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- PDB-7bp1: Crystal structure of 2, 3-dihydroxybenzoic acid decarboxylase fro... -

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Basic information

Entry
Database: PDB / ID: 7bp1
TitleCrystal structure of 2, 3-dihydroxybenzoic acid decarboxylase from Fusarium oxysporum in complex with Catechol
Components2,3-dihydroxybenzoate decarboxylase
KeywordsBIOSYNTHETIC PROTEIN / 2 / 3-dihydroxybenzoic acid decarboxylase
Function / homology
Function and homology information


secondary metabolic process / carboxy-lyase activity / hydrolase activity / metal ion binding / 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 / Uncharacterized protein / 2,3-dihydroxybenzoate decarboxylase
Similarity search - Component
Biological speciesFusarium oxysporum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsSong, M.K. / Feng, J.H. / Liu, W.D. / Wu, Q.Q. / Zhu, D.M.
CitationJournal: Chembiochem / Year: 2020
Title: 2,3-Dihydroxybenzoic Acid Decarboxylase from Fusarium oxysporum: Crystal Structures and Substrate Recognition Mechanism.
Authors: Song, M. / Zhang, X. / Liu, W. / Feng, J. / Cui, Y. / Yao, P. / Wang, M. / Guo, R.T. / Wu, Q. / Zhu, D.
History
DepositionMar 21, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 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

Downloads & links

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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)157,5578
Polymers157,1624
Non-polymers3964
Water21,2761181
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16190 Å2
ΔGint-107 kcal/mol
Surface area42930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.020, 131.374, 141.007
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(CHAIN A AND RESID 2 THROUGH 332)
21(CHAIN B AND RESID 2 THROUGH 332)
31(CHAIN C AND RESID 2 THROUGH 332)
41(CHAIN D AND RESID 2 THROUGH 332)

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(CHAIN A AND RESID 2 THROUGH 332)A0
211(CHAIN B AND RESID 2 THROUGH 332)B0
311(CHAIN C AND RESID 2 THROUGH 332)C0
411(CHAIN D AND RESID 2 THROUGH 332)D0

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Components

#1: Protein
2,3-dihydroxybenzoate decarboxylase


Mass: 39290.387 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fusarium oxysporum (fungus) / Gene: BFJ70_g2310 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A420U2F4, UniProt: N1S495*PLUS
#2: Chemical ChemComp-CAQ / CATECHOL / 1,2-DIHYDROXYBENZENE


Mass: 110.111 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H6O2
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1181 / 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: 2.28 Å3/Da / Density % sol: 45.96 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.1 mol/L tri-potassium citrate, 20% (w/v) PEG 3350 and 10% (v/v) glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.97→25 Å / Num. obs: 102008 / % possible obs: 99.7 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 11.8
Reflection shellResolution: 1.97→2.04 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.609 / Num. unique obs: 9853 / % possible all: 98.1

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Processing

Software
NameVersionClassification
PHENIX1.17.1refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DVT

2dvt


Resolution: 1.97→24.87 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1963 5072 5.01 %
Rwork0.1655 --
obs0.167 101301 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 86.43 Å2 / Biso mean: 30.08 Å2 / Biso min: 15.74 Å2
Refinement stepCycle: final / Resolution: 1.97→24.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10784 0 43 1186 12013
Biso mean--33.26 36.74 -
Num. residues----1338
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A4024X-RAY DIFFRACTIONPOSITIONAL0
12B4024X-RAY DIFFRACTIONPOSITIONAL0
13C4024X-RAY DIFFRACTIONPOSITIONAL0
14D4024X-RAY DIFFRACTIONPOSITIONAL0
LS refinement shellResolution: 1.97→2.04 Å
RfactorNum. reflection% reflection
Rfree0.2807 --
Rwork0.2395 --
obs-9853 98 %

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