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- PDB-7wjr: Crystal structure of dihydroxybenzoate decarboxylase mutant A63S ... -

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Basic information

Entry
Database: PDB / ID: 7wjr
TitleCrystal structure of dihydroxybenzoate decarboxylase mutant A63S from Aspergillus oryzae in complex with catechol
Components2,3-dihydroxybenzoate decarboxylase
KeywordsHYDROLASE
Function / homology
Function and homology information


o-pyrocatechuate decarboxylase / o-pyrocatechuate decarboxylase activity / benzoate catabolic process via hydroxylation / secondary metabolic process / hydrolase activity / cytosol
Similarity search - Function
2-amino-3-carboxymuconate-6-semialdehyde decarboxylase / Amidohydrolase / Amidohydrolase-related / Metal-dependent hydrolases / Metal-dependent hydrolase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
CATECHOL / 2,3-dihydroxybenzoate decarboxylase
Similarity search - Component
Biological speciesAspergillus oryzae RIB40 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsYan, F. / Song, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21877110 China
CitationJournal: To Be Published
Title: Molecular mechanism of reversible decarboxylase with efficient CO2 fixation
Authors: Yan, F. / Song, X.
History
DepositionJan 7, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2,3-dihydroxybenzoate decarboxylase
B: 2,3-dihydroxybenzoate decarboxylase
C: 2,3-dihydroxybenzoate decarboxylase
D: 2,3-dihydroxybenzoate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,77812
Polymers156,2404
Non-polymers5388
Water31,5261750
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17230 Å2
ΔGint-104 kcal/mol
Surface area41520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.932, 105.842, 181.689
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein
2,3-dihydroxybenzoate decarboxylase / 2 / 3-DHBA decarboxylase / DHBD / o-pyrocatechuate decarboxylase


Mass: 39060.004 Da / Num. of mol.: 4 / Mutation: A63S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus oryzae RIB40 (mold) / Strain: RIB 40 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P80402, o-pyrocatechuate decarboxylase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CAQ / CATECHOL / 1,2-DIHYDROXYBENZENE


Mass: 110.111 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H6O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1750 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.37 Å3/Da / Density % sol: 48.04 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2 M Sodium Chloride, 0.1 M Bis-Tris pH 5.5, 25% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9792 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: May 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.99→30 Å / Num. obs: 98188 / % possible obs: 96.8 % / Redundancy: 3.4 % / Biso Wilson estimate: 19.25 Å2 / Rmerge(I) obs: 0.1273 / Rrim(I) all: 0.1503 / Net I/σ(I): 6.35
Reflection shellResolution: 1.99→2.06 Å / Rmerge(I) obs: 0.474 / Mean I/σ(I) obs: 1.98 / Num. unique obs: 9464 / Rrim(I) all: 0.5666 / % possible all: 94.2

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-3000721.3data reduction
HKL-3000721.3data scaling
PHENIX1.16_3549phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DVU

2dvu


Resolution: 2→27.68 Å / SU ML: 0.1869 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.523
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1755 1998 2.04 %
Rwork0.1438 96147 -
obs0.1444 98145 96.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.36 Å2
Refinement stepCycle: LAST / Resolution: 2→27.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11020 0 36 1750 12806
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008811368
X-RAY DIFFRACTIONf_angle_d1.078815420
X-RAY DIFFRACTIONf_chiral_restr0.07171612
X-RAY DIFFRACTIONf_plane_restr0.00861992
X-RAY DIFFRACTIONf_dihedral_angle_d3.80756616
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.23271340.19266459X-RAY DIFFRACTION92.2
2.05-2.10.21841420.18236845X-RAY DIFFRACTION98.01
2.1-2.160.24481440.17766906X-RAY DIFFRACTION98.27
2.16-2.230.21041420.17236859X-RAY DIFFRACTION97.7
2.23-2.310.22811440.16126913X-RAY DIFFRACTION98.15
2.31-2.40.19661440.15566915X-RAY DIFFRACTION97.8
2.4-2.510.18391420.14886844X-RAY DIFFRACTION97.41
2.51-2.650.19691420.15126810X-RAY DIFFRACTION96.37
2.65-2.810.21011420.14976859X-RAY DIFFRACTION97.18
2.81-3.030.16461420.14496828X-RAY DIFFRACTION95.95
3.03-3.330.16691460.1387020X-RAY DIFFRACTION98.77
3.33-3.810.14911470.12867020X-RAY DIFFRACTION98.18
3.81-4.80.12841450.10866995X-RAY DIFFRACTION96.84
4.8-27.680.14571420.13586874X-RAY DIFFRACTION92.1

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