931.7451,299.7
5.35-503.60.03216261.5311,299.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.7.0032refinement
PDB_EXTRACT3.15data extraction
HKL-2000data collection
HKL-2000data reduction
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.97→48.08 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.939 / SU B: 4.547 / SU ML: 0.127 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.192 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2235 1535 5 %RANDOM
Rwork0.1602 ---
obs0.1634 28990 96.94 %-
all-30525 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 146.26 Å2 / Biso mean: 28.437 Å2 / Biso min: 12.52 Å2
Baniso -1Baniso -2Baniso -3
1--2.23 Å20 Å2-1.48 Å2
2--1.72 Å20 Å2
3---0.83 Å2
Refinement stepCycle: LAST / Resolution: 1.97→48.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3889 0 59 262 4210
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0194060
X-RAY DIFFRACTIONr_bond_other_d0.0010.023821
X-RAY DIFFRACTIONr_angle_refined_deg1.6941.9735501
X-RAY DIFFRACTIONr_angle_other_deg0.84838835
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.45492
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.3924.725182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.92515702
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5061512
X-RAY DIFFRACTIONr_chiral_restr0.10.2598
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214540
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02935
X-RAY DIFFRACTIONr_mcbond_it2.2982.6491959
X-RAY DIFFRACTIONr_mcbond_other2.2952.6471958
X-RAY DIFFRACTIONr_mcangle_it3.5083.9642448
LS refinement shellResolution: 1.97→2.022 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 93 -
Rwork0.224 1883 -
all-1976 -
obs--84.01 %

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