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

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Basic information

Entry
Database: PDB / ID: 7bpc
TitleCrystal structure of 2, 3-dihydroxybenzoic acid decarboxylase from Fusarium oxysporum in complex with 2,5-DHBA
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
2,5-dihydroxybenzoic acid / Uncharacterized protein / 2,3-dihydroxybenzoate decarboxylase
Similarity search - Component
Biological speciesFusarium oxysporum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 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 22, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)157,7559
Polymers157,1624
Non-polymers5935
Water5,134285
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15040 Å2
ΔGint-165 kcal/mol
Surface area43530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.769, 129.739, 140.557
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 17 or resid 26 through 330))
21(chain B and (resid 2 through 17 or resid 26 through 330))
31(chain C and (resid 2 through 17 or resid 26 through 330))
41chain D

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETHISHIS(chain A and (resid 2 through 17 or resid 26 through 330))AA2 - 172 - 17
12GLYGLYPROPRO(chain A and (resid 2 through 17 or resid 26 through 330))AA26 - 33026 - 330
21METMETHISHIS(chain B and (resid 2 through 17 or resid 26 through 330))BB2 - 172 - 17
22GLYGLYPROPRO(chain B and (resid 2 through 17 or resid 26 through 330))BB26 - 33026 - 330
31METMETHISHIS(chain C and (resid 2 through 17 or resid 26 through 330))CC2 - 172 - 17
32GLYGLYPROPRO(chain C and (resid 2 through 17 or resid 26 through 330))CC26 - 33026 - 330
41METMETPROPROchain DDD2 - 3302 - 330

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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 / Plasmid: pET-21a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A420U2F4, UniProt: N1S495*PLUS
#2: Chemical ChemComp-GTQ / 2,5-dihydroxybenzoic acid


Mass: 154.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H6O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 285 / 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: 2.23 Å3/Da / Density % sol: 44.77 % / Mosaicity: 1.423 °
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8
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: BL17B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 26, 2019
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.45→25 Å / Num. obs: 53445 / % possible obs: 99.9 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.182 / Rpim(I) all: 0.069 / Rrim(I) all: 0.196 / Χ2: 1.133 / Net I/σ(I): 5.3 / Num. measured all: 409878
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.45-2.546.50.80452570.7870.3370.8730.699100
2.54-2.647.10.73152570.8490.2910.7880.772100
2.64-2.767.50.62553040.8910.2390.670.879100
2.76-2.97.80.52652920.9210.1960.5621.028100
2.9-3.097.90.40452980.9520.1480.4311.399.9
3.09-3.3280.31353030.960.1160.3351.25799.9
3.32-3.667.90.23653330.970.0880.2531.43299.9
3.66-4.187.80.17653520.9790.0670.1891.47399.6
4.18-5.267.80.12754160.9840.0490.1361.35199.8
5.26-258.30.10756330.9890.040.1151.00599.9

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DVT

2dvt


Resolution: 2.45→24.77 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 25.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2472 2591 4.97 %
Rwork0.1931 49578 -
obs0.1957 52169 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 110.41 Å2 / Biso mean: 46.5965 Å2 / Biso min: 14.3 Å2
Refinement stepCycle: final / Resolution: 2.45→24.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10668 0 50 285 11003
Biso mean--56.57 43.23 -
Num. residues----1326
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3876X-RAY DIFFRACTION11.163TORSIONAL
12B3876X-RAY DIFFRACTION11.163TORSIONAL
13C3876X-RAY DIFFRACTION11.163TORSIONAL
14D3876X-RAY DIFFRACTION11.163TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.45-2.540.29992500.236749065156100
2.54-2.640.32332540.240449055159100
2.64-2.760.2722590.23649055164100
2.76-2.90.28262490.228749145163100
2.9-3.090.28342570.2349405197100
3.09-3.320.28182380.227249485186100
3.32-3.660.27572510.210149435194100
3.66-4.180.21732780.17754919519799
4.18-5.260.1972790.1594985526499
5.26-24.770.23592760.162452135489100

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