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- PDB-3ixl: Crystal structure of the Gly74Cys-Cys188Ser mutant of arylmalonat... -

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Basic information

Entry
Database: PDB / ID: 3ixl
TitleCrystal structure of the Gly74Cys-Cys188Ser mutant of arylmalonate decarboxylase in the liganded form
ComponentsArylmalonate decarboxylase
KeywordsLYASE / enantioselective decarboxylation / Decarboxylase
Function / homology
Function and homology information


arylmalonate decarboxylase / arylmalonate decarboxylase activity
Similarity search - Function
Maleate isomerase/Arylmalonate decarboxylase / Arylmalonate decarboxylase / Rossmann fold - #12500 / : / Ribulose-phosphate binding barrel / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2-PHENYLACETIC ACID / Arylmalonate decarboxylase
Similarity search - Component
Biological speciesBordetella bronchiseptica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsNakasako, M. / Obata, R.
Citation
Journal: Biochemistry / Year: 2010
Title: Structural Basis for Inverting the Enantioselectivity of Arylmalonate Decarboxylase Revealed by the Structural Analysis of the Gly74Cys/Cys188Ser Mutant in the Liganded Form
Authors: Obata, R. / Nakasako, M.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2008
Title: Crystallization and preliminary X-ray diffraction experiments of arylmalonate decarboxylase from Alcaligenes bronchisepticus
Authors: Nakasako, M. / Obata, R. / Okubo, R. / Nakayama, S. / Miyamoto, K. / Ohta, H.
History
DepositionSep 4, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Arylmalonate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1864
Polymers24,8621
Non-polymers3243
Water4,468248
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.392, 63.353, 82.413
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221
Components on special symmetry positions
IDModelComponents
11A-1067-

HOH

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Components

#1: Protein Arylmalonate decarboxylase / AMDase


Mass: 24861.502 Da / Num. of mol.: 1 / Mutation: G74C, C188S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella bronchiseptica (bacteria) / Strain: KU1201 / Plasmid: pAMD101 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha-MCR / References: UniProt: Q05115, arylmalonate decarboxylase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PAC / 2-PHENYLACETIC ACID


Mass: 136.148 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H8O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.02 Å3/Da / Density % sol: 38.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 1.2M ammonium sulfate, 15%(w/v) PEG 5000, 10mM alpha-bromophenylacetate, 1%(v/v) dioxan, 70mM HEPES, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 25, 2008 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→100 Å / Num. obs: 35026 / % possible obs: 98.8 % / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.054 / Num. measured all: 370811
Reflection shellResolution: 1.45→1.48 Å / Rmerge(I) obs: 0.246 / Mean I/σ(I) obs: 5.14 / % possible all: 70.8

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Processing

Software
NameVersionClassification
AMoREphasing
REFMAC5.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3DTV

3dtv


Resolution: 1.45→20 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.945 / SU B: 0.959 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R: 0.071 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19347 1756 5 %RANDOM
Rwork0.17072 ---
obs0.17185 33171 95.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.309 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20 Å20 Å2
2---0.3 Å20 Å2
3---0.48 Å2
Refinement stepCycle: LAST / Resolution: 1.45→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1703 0 21 248 1972
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0221750
X-RAY DIFFRACTIONr_angle_refined_deg1.2982.0082382
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5375234
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.4612260
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.84315259
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5261517
X-RAY DIFFRACTIONr_chiral_restr0.0840.2284
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021313
X-RAY DIFFRACTIONr_nbd_refined0.1950.2867
X-RAY DIFFRACTIONr_nbtor_refined0.3050.21227
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0840.2174
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1540.256
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1040.251
X-RAY DIFFRACTIONr_mcbond_it0.6681.51189
X-RAY DIFFRACTIONr_mcangle_it1.09221857
X-RAY DIFFRACTIONr_scbond_it1.8133619
X-RAY DIFFRACTIONr_scangle_it2.9344.5525
LS refinement shellResolution: 1.45→1.487 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 90 -
Rwork0.207 1866 -
obs--73.78 %

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