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- PDB-6jrl: Crystal structure of Drosophila alpha methyldopa-resistant protei... -

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Basic information

Entry
Database: PDB / ID: 6jrl
TitleCrystal structure of Drosophila alpha methyldopa-resistant protein/3,4-dihydroxyphenylacetaldehyde synthase
Components3,4-dihydroxyphenylacetaldehyde synthase
KeywordsOXIDOREDUCTASE / synthase
Function / homology
Function and homology information


3,4-dihydroxyphenylacetaldehyde synthase / structural constituent of cuticle / 3,4-dihydroxyphenylacetaldehyde synthase activity / chitin-based cuticle development / aromatic-L-amino-acid decarboxylase activity / cuticle development / catecholamine metabolic process / carboxylic acid metabolic process / carboxy-lyase activity / amino acid metabolic process ...3,4-dihydroxyphenylacetaldehyde synthase / structural constituent of cuticle / 3,4-dihydroxyphenylacetaldehyde synthase activity / chitin-based cuticle development / aromatic-L-amino-acid decarboxylase activity / cuticle development / catecholamine metabolic process / carboxylic acid metabolic process / carboxy-lyase activity / amino acid metabolic process / pyridoxal phosphate binding / cytoplasm
Similarity search - Function
Aromatic-L-amino-acid decarboxylase / Pyridoxal-phosphate binding site / DDC / GAD / HDC / TyrDC pyridoxal-phosphate attachment site. / Pyridoxal phosphate-dependent decarboxylase / Pyridoxal-dependent decarboxylase conserved domain / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
3,4-dihydroxyphenylacetaldehyde synthase
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsWei, S. / Vavrick, C.J. / Guan, H. / Liao, C. / Robinson, H. / Liang, J. / Wang, D. / Han, Q. / Li, J.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China31860702 China
National Natural Science Foundation of China31472186 China
CitationJournal: To Be Published
Title: Structural basis for the bifunctional mechanism of Drosophila alpha methyldopa-resistant protein/3,4-dihydroxyphenylacetaldehyde synthase
Authors: Wei, S. / Vavricka, C.J. / Guan, H. / Liao, C. / Robinson, H. / Liang, J. / Wang, D. / Han, Q. / Li, J.
History
DepositionApr 4, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3,4-dihydroxyphenylacetaldehyde synthase


Theoretical massNumber of molelcules
Total (without water)57,3201
Polymers57,3201
Non-polymers00
Water2,522140
1
A: 3,4-dihydroxyphenylacetaldehyde synthase

A: 3,4-dihydroxyphenylacetaldehyde synthase


Theoretical massNumber of molelcules
Total (without water)114,6402
Polymers114,6402
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area11190 Å2
ΔGint-95 kcal/mol
Surface area30960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.469, 117.307, 139.801
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein 3,4-dihydroxyphenylacetaldehyde synthase / DHPAA synthase / isoform A / Alpha-methyldopa hypersensitive protein


Mass: 57319.965 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: alpha methyldopa-resistant gene
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P18486, EC: 1.13.12.15
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 2.59 Å3/Da / Density % sol: 52.54 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.16M MgCl, 0.085M NaCl, pH 6.5, 25.5% w/v PEG 8000, 15% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 8, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 30527 / % possible obs: 100 % / Redundancy: 14.5 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 32.9
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.577 / Num. unique obs: 3001

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
HKL-2000data reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3K40

3k40


Resolution: 2.2→37.18 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.896 / Cross valid method: THROUGHOUT / ESU R: 0.256 / ESU R Free: 0.217 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26708 1543 5 %RANDOM
Rwork0.21778 ---
obs0.22028 29057 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 45.753 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.2→37.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3668 0 0 141 3809
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0223750
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3061.965084
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9855463
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.89723.75176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.23515628
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3891528
X-RAY DIFFRACTIONr_chiral_restr0.0950.2557
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212862
X-RAY DIFFRACTIONr_gen_planes_other
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_it4.8871.52312
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it7.24623710
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.46131438
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it9.3944.51374
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.198→2.255 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 101 -
Rwork0.286 2131 -
obs--98.76 %

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