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- PDB-6m53: Crystal structure of 2, 3-dihydroxybenzoic acid decarboxylase fro... -

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Basic information

Entry
Database: PDB / ID: 6m53
TitleCrystal structure of 2, 3-dihydroxybenzoic acid decarboxylase from Fusarium oxysporum
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
Uncharacterized protein / 2,3-dihydroxybenzoate decarboxylase
Similarity search - Component
Biological speciesFusarium oxysporum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 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 9, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2020Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / struct_conn
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
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

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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)157,69911
Polymers157,1624
Non-polymers5387
Water29,1661619
1
B: 2,3-dihydroxybenzoate decarboxylase
D: 2,3-dihydroxybenzoate decarboxylase
hetero molecules

A: 2,3-dihydroxybenzoate decarboxylase
hetero molecules

C: 2,3-dihydroxybenzoate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,69911
Polymers157,1624
Non-polymers5387
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
crystal symmetry operation4_555x+1/2,-y+1/2,-z1
Buried area16270 Å2
ΔGint-231 kcal/mol
Surface area43270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.625, 132.246, 140.593
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1619 / 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: 2.3 Å3/Da / Density % sol: 46.42 % / Mosaicity: 0.415 °
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: RAYONIX MX300HE / 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: 1.55→25 Å / Num. obs: 207763 / % possible obs: 99 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.038 / Rpim(I) all: 0.022 / Rrim(I) all: 0.044 / Χ2: 1.589 / Net I/σ(I): 16.2 / Num. measured all: 796743
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.55-1.613.70.493202880.7990.2910.5751.19997.8
1.61-1.673.70.354204160.8870.2080.4121.23998.1
1.67-1.753.70.251205760.9390.1480.2921.26198.7
1.75-1.843.70.173206950.9690.1010.2021.31499.3
1.84-1.953.80.128208160.9820.0750.1491.62199.7
1.95-2.13.80.09208880.990.0530.1052.02399.8
2.1-2.3140.06209220.9960.0340.071.812100
2.31-2.654.10.047210000.9970.0260.0541.98899.8
2.65-3.3440.034210710.9980.0190.0392.09699.5
3.34-253.90.02210910.9990.0110.0231.16297

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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: 1.55→24.77 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 21.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1993 10338 4.99 %
Rwork0.186 196845 -
obs0.1867 207183 98.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 75.99 Å2 / Biso mean: 26.3993 Å2 / Biso min: 11.13 Å2
Refinement stepCycle: final / Resolution: 1.55→24.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10746 0 22 1619 12387
Biso mean--26.39 35.7 -
Num. residues----1333
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 (%)
1.55-1.610.291410330.2597192202025398
1.61-1.670.284110100.2519193682037898
1.67-1.750.276310150.2324194922050799
1.75-1.840.24249840.2192196712065599
1.84-1.950.24689930.21521974820741100
1.95-2.10.234410210.20361980420825100
2.1-2.310.214210830.19471979720880100
2.31-2.650.21710800.18561986520945100
2.65-3.340.197210750.17391993221007100
3.34-24.770.150810440.159199482099297

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