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- PDB-7a19: 2,3-Dihydroxybenzoate Decarboxylase of Aspergillus oryzae -

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Basic information

Entry
Database: PDB / ID: 7a19
Title2,3-Dihydroxybenzoate Decarboxylase of Aspergillus oryzae
ComponentsAmidohydrolase 2
KeywordsMETAL BINDING PROTEIN
Function / homology
Function and homology information


o-pyrocatechuate decarboxylase / o-pyrocatechuate decarboxylase activity / benzoate catabolic process via hydroxylation / secondary metabolic process / carboxy-lyase activity / hydrolase activity / cytosol
Similarity search - Function
2-amino-3-carboxymuconate-6-semialdehyde decarboxylase / Amidohydrolase / Amidohydrolase-related / Metal-dependent hydrolase
Similarity search - Domain/homology
Amidohydrolase 2 / 2,3-dihydroxybenzoate decarboxylase
Similarity search - Component
Biological speciesAspergillus oryzae (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.21 Å
AuthorsHofer, G. / Keller, W.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science FundF04604 Austria
CitationJournal: Chembiochem / Year: 2021
Title: Metal Ion Promiscuity and Structure of 2,3-Dihydroxybenzoic Acid Decarboxylase of Aspergillus oryzae.
Authors: Hofer, G. / Sheng, X. / Braeuer, S. / Payer, S.E. / Plasch, K. / Goessler, W. / Faber, K. / Keller, W. / Himo, F. / Glueck, S.M.
History
DepositionAug 12, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 21, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 24, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Jan 31, 2024Group: 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: Amidohydrolase 2
B: Amidohydrolase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,2275
Polymers82,1542
Non-polymers733
Water21,3841187
1
A: Amidohydrolase 2
B: Amidohydrolase 2
hetero molecules

A: Amidohydrolase 2
B: Amidohydrolase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,45510
Polymers164,3094
Non-polymers1466
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_667-y+1,-x+1,-z+5/21
Buried area15990 Å2
ΔGint-128 kcal/mol
Surface area41820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.794, 99.794, 129.177
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Amidohydrolase 2


Mass: 41077.223 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus oryzae (mold) / Gene: OAory_01010140 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1S9DW14, UniProt: P80402*PLUS
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1187 / 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: 1.96 Å3/Da / Density % sol: 37.16 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M magnesium chloride 0.1 M Na HEPES 7.5 10 % w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.21→47.64 Å / Num. obs: 165014 / % possible obs: 83.12 % / Redundancy: 4.2 % / Biso Wilson estimate: 11.53 Å2 / CC1/2: 0.986 / CC star: 0.997 / Rmerge(I) obs: 0.1235 / Net I/σ(I): 6.99
Reflection shellResolution: 1.21→1.254 Å / Rmerge(I) obs: 0.764 / Mean I/σ(I) obs: 1.07 / Num. unique obs: 2990

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Processing

Software
NameVersionClassification
DIALSdata reduction
PHENIX1.18.2_3874refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DVT

2dvt


Resolution: 1.21→47.64 Å / SU ML: 0.0986 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.9298
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1713 8097 4.94 %
Rwork0.1411 155787 -
obs0.1426 163884 83.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.11 Å2
Refinement stepCycle: LAST / Resolution: 1.21→47.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5510 0 3 1187 6700
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00745741
X-RAY DIFFRACTIONf_angle_d0.99377803
X-RAY DIFFRACTIONf_chiral_restr0.076816
X-RAY DIFFRACTIONf_plane_restr0.00761014
X-RAY DIFFRACTIONf_dihedral_angle_d19.13972087
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.21-1.220.3287110.3132261X-RAY DIFFRACTION4.21
1.22-1.240.3408450.2802837X-RAY DIFFRACTION13.55
1.24-1.250.2762820.22831754X-RAY DIFFRACTION28.26
1.25-1.270.2381230.20292413X-RAY DIFFRACTION39.08
1.27-1.290.24621610.20193122X-RAY DIFFRACTION50.6
1.29-1.30.39071990.30813733X-RAY DIFFRACTION60.46
1.3-1.320.21862350.18444415X-RAY DIFFRACTION71.28
1.32-1.340.2292700.15824838X-RAY DIFFRACTION78.73
1.34-1.360.20412720.15825226X-RAY DIFFRACTION84.34
1.36-1.390.20092920.15785545X-RAY DIFFRACTION89.18
1.39-1.410.1843030.14795833X-RAY DIFFRACTION94.3
1.41-1.430.19463100.13865959X-RAY DIFFRACTION96.67
1.43-1.460.18243200.1326038X-RAY DIFFRACTION97.31
1.46-1.490.22093120.15166191X-RAY DIFFRACTION99.65
1.49-1.520.16773310.12046209X-RAY DIFFRACTION99.98
1.52-1.560.16553190.1186219X-RAY DIFFRACTION99.92
1.56-1.60.1523230.11986206X-RAY DIFFRACTION99.95
1.6-1.640.15283160.12076220X-RAY DIFFRACTION99.85
1.64-1.690.16813150.13466250X-RAY DIFFRACTION99.88
1.69-1.750.18613240.13926219X-RAY DIFFRACTION99.94
1.75-1.810.17023420.13846214X-RAY DIFFRACTION99.97
1.81-1.880.17163370.13926252X-RAY DIFFRACTION99.95
1.88-1.970.26023000.21475857X-RAY DIFFRACTION93.5
1.97-2.070.14663300.11766275X-RAY DIFFRACTION99.98
2.07-2.20.14373260.11716270X-RAY DIFFRACTION99.97
2.2-2.370.16562740.1485658X-RAY DIFFRACTION89.27
2.37-2.610.13873050.12036332X-RAY DIFFRACTION99.83
2.61-2.980.1533110.12976380X-RAY DIFFRACTION100
2.98-3.760.15823700.13946374X-RAY DIFFRACTION99.63
3.76-47.640.1583390.13966687X-RAY DIFFRACTION99.32

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