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- PDB-7wkm: Crystal Structure of 2,3-Dihydroxybenzoate Decarboxylase Complexe... -

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Basic information

Entry
Database: PDB / ID: 7wkm
TitleCrystal Structure of 2,3-Dihydroxybenzoate Decarboxylase Complexed with Catechol
ComponentsAmidohydrolase 2
KeywordsHYDROLASE
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 hydrolases / Metal-dependent hydrolase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
CATECHOL / Amidohydrolase 2
Similarity search - Component
Biological speciesAspergillus oryzae (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 10, 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)78,3576
Polymers78,0882
Non-polymers2694
Water14,340796
1
A: Amidohydrolase 2
B: Amidohydrolase 2
hetero molecules

A: Amidohydrolase 2
B: Amidohydrolase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,71412
Polymers156,1764
Non-polymers5388
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area17310 Å2
ΔGint-105 kcal/mol
Surface area41650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.415, 99.415, 128.921
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: 39044.004 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus oryzae (mold) / 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.: 796 / 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: 2.04 Å3/Da / Density % sol: 39.7 %
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: Aug 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 60515 / % possible obs: 99.89 % / Redundancy: 23.4 % / Biso Wilson estimate: 19.27 Å2 / Rmerge(I) obs: 0.0822 / Rrim(I) all: 0.084 / Net I/σ(I): 30.5
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.6107 / Mean I/σ(I) obs: 5.17 / Num. unique obs: 6322 / Rrim(I) all: 0.6254

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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: 1.8→24.96 Å / SU ML: 0.1499 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.0824
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1775 1999 3.3 %
Rwork0.1425 58516 -
obs0.1437 60515 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.55 Å2
Refinement stepCycle: LAST / Resolution: 1.8→24.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5508 0 18 796 6322
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00615682
X-RAY DIFFRACTIONf_angle_d0.85637708
X-RAY DIFFRACTIONf_chiral_restr0.0551806
X-RAY DIFFRACTIONf_plane_restr0.006996
X-RAY DIFFRACTIONf_dihedral_angle_d3.15783306
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.840.19971390.17874098X-RAY DIFFRACTION99.91
1.84-1.890.24031420.16244120X-RAY DIFFRACTION99.98
1.89-1.950.22121400.15314117X-RAY DIFFRACTION99.95
1.95-2.010.19141420.15024135X-RAY DIFFRACTION100
2.01-2.080.17571410.14224118X-RAY DIFFRACTION99.95
2.08-2.170.1891410.14094139X-RAY DIFFRACTION99.95
2.17-2.270.21211420.14664145X-RAY DIFFRACTION99.93
2.27-2.380.18231400.14624145X-RAY DIFFRACTION99.93
2.38-2.530.17371430.14784147X-RAY DIFFRACTION99.95
2.53-2.730.23061420.15414179X-RAY DIFFRACTION100
2.73-30.18581440.154219X-RAY DIFFRACTION100
3-3.440.17551440.1414209X-RAY DIFFRACTION100
3.44-4.330.14051460.1194274X-RAY DIFFRACTION100
4.33-24.960.14991530.14034471X-RAY DIFFRACTION99.85

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