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- PDB-1gp5: Anthocyanidin synthase from Arabidopsis thaliana complexed with t... -

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Basic information

Entry
Database: PDB / ID: 1gp5
TitleAnthocyanidin synthase from Arabidopsis thaliana complexed with trans-dihydroquercetin
ComponentsLEUCOANTHOCYANIDIN DIOXYGENASE
KeywordsOXIDOREDUCTASE / DIOXYGENASE / 2-OXOGLUTARATE DEPENDENT DIOXYGENASE / FLAVONOID BIOSYNTHESIS
Function / homology
Function and homology information


anthocyanidin synthase / proanthocyanidin biosynthetic process / leucocyanidin oxygenase activity / anthocyanin-containing compound biosynthetic process / response to jasmonic acid / vacuole organization / L-ascorbic acid binding / response to wounding / metal ion binding
Similarity search - Function
: / B-lactam Antibiotic, Isopenicillin N Synthase; Chain / Non-haem dioxygenase N-terminal domain / non-haem dioxygenase in morphine synthesis N-terminal / Isopenicillin N synthase-like, Fe(2+) 2OG dioxygenase domain / 2OG-Fe(II) oxygenase superfamily / Isopenicillin N synthase-like superfamily / Oxoglutarate/iron-dependent dioxygenase / Fe(2+) 2-oxoglutarate dioxygenase domain profile. / Jelly Rolls ...: / B-lactam Antibiotic, Isopenicillin N Synthase; Chain / Non-haem dioxygenase N-terminal domain / non-haem dioxygenase in morphine synthesis N-terminal / Isopenicillin N synthase-like, Fe(2+) 2OG dioxygenase domain / 2OG-Fe(II) oxygenase superfamily / Isopenicillin N synthase-like superfamily / Oxoglutarate/iron-dependent dioxygenase / Fe(2+) 2-oxoglutarate dioxygenase domain profile. / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
2-OXOGLUTARIC ACID / Chem-DH2 / Chem-DQH / : / Leucoanthocyanidin dioxygenase
Similarity search - Component
Biological speciesARABIDOPSIS THALIANA (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsWilmouth, R.C. / Turnbull, J.J. / Welford, R.W.D. / Clifton, I.J. / Prescott, A.G. / Schofield, C.J.
Citation
Journal: Structure / Year: 2002
Title: Structure and Mechanism of Anthocyanidin Synthase from Arabidopsis Thaliana.
Authors: Wilmouth, R.C. / Turnbull, J.J. / Welford, R.W.D. / Clifton, I.J. / Prescott, A.G. / Schofield, C.J.
#1: Journal: Chem. Commun. / Year: 2000
Title: Are Anthocyanidins the Immediate Products of Anthocyanidin Synthase?
Authors: Turnbull, J.J. / Sobey, W.J. / Aplin, R.T. / Hassan, A. / Firmin, J.L. / Schofield, C.J. / Prescott, A.G.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Purification, Crystallization and Preliminary X-Ray Diffraction of Anthocyanidin Synthase from Arabidopsis Thaliana
Authors: Turnbull, J.J. / Prescott, A.G. / Schofield, C.J. / Wilmouth, R.C.
#3: Journal: Plant J. / Year: 1999
Title: Direct Evidence for Anthocyanidin Synthase as a 2-Oxoglutarate-Dependent Oxygenase: Molecular Cloning and Functional Expression of Cdna from a Red Forma of Perilla Frutescens
Authors: Saito, K. / Kobayashi, M. / Gong, Z. / Tanaka, Y. / Yamazaki, M.
History
DepositionOct 30, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 21, 2002Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2013Group: Database references / Derived calculations ...Database references / Derived calculations / Refinement description / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_conn.ptnr2_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

Downloads & links

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Assembly

Deposited unit
A: LEUCOANTHOCYANIDIN DIOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6527
Polymers40,4511
Non-polymers1,2016
Water3,783210
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.033, 74.362, 88.109
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein LEUCOANTHOCYANIDIN DIOXYGENASE / ANTHOCYANIDIN SYNTHASE


Mass: 40451.352 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARABIDOPSIS THALIANA (thale cress) / Plasmid: PET-24A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q96323, EC: 1.14.11.19

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Non-polymers , 6 types, 216 molecules

#2: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical ChemComp-DQH / (2R,3R)-2-(3,4-DIHYDROXYPHENYL)-3,5,7-TRIHYDROXY-2,3-DIHYDRO-4H-CHROMEN-4-ONE / (2R,3R)-TRANS-DIHYDROQUERCETIN


Mass: 304.252 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H12O7
#5: Chemical ChemComp-DH2 / (2S,3S)-2-(3,4-DIHYDROXYPHENYL)-3,5,7-TRIHYDROXY-2,3-DIHYDRO-4H-CHROMEN-4-ONE / (2S,3S)-TRANS-DIHYDROQUERCETIN


Mass: 304.252 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H12O7
#6: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / 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: 2.52 Å3/Da / Density % sol: 50.7 %
Crystal growpH: 6.5
Details: 18% (W/V) PEG 2000 MONOMETHYLETHER, 50 MM MES,200 MM AMMONIUM ACETATE, 2 MM IRON(II) SULPHATE, 10 MM POTASSIUM ALPHA-KETOGLUTARATE, 10 MM SODIUM ASCORBATE, 10 MM DIHYDROQUERCETIN (IN MEOH TO ...Details: 18% (W/V) PEG 2000 MONOMETHYLETHER, 50 MM MES,200 MM AMMONIUM ACETATE, 2 MM IRON(II) SULPHATE, 10 MM POTASSIUM ALPHA-KETOGLUTARATE, 10 MM SODIUM ASCORBATE, 10 MM DIHYDROQUERCETIN (IN MEOH TO GIVE A FINAL CONC. OF 10%(V/V) MEOH), PH 6.5, ANAEROBIC (AR ATMOSPHERE,< 0.5 PPM OXYGEN)
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: Turnbull, J.J., (2001) Acta Crystallogr.,Sect.D, D57, 425.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
118 %(w/v)PEG2000 MME1reservoir
250 mMMES1reservoir
3200 mMammonium acetate1reservoir
42 mM1reservoirFeSO4
510 mMpotassium alpha-ketoglutarate1reservoir
610 mMsodium ascorbate1reservoir
710 mMDHQ1reservoir
810 %(v/v)1reservoirMeOHpH6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 15, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 20932 / % possible obs: 98.8 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 25.9 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 13
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 3.9 / % possible all: 99.2
Reflection
*PLUS
Num. measured all: 243242
Reflection shell
*PLUS
% possible obs: 99.2 % / Rmerge(I) obs: 0.28

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GP4

1gp4


Resolution: 2.2→25 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1581903.05 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.237 876 4.2 %RANDOM
Rwork0.204 ---
obs0.204 20926 98.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.6 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 26.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.89 Å20 Å20 Å2
2--9.47 Å20 Å2
3----8.59 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2.2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2709 0 79 210 2998
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0071
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.29
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.291.5
X-RAY DIFFRACTIONc_mcangle_it2.052
X-RAY DIFFRACTIONc_scbond_it2.092
X-RAY DIFFRACTIONc_scangle_it3.052.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.278 146 4.2 %
Rwork0.234 3303 -
obs--98.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 1.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.8
LS refinement shell
*PLUS
Rfactor obs: 0.234

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