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- PDB-7a1a: 2,3-Dihydroxybenzoate Decarboxylase of Aspergillus oryzae -

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Basic information

Entry
Database: PDB / ID: 7a1a
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: 1.53 Å
AuthorsHofer, G. / Keller, W.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science FundF04604 Austria
Citation
Journal: 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)82,2435
Polymers82,1542
Non-polymers893
Water12,881715
1
A: Amidohydrolase 2
B: Amidohydrolase 2
hetero molecules

A: Amidohydrolase 2
B: Amidohydrolase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,48610
Polymers164,3094
Non-polymers1776
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_667-y+1,-x+1,-z+5/21
Buried area15990 Å2
ΔGint-130 kcal/mol
Surface area42370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.894, 99.894, 129.168
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.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 715 / 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: 37.28 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.1M calcium acetate, 0.1M sodium acetate 4.5, 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 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.53→49.95 Å / Num. obs: 98740 / % possible obs: 99.64 % / Redundancy: 23.7 % / Biso Wilson estimate: 15.44 Å2 / CC1/2: 0.986 / CC star: 0.997 / Rmerge(I) obs: 0.2276 / Rpim(I) all: 0.05 / Rrim(I) all: 0.2332 / Net I/σ(I): 8.94
Reflection shellResolution: 1.53→1.584 Å / Redundancy: 24.5 % / Rmerge(I) obs: 0.8963 / Mean I/σ(I) obs: 1.82 / Num. unique obs: 9747 / CC1/2: 0.959 / CC star: 0.989 / % possible all: 99.08

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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: 1.53→49.95 Å / SU ML: 0.1772 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.8959
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2247 4845 4.92 %
Rwork0.192 93612 -
obs0.1936 98457 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.52 Å2
Refinement stepCycle: LAST / Resolution: 1.53→49.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5510 0 3 715 6228
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075703
X-RAY DIFFRACTIONf_angle_d0.84717746
X-RAY DIFFRACTIONf_chiral_restr0.051811
X-RAY DIFFRACTIONf_plane_restr0.00611005
X-RAY DIFFRACTIONf_dihedral_angle_d19.87192060
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.53-1.550.38271650.36782992X-RAY DIFFRACTION97.38
1.55-1.570.2241680.19473092X-RAY DIFFRACTION99.91
1.57-1.580.23411410.18673122X-RAY DIFFRACTION99.97
1.58-1.60.26391480.18413087X-RAY DIFFRACTION99.94
1.6-1.630.23631530.18473073X-RAY DIFFRACTION99.91
1.63-1.650.2311590.18293105X-RAY DIFFRACTION99.91
1.65-1.670.2391600.18493083X-RAY DIFFRACTION99.97
1.67-1.70.25271690.19563085X-RAY DIFFRACTION99.97
1.7-1.720.35811840.283097X-RAY DIFFRACTION99.79
1.72-1.750.32331470.25293083X-RAY DIFFRACTION99.94
1.75-1.780.23861540.20723100X-RAY DIFFRACTION100
1.78-1.810.23821760.21313103X-RAY DIFFRACTION99.94
1.81-1.850.261690.21683075X-RAY DIFFRACTION99.97
1.85-1.890.31611800.30473101X-RAY DIFFRACTION99.85
1.89-1.930.54291630.47543016X-RAY DIFFRACTION97.7
1.93-1.970.33241470.2653094X-RAY DIFFRACTION99.57
1.97-2.020.23211620.19873117X-RAY DIFFRACTION99.97
2.02-2.080.40411520.29623107X-RAY DIFFRACTION99.66
2.08-2.140.2421760.19723101X-RAY DIFFRACTION99.91
2.14-2.210.18871590.17243142X-RAY DIFFRACTION100
2.21-2.280.27741620.2593008X-RAY DIFFRACTION96.62
2.28-2.380.18011430.15653153X-RAY DIFFRACTION100
2.38-2.480.17331570.1463149X-RAY DIFFRACTION100
2.48-2.620.20661370.1493166X-RAY DIFFRACTION99.97
2.62-2.780.19981510.16423165X-RAY DIFFRACTION99.94
2.78-2.990.17611620.14953172X-RAY DIFFRACTION100
2.99-3.30.16481880.15383151X-RAY DIFFRACTION100
3.3-3.770.18271640.15923204X-RAY DIFFRACTION99.97
3.77-4.750.13141720.12883259X-RAY DIFFRACTION99.97
4.75-49.950.17041770.1453410X-RAY DIFFRACTION99.81

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