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- PDB-3ip8: Crystal structure of arylmalonate decarboxylase (AMDase) from Bor... -

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Basic information

Entry
Database: PDB / ID: 3ip8
TitleCrystal structure of arylmalonate decarboxylase (AMDase) from Bordatella bronchiseptic in complex with benzylphosphonate
ComponentsArylmalonate decarboxylase
KeywordsLYASE / arylmalonate decarboxylase benzylphosphonate complex / 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
benzylphosphonic acid / Arylmalonate decarboxylase
Similarity search - Component
Biological speciesBordetella bronchiseptica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.498 Å
AuthorsOkrasa, K. / Levy, C. / Leys, D. / Micklefield, J.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2009
Title: Structure-Guided Directed Evolution of Alkenyl and Arylmalonate Decarboxylases.
Authors: Okrasa, K. / Levy, C. / Wilding, M. / Goodall, M. / Baudendistel, N. / Hauer, B. / Leys, D. / Micklefield, J.
History
DepositionAug 17, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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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)25,9992
Polymers25,8271
Non-polymers1721
Water5,278293
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.640, 65.600, 41.880
Angle α, β, γ (deg.)90.00, 110.42, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Arylmalonate decarboxylase / AMDase


Mass: 25826.512 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella bronchiseptica (bacteria) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q05115, arylmalonate decarboxylase
#2: Chemical ChemComp-B85 / benzylphosphonic acid


Mass: 172.118 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H9O3P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 293 / 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: 1.93 Å3/Da / Density % sol: 36.14 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8
Details: well solution 0.1M Tris pH 8.0 and 30% Peg 10K, Protein 10-15mg/ml in Tris pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9756 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 13, 2008 / Details: Monochromator
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9756 Å / Relative weight: 1
ReflectionResolution: 1.498→50 Å / Num. all: 63157 / Num. obs: 29865 / Observed criterion σ(F): 1 / Rmerge(I) obs: 0.061 / Net I/σ(I): 12.6

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Processing

Software
NameVersionClassification
DNAdata collection
PHENIXmodel building
PHENIX(phenix.refine)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.498→32.955 Å / SU ML: 0.18 / σ(F): 1.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1806 1511 5.06 %
Rwork0.1582 --
obs0.1594 29863 94.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 72.626 Å2 / ksol: 0.394 e/Å3
Displacement parametersBiso max: 44.54 Å2 / Biso mean: 16.151 Å2 / Biso min: 7.38 Å2
Baniso -1Baniso -2Baniso -3
1--2.991 Å2-0 Å2-1.61 Å2
2---4.294 Å2-0 Å2
3---2.556 Å2
Refinement stepCycle: LAST / Resolution: 1.498→32.955 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1671 0 11 293 1975
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091710
X-RAY DIFFRACTIONf_angle_d1.3512330
X-RAY DIFFRACTIONf_dihedral_angle_d15.551607
X-RAY DIFFRACTIONf_chiral_restr0.085279
X-RAY DIFFRACTIONf_plane_restr0.007303
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.498-1.54650.25521300.20342494X-RAY DIFFRACTION92
1.5465-1.60170.23231340.18182581X-RAY DIFFRACTION96
1.6017-1.66590.19611400.17512586X-RAY DIFFRACTION96
1.6659-1.74170.21671440.16042605X-RAY DIFFRACTION96
1.7417-1.83350.19451420.15662580X-RAY DIFFRACTION95
1.8335-1.94840.2121290.15722620X-RAY DIFFRACTION96
1.9484-2.09880.18731320.15672643X-RAY DIFFRACTION97
2.0988-2.30990.17921450.15322599X-RAY DIFFRACTION96
2.3099-2.6440.19391230.16032597X-RAY DIFFRACTION95
2.644-3.33070.16741430.1582550X-RAY DIFFRACTION93
3.3307-32.96290.14231490.14132497X-RAY DIFFRACTION90

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