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- PDB-1gp4: Anthocyanidin synthase from Arabidopsis thaliana (selenomethionin... -

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Basic information

Entry
Database: PDB / ID: 1gp4
TitleAnthocyanidin synthase from Arabidopsis thaliana (selenomethionine substituted)
ComponentsANTHOCYANIDIN SYNTHASE
KeywordsOXIDOREDUCTASE / OXYGENASE / 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 / Leucoanthocyanidin dioxygenase
Similarity search - Component
Biological speciesARABIDOPSIS THALIANA (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 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 1.2Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / 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 / _struct_conn.pdbx_leaving_atom_flag / _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: ANTHOCYANIDIN SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1213
Polymers40,7801
Non-polymers3412
Water5,188288
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.073, 72.993, 87.425
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ANTHOCYANIDIN SYNTHASE / LEUCOANTHOCYANIDIN DIOXYGENASE


Mass: 40779.617 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
#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.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 288 / 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: 2.41 Å3/Da / Density % sol: 48.6 %
Crystal growpH: 6.5
Details: 30% (W/V) PEG 2000 MONOMETHYLETHER, 50 MM MES, 100 MM SODIUM CITRATE, 200 MM AMMONIUM ACETATE, 5 MM IRON(II) SULPHATE, 10 MM POTASSIUM ALPHA-KETOGLUTARATE, 10 MM SODIUM ASCORBATE, PH 6.5, ...Details: 30% (W/V) PEG 2000 MONOMETHYLETHER, 50 MM MES, 100 MM SODIUM CITRATE, 200 MM AMMONIUM ACETATE, 5 MM IRON(II) SULPHATE, 10 MM POTASSIUM ALPHA-KETOGLUTARATE, 10 MM SODIUM ASCORBATE, 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
130 %(w/v)PEG2000 MME1reservoir
250 mMMES1reservoir
3100 mMsodium citrate1reservoir
4200 mMammonium acetate1reservoir
55 mM1reservoirFeSO4
610 mMpotassium alpha-ketoglutarate1reservoir
710 mMsodium ascorbate1reservoirpH6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.91841,0.97855,0.97885
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 15, 2000 / Details: MIRRORS
RadiationMonochromator: SI / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918411
20.978551
30.978851
ReflectionResolution: 2.1→36.5 Å / Num. obs: 23462 / % possible obs: 99.9 % / Redundancy: 5.4 % / Biso Wilson estimate: 27.3 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 9.8
Reflection shellResolution: 2.1→2.21 Å / Rmerge(I) obs: 0.251 / Mean I/σ(I) obs: 2.8 / % possible all: 100
Reflection
*PLUS
Num. measured all: 348658
Reflection shell
*PLUS
Highest resolution: 2.1 Å / % possible obs: 100 %

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→20 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1571181.72 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.233 964 4.1 %RANDOM
Rwork0.195 ---
obs0.195 23357 99.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.5 Å2 / ksol: 0.336 e/Å3
Displacement parametersBiso mean: 26.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.085 Å20 Å20 Å2
2---5.614 Å20 Å2
3---5.528 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.23 Å
Luzzati d res low-20 Å
Luzzati sigma a0.18 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2708 0 22 288 3018
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0052
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_deg1.32
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.3131.5
X-RAY DIFFRACTIONc_mcangle_it2.2022
X-RAY DIFFRACTIONc_scbond_it2.0352
X-RAY DIFFRACTIONc_scangle_it3.1732.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.245 146 3.8 %
Rwork0.192 3699 -
obs--99.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.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_deg22.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.81
LS refinement shell
*PLUS
Rfactor obs: 0.192

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