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- PDB-3cqn: Crystal Structure of the Lipocalin domain of Violaxanthin de-epox... -

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Basic information

Entry
Database: PDB / ID: 3cqn
TitleCrystal Structure of the Lipocalin domain of Violaxanthin de-epoxidase (VDE) at pH7
ComponentsViolaxanthin de-epoxidase, chloroplast
KeywordsOXIDOREDUCTASE / Lipocalin / Enzyme / de-epoxidase / Xanthophyll cycle / non photochemical quenching / NPQ / Violaxanthin / Antheraxanthin / Zeaxanthin / pH dependant transition / Chloroplast / Membrane / Thylakoid / Transit peptide
Function / homology
Function and homology information


violaxanthin de-epoxidase / xanthophyll cycle / violaxanthin de-epoxidase activity / chlorophyll metabolic process / thylakoid lumen / chloroplast thylakoid / chloroplast thylakoid membrane / chloroplast / fatty acid metabolic process / response to heat ...violaxanthin de-epoxidase / xanthophyll cycle / violaxanthin de-epoxidase activity / chlorophyll metabolic process / thylakoid lumen / chloroplast thylakoid / chloroplast thylakoid membrane / chloroplast / fatty acid metabolic process / response to heat / protein domain specific binding / extracellular region / cytosol
Similarity search - Function
VDE lipocalin domain / Violaxanthin de-epoxidase / VDE lipocalin domain / Lipocalin family conserved site / Calycin beta-barrel core domain / Calycin / Lipocalin / Lipocalin signature. / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Violaxanthin de-epoxidase, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsArnoux, P. / Morosinotto, T. / Pignol, D.
CitationJournal: Plant Cell / Year: 2009
Title: A structural basis for the pH-dependent xanthophyll cycle in Arabidopsis thaliana.
Authors: Arnoux, P. / Morosinotto, T. / Saga, G. / Bassi, R. / Pignol, D.
History
DepositionApr 3, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 26, 2012Group: Database references
Revision 1.3Apr 3, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Violaxanthin de-epoxidase, chloroplast
B: Violaxanthin de-epoxidase, chloroplast


Theoretical massNumber of molelcules
Total (without water)42,6872
Polymers42,6872
Non-polymers00
Water2,846158
1
A: Violaxanthin de-epoxidase, chloroplast


Theoretical massNumber of molelcules
Total (without water)21,3431
Polymers21,3431
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Violaxanthin de-epoxidase, chloroplast


Theoretical massNumber of molelcules
Total (without water)21,3431
Polymers21,3431
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.634, 52.458, 54.605
Angle α, β, γ (deg.)82.520, 75.990, 74.540
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: 4 / Auth seq-ID: 83 - 250 / Label seq-ID: 7 - 174

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
Detailsbiological unit is a monomer at pH7 and a dimer at pH5. There are two biological units in the asymmetric unit at pH7 (chain A and chain B)

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Components

#1: Protein Violaxanthin de-epoxidase, chloroplast / / Protein NON-PHOTOCHEMICAL QUENCHING 1 / AtVxDE


Mass: 21343.457 Da / Num. of mol.: 2 / Fragment: Lipocalin Domain (UNP residues 191-366)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: VDE1, AVDE1, NPQ1, VXDE / Plasmid: pQE60 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q39249, EC: 1.10.99.3
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 2.36 Å3/Da / Density % sol: 43.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7
Details: PEG3350, MgNO3, Benzamidine HCl, pH 7, vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97625 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 19, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 23574 / Num. obs: 23574 / % possible obs: 96.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2 % / Biso Wilson estimate: 20.7 Å2 / Rmerge(I) obs: 0.088 / Rsym value: 0.088 / Net I/σ(I): 6.2
Reflection shellResolution: 2→2.11 Å / Redundancy: 2 % / Rmerge(I) obs: 0.344 / Mean I/σ(I) obs: 1.6 / Num. unique all: 6787 / Rsym value: 0.344 / % possible all: 97.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
DNAdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AtVDE at pH5

Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.903 / SU B: 9.915 / SU ML: 0.139 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.201 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.272 1199 5.1 %RANDOM
Rwork0.196 ---
all0.2 22270 --
obs0.2 22270 96.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.02 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å2-0.02 Å2-0.11 Å2
2--0.09 Å20.02 Å2
3---0.2 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2603 0 0 158 2761
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0222693
X-RAY DIFFRACTIONr_angle_refined_deg2.2051.9243666
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.2265323
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.22724.266143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.42115407
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.7921514
X-RAY DIFFRACTIONr_chiral_restr0.1910.2379
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022137
X-RAY DIFFRACTIONr_nbd_refined0.2570.21143
X-RAY DIFFRACTIONr_nbtor_refined0.3260.21804
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2120.2146
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2570.261
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2150.213
X-RAY DIFFRACTIONr_mcbond_it1.3891.51651
X-RAY DIFFRACTIONr_mcangle_it2.18922614
X-RAY DIFFRACTIONr_scbond_it3.34431214
X-RAY DIFFRACTIONr_scangle_it4.8384.51050
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1278 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
MEDIUM POSITIONAL0.520.5
MEDIUM THERMAL1.212
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 81 -
Rwork0.237 1634 -
all-1715 -
obs--96.08 %

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