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- PDB-3hfs: Structure of apo anthocyanidin reductase from vitis vinifera -

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Basic information

Entry
Database: PDB / ID: 3hfs
TitleStructure of apo anthocyanidin reductase from vitis vinifera
ComponentsAnthocyanidin reductase
KeywordsOXIDOREDUCTASE / flavonoids / Rossmann fold / short chain dehydrogenase reductase
Function / homology
Function and homology information


anthocyanidin reductase [(2S)-flavan-3-ol-forming] / anthocyanidin reductase activity / racemase and epimerase activity / flavonoid biosynthetic process / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / NADP binding
Similarity search - Function
NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Anthocyanidin reductase ((2S)-flavan-3-ol-forming)
Similarity search - Component
Biological speciesVitis vinifera (wine grape)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.17 Å
AuthorsGargouri, M. / Mauge, C. / Langlois d'Estaintot, B. / Granier, T. / Manigan, C. / Gallois, B.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2009
Title: Structure and epimerase activity of anthocyanidin reductase from Vitis vinifera.
Authors: Gargouri, M. / Manigand, C. / Mauge, C. / Granier, T. / Langlois d'Estaintot, B. / Cala, O. / Pianet, I. / Bathany, K. / Chaudiere, J. / Gallois, B.
History
DepositionMay 12, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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_site
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.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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: Anthocyanidin reductase
B: Anthocyanidin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,6794
Polymers73,6092
Non-polymers712
Water00
1
A: Anthocyanidin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8402
Polymers36,8041
Non-polymers351
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Anthocyanidin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8402
Polymers36,8041
Non-polymers351
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.518, 51.012, 86.113
Angle α, β, γ (deg.)90.00, 110.31, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B

NCS domain segments:

Component-ID: 1 / Refine code: 4

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSHISHISAA9 - 929 - 92
21LYSLYSHISHISBB9 - 929 - 92
12ILEILELYSLYSAA103 - 150103 - 150
22ILEILELYSLYSBB103 - 150103 - 150
13THRTHRGLNGLNAA165 - 337165 - 337
23THRTHRGLNGLNBB165 - 337165 - 337

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Anthocyanidin reductase


Mass: 36804.285 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vitis vinifera (wine grape) / Gene: VvANR / Plasmid: pETGB-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5FB34, EC: 1.3.1.77
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 47.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.85
Details: 0.12 M MGCL2, 0.1 M BIS6TRIS PH 6.85, 21% PEG 3350, 2.5 % GLYCEROL, TEMERATURE 293K, VAPOR DIFFUSION, HANGING DROP, temperature 100K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 27, 2008 / Details: mirrors
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 3.17→80.84 Å / Num. all: 11952 / Num. obs: 11952 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rsym value: 0.089 / Net I/σ(I): 6
Reflection shellResolution: 3.17→3.34 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 2 / Rsym value: 0.389 / % possible all: 99.9

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Processing

Software
NameVersionClassification
DNAdata collection
MOLREPphasing
REFMAC5.5.0072refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2rh8

2rh8


Resolution: 3.17→79.31 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.834 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.593 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29912 576 4.8 %RANDOM
Rwork0.22141 ---
obs0.22518 11368 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.397 Å2
Baniso -1Baniso -2Baniso -3
1--2.39 Å20 Å20.9 Å2
2--0.59 Å20 Å2
3---2.43 Å2
Refinement stepCycle: LAST / Resolution: 3.17→79.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4286 0 2 0 4288
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0224366
X-RAY DIFFRACTIONr_bond_other_d00.022640
X-RAY DIFFRACTIONr_angle_refined_deg1.3091.9575972
X-RAY DIFFRACTIONr_angle_other_deg4.64236517
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2545616
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.44424.56125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.92115567
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.631156
X-RAY DIFFRACTIONr_chiral_restr0.0670.2736
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215030
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02852
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4791.53087
X-RAY DIFFRACTIONr_mcbond_other01.51259
X-RAY DIFFRACTIONr_mcangle_it0.89324861
X-RAY DIFFRACTIONr_scbond_it0.7931279
X-RAY DIFFRACTIONr_scangle_it1.4084.51111
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A866medium positional0.270.5
21A441medium positional0.370.5
31A1973medium positional0.330.5
12B866medium thermal0.322
22B441medium thermal0.32
32B1973medium thermal0.282
LS refinement shellResolution: 3.17→3.252 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 37 -
Rwork0.278 844 -
obs--99.66 %

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