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- PDB-7wmb: Crystal structure of 2,3-dihydroxybenzoate decarboxylase mutant W... -

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Basic information

Entry
Database: PDB / ID: 7wmb
TitleCrystal structure of 2,3-dihydroxybenzoate decarboxylase mutant W23Y from Aspergillus oryzae in complex with catechol
ComponentsAmidohydrolase 2
KeywordsHYDROLASE / dihydroxybenzoate decarboxylase
Function / homology
Function and homology information


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
CATECHOL / Amidohydrolase 2
Similarity search - Component
Biological speciesAspergillus oryzae (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsFan, Y. / Xue, S.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21877110 China
CitationJournal: Appl.Microbiol.Biotechnol. / Year: 2023
Title: The catalytic mechanism of direction-dependent interactions for 2,3-dihydroxybenzoate decarboxylase
Authors: Fan, Y. / Wu, S. / Shi, J. / Li, X. / Yang, Y. / Feng, Y. / Xue, S.
History
DepositionJan 14, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Jan 3, 2024Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.country ..._audit_author.name / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Amidohydrolase 2
B: Amidohydrolase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,3116
Polymers78,0422
Non-polymers2694
Water7,746430
1
A: Amidohydrolase 2
B: Amidohydrolase 2
hetero molecules

A: Amidohydrolase 2
B: Amidohydrolase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,62212
Polymers156,0844
Non-polymers5388
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area17250 Å2
ΔGint-106 kcal/mol
Surface area42790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.711, 99.711, 129.675
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: 39020.969 Da / Num. of mol.: 2 / Mutation: W23Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus oryzae (mold) / Gene: OAory_01010140 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A1S9DW14
#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-CAQ / CATECHOL / 1,2-DIHYDROXYBENZENE


Mass: 110.111 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H6O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 430 / 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: 2.07 Å3/Da / Density % sol: 40.44 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2 M Sodium Chloride, 0.1 M Bis-Tris pH 5.5, 25% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9792 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Nov 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.19→36 Å / Num. obs: 33777 / % possible obs: 99.52 % / Redundancy: 13.1 % / Biso Wilson estimate: 27.13 Å2 / Rmerge(I) obs: 0.156 / Rrim(I) all: 0.162 / Net I/σ(I): 5.3
Reflection shellResolution: 2.19→2.27 Å / Rmerge(I) obs: 0.501 / Mean I/σ(I) obs: 4.22 / Num. unique obs: 6298 / Rrim(I) all: 0.523

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-3000721.3data reduction
HKL-3000721.3data scaling
PHENIX1.16_3549phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DVU

2dvu


Resolution: 2.2→35.25 Å / SU ML: 0.222 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.0511
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2076 1621 4.8 %
Rwork0.1592 32118 -
obs0.1616 33739 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.76 Å2
Refinement stepCycle: LAST / Resolution: 2.2→35.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5522 0 0 430 5952
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00685676
X-RAY DIFFRACTIONf_angle_d0.82427698
X-RAY DIFFRACTIONf_chiral_restr0.0479806
X-RAY DIFFRACTIONf_plane_restr0.0053996
X-RAY DIFFRACTIONf_dihedral_angle_d3.13313308
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.260.27611380.18992568X-RAY DIFFRACTION97.41
2.26-2.340.24651360.17372628X-RAY DIFFRACTION100
2.34-2.420.23161360.16742642X-RAY DIFFRACTION99.96
2.42-2.520.25321310.1672649X-RAY DIFFRACTION100
2.52-2.630.24081340.17262657X-RAY DIFFRACTION99.89
2.63-2.770.26861200.1732688X-RAY DIFFRACTION99.93
2.77-2.940.23131390.17582638X-RAY DIFFRACTION99.89
2.94-3.170.22151450.17282660X-RAY DIFFRACTION99.89
3.17-3.490.21721390.16442694X-RAY DIFFRACTION99.93
3.49-3.990.17921300.13842717X-RAY DIFFRACTION99.86
3.99-5.030.15341230.12682757X-RAY DIFFRACTION99.9
5.03-35.250.17651500.16922820X-RAY DIFFRACTION97.5

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