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

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Basic information

Entry
Database: PDB / ID: 3cqr
TitleCrystal Structure of the Lipocalin domain of Violaxanthin de-epoxidase (VDE) at pH5
ComponentsViolaxanthin de-epoxidase, chloroplast
KeywordsOXIDOREDUCTASE / Lipocalin / Enzyme / de-epoxidase / Xanthophyll cycle / non photochemical quenching / NPQ / Violaxanthin / Antheraxanthin / Zeaxanthin / 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
GADOLINIUM ATOM / Violaxanthin de-epoxidase, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / 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 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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: Violaxanthin de-epoxidase, chloroplast
B: Violaxanthin de-epoxidase, chloroplast
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1595
Polymers42,6872
Non-polymers4723
Water3,207178
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2770 Å2
ΔGint-28.6 kcal/mol
Surface area17960 Å2
MethodPISA
2
A: Violaxanthin de-epoxidase, chloroplast
hetero molecules

B: Violaxanthin de-epoxidase, chloroplast
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1595
Polymers42,6872
Non-polymers4723
Water362
TypeNameSymmetry operationNumber
crystal symmetry operation5_555-x+1/2,y,-z+3/41
identity operation1_555x,y,z1
Buried area4120 Å2
ΔGint-33.6 kcal/mol
Surface area16610 Å2
MethodPISA
3
A: Violaxanthin de-epoxidase, chloroplast
B: Violaxanthin de-epoxidase, chloroplast
hetero molecules

A: Violaxanthin de-epoxidase, chloroplast
B: Violaxanthin de-epoxidase, chloroplast
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,31710
Polymers85,3744
Non-polymers9446
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555-x+1/2,y,-z+3/41
Buried area15760 Å2
ΔGint-118.8 kcal/mol
Surface area25700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.297, 122.297, 158.337
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-437-

HOH

21B-496-

HOH

31B-513-

HOH

Detailsbiological unit is a monomer at pH7 and a dimer at pH5. There is one biological unit in the asymmetric unit at pH5 (chains A, 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: Chemical ChemComp-GD / GADOLINIUM ATOM


Mass: 157.250 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Gd
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.77 Å3/Da / Density % sol: 67.38 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5
Details: Sodium Acetate trihydrate pH5, Ammonium Sulfate 2.0M, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.97972 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 10, 2007
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97972 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 39345 / Num. obs: 39345 / % possible obs: 98.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.9 % / Biso Wilson estimate: 29.3 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 5.6
Reflection shellResolution: 2→2.11 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.267 / Mean I/σ(I) obs: 1.3 / Num. unique all: 5796 / Rsym value: 0.267 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3.005data extraction
DNAdata collection
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
RefinementResolution: 2→29.2 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.923 / SU B: 2.965 / SU ML: 0.085 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.144 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.234 1996 5 %RANDOM
Rwork0.208 ---
all0.209 39865 --
obs0.209 37869 98.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.205 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å20 Å2
2---0.09 Å20 Å2
3---0.18 Å2
Refinement stepCycle: LAST / Resolution: 2→29.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2773 0 3 178 2954
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222889
X-RAY DIFFRACTIONr_angle_refined_deg1.7971.9243941
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.6095345
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.54424.304158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.88415433
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8711515
X-RAY DIFFRACTIONr_chiral_restr0.180.2402
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022323
X-RAY DIFFRACTIONr_nbd_refined0.2140.21151
X-RAY DIFFRACTIONr_nbtor_refined0.3140.21928
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2180
X-RAY DIFFRACTIONr_metal_ion_refined0.0260.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2360.2126
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2610.225
X-RAY DIFFRACTIONr_mcbond_it1.3281.51758
X-RAY DIFFRACTIONr_mcangle_it2.21522791
X-RAY DIFFRACTIONr_scbond_it3.41231317
X-RAY DIFFRACTIONr_scangle_it5.1524.51150
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 135 -
Rwork0.229 2645 -
all-2780 -
obs--99.78 %

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