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- PDB-3ixm: Structure of the Gly74Cys mutant of arylmalonate decarboxylase in... -

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Basic information

Entry
Database: PDB / ID: 3ixm
TitleStructure of the Gly74Cys mutant of arylmalonate decarboxylase in the sulfate ion associated form
ComponentsArylmalonate decarboxylase
KeywordsLYASE / enantioselective racemase / 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
Arylmalonate decarboxylase
Similarity search - Component
Biological speciesBordetella bronchiseptica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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_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_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

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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)24,9943
Polymers24,8011
Non-polymers1922
Water2,900161
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)100.730, 100.730, 54.165
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Arylmalonate decarboxylase / AMDase


Mass: 24801.449 Da / Num. of mol.: 1 / Mutation: G74C
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.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H2O

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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: 2.13 Å3/Da / Density % sol: 42.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 1.2M ammonium sulfate, 15%(w/v) glycerol, 0.1M HEPES, pH 6.2, 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: Apr 22, 2008 / Details: mirror
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→100 Å / Num. obs: 16054 / % possible obs: 94.2 % / Observed criterion σ(F): 1 / Rmerge(I) obs: 0.053 / Num. measured all: 174138
Reflection shellResolution: 1.9→1.93 Å / Rmerge(I) obs: 0.129 / % possible all: 100

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Processing

Software
NameVersionClassification
AMoREphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3DTV

3dtv


Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.916 / SU B: 3.484 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.17 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24462 804 5 %RANDOM
Rwork0.18002 ---
obs0.18311 15236 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.296 Å2
Baniso -1Baniso -2Baniso -3
1--0.5 Å2-0.25 Å20 Å2
2---0.5 Å20 Å2
3---0.75 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1673 0 10 161 1844
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221717
X-RAY DIFFRACTIONr_angle_refined_deg1.7181.9972341
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3475232
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.09521.86459
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.50115256
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9031517
X-RAY DIFFRACTIONr_chiral_restr0.1210.2281
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021282
X-RAY DIFFRACTIONr_nbd_refined0.2240.2834
X-RAY DIFFRACTIONr_nbtor_refined0.3080.21199
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.20.2117
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2390.263
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2890.229
X-RAY DIFFRACTIONr_mcbond_it1.0971.51175
X-RAY DIFFRACTIONr_mcangle_it1.82421836
X-RAY DIFFRACTIONr_scbond_it2.9583594
X-RAY DIFFRACTIONr_scangle_it4.7394.5505
LS refinement shellResolution: 1.902→1.951 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 65 -
Rwork0.215 1109 -
obs--100 %

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