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- PDB-7wkl: Crystal structure of dihydroxybenzoate decarboxylase mutant F296Y... -

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Basic information

Entry
Database: PDB / ID: 7wkl
TitleCrystal structure of dihydroxybenzoate decarboxylase mutant F296Y from Aspergillus oryzae in complex with catechol
ComponentsAmidohydrolase 2
KeywordsHYDROLASE
Function / homology
Function and homology information


secondary metabolic process / carboxy-lyase activity / 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 / Amidohydrolase 2
Similarity search - Component
Biological speciesAspergillus oryzae (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsFan, Y. / Xue, S.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21877110 China
CitationJournal: Appl.Microbiol.Biotechnol. / Year: 2023
Title: The catalytic mechanism of direction-dependent interactions for 2,3-dihydroxybenzoate decarboxylase
Authors: Fan, Y. / Wu, S. / Shi, J. / Li, X. / Yang, Y. / Feng, Y. / Xue, S.
History
DepositionJan 10, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 25, 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
Revision 1.2Jan 3, 2024Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.country ..._audit_author.name / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Amidohydrolase 2
B: Amidohydrolase 2
C: Amidohydrolase 2
D: Amidohydrolase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,16216
Polymers156,2404
Non-polymers92212
Water30,0671669
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18050 Å2
ΔGint-161 kcal/mol
Surface area41670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.282, 105.708, 181.659
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
Amidohydrolase 2


Mass: 39060.004 Da / Num. of mol.: 4 / Mutation: F296Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus oryzae (mold) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A1S9DW14
#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: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1669 / 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: 48.2 %
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: 1.87→30 Å / Num. obs: 118580 / % possible obs: 97.44 % / Redundancy: 11.5 % / Biso Wilson estimate: 19.49 Å2 / Rmerge(I) obs: 0.1774 / Rrim(I) all: 0.1855 / Net I/σ(I): 9.78
Reflection shellResolution: 1.87→1.94 Å / Rmerge(I) obs: 0.5524 / Mean I/σ(I) obs: 4.75 / Num. unique obs: 11301 / Rrim(I) all: 0.5766 / % possible all: 94.03

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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: 1.88→26.47 Å / SU ML: 0.1494 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.5844
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1775 5938 5.01 %
Rwork0.1392 112630 -
obs0.1411 118568 97.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.21 Å2
Refinement stepCycle: LAST / Resolution: 1.88→26.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11020 0 56 1669 12745
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006311384
X-RAY DIFFRACTIONf_angle_d0.813715448
X-RAY DIFFRACTIONf_chiral_restr0.05121612
X-RAY DIFFRACTIONf_plane_restr0.0061992
X-RAY DIFFRACTIONf_dihedral_angle_d3.22136616
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.88-1.90.23531770.17553451X-RAY DIFFRACTION90.75
1.9-1.920.22931810.16513634X-RAY DIFFRACTION95.28
1.92-1.950.23591710.16033664X-RAY DIFFRACTION95.47
1.95-1.970.21042110.15323590X-RAY DIFFRACTION95.55
1.97-20.21422110.15293670X-RAY DIFFRACTION96.06
2-2.020.21491710.15123658X-RAY DIFFRACTION95.7
2.02-2.050.20532020.14543655X-RAY DIFFRACTION95.78
2.05-2.080.18352130.14383633X-RAY DIFFRACTION95.65
2.08-2.120.1852070.1433655X-RAY DIFFRACTION96.72
2.12-2.150.20762000.14243662X-RAY DIFFRACTION95.62
2.15-2.190.17651900.13913678X-RAY DIFFRACTION96.72
2.19-2.230.17621850.14293691X-RAY DIFFRACTION96.49
2.23-2.270.17761850.14693698X-RAY DIFFRACTION95.95
2.27-2.320.20321760.1463721X-RAY DIFFRACTION97.6
2.32-2.370.19671960.14323756X-RAY DIFFRACTION97.51
2.37-2.420.20661990.14413766X-RAY DIFFRACTION98
2.42-2.480.18751980.13813764X-RAY DIFFRACTION98.22
2.48-2.550.18271790.14293765X-RAY DIFFRACTION98.21
2.55-2.620.19161910.14613827X-RAY DIFFRACTION98.87
2.62-2.710.19461900.14533826X-RAY DIFFRACTION98.84
2.71-2.810.19572030.14563777X-RAY DIFFRACTION98.59
2.81-2.920.19362310.14683819X-RAY DIFFRACTION99.66
2.92-3.050.16722230.13923822X-RAY DIFFRACTION99.68
3.05-3.210.17572090.13983856X-RAY DIFFRACTION99.66
3.21-3.410.17292290.13393839X-RAY DIFFRACTION99.71
3.41-3.670.14751990.1333897X-RAY DIFFRACTION99.68
3.67-4.040.15051970.11623869X-RAY DIFFRACTION99.29
4.04-4.630.12581950.11123916X-RAY DIFFRACTION99.59
4.63-5.820.14822220.12863961X-RAY DIFFRACTION99.86
5.82-26.470.19161970.16064110X-RAY DIFFRACTION98.88

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