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- PDB-3eis: Crystal Structure of Arylmalonate Decarboxylase -

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Basic information

Entry
Database: PDB / ID: 3eis
TitleCrystal Structure of Arylmalonate Decarboxylase
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
Arylmalonate decarboxylase
Similarity search - Component
Biological speciesBordetella bronchiseptica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.1 Å
AuthorsNakasako, M. / Obata, R. / Miyamoto, K. / Ohta, H.
CitationJournal: To be Published
Title: Structural Basis of the Enantioselective Decarboxylation by Arylmalonate Decarboxylase
Authors: Nakasako, M. / Obata, R. / Miyamoto, K. / Ohta, H.
History
DepositionSep 17, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_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
B: Arylmalonate decarboxylase
C: Arylmalonate decarboxylase
D: Arylmalonate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,47913
Polymers99,6304
Non-polymers8499
Water7,314406
1
A: Arylmalonate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1884
Polymers24,9081
Non-polymers2803
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Arylmalonate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0963
Polymers24,9081
Non-polymers1882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Arylmalonate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1003
Polymers24,9081
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Arylmalonate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0963
Polymers24,9081
Non-polymers1882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
B: Arylmalonate decarboxylase
hetero molecules

C: Arylmalonate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1956
Polymers49,8152
Non-polymers3804
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_656-x+1,y+1/2,-z+3/21
Buried area2310 Å2
ΔGint-41 kcal/mol
Surface area19370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.508, 99.395, 139.981
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Arylmalonate decarboxylase / AMDase


Mass: 24907.592 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella bronchiseptica (bacteria) / Strain: KU1201 / Plasmid: PAMD 101 / 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.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 406 / 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: 2.92 Å3/Da / Density % sol: 57.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.5M AMMONIUM SULFATE, 12% (W/V) GLYCEROL, 0.1M TRIS-HCL, pH 8.00, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 15, 2007 / Details: TOROIDAL MIRROR
RadiationMonochromator: DOUBLE CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 68612 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.2 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 30.1 / Num. measured all: 493346
Reflection shellResolution: 2.1→2.14 Å / Rmerge(I) obs: 0.393 / Mean I/σ(I) obs: 3.2 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
MLPHAREphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MIR / Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.926 / SU B: 8.639 / SU ML: 0.119 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.186 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24 3453 5 %RANDOM
Rwork0.195 ---
obs0.197 65102 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.629 Å2
Baniso -1Baniso -2Baniso -3
1-2.2 Å20 Å20 Å2
2---1.12 Å20 Å2
3----1.08 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6757 0 49 406 7212
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0226903
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9752.0069389
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5355925
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.56421.933238
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.884151020
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5481568
X-RAY DIFFRACTIONr_chiral_restr0.1720.21120
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025148
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2510.33330
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.320.54778
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2130.5686
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2240.3137
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2930.560
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.73424721
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.65437335
X-RAY DIFFRACTIONr_scbond_it2.14222426
X-RAY DIFFRACTIONr_scangle_it3.12732054
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 222 -
Rwork0.207 4741 -
obs--99.96 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.17670.76640.34792.08191.35151.96910.04260.03540.14180.01580.0960.2341-0.07020.0794-0.1387-0.025-0.0317-0.0611-0.11090.0242-0.02924.23055.651283.8727
21.17980.6268-0.05031.0128-0.18740.6831-0.10010.0632-0.1053-0.23960.10830.05120.1787-0.0328-0.00820.0284-0.0370.0296-0.07740.0465-0.044434.841442.146383.0535
30.5378-0.0827-0.02821.3515-0.59980.7628-0.16710.14050.06810.09240.20610.054-0.0066-0.1303-0.039-0.045-0.03220.00550.01460.0225-0.094136.323826.1917116.819
40.78970.07490.14061.79111.05721.6638-0.0894-0.10620.11820.06120.1512-0.42940.1480.0955-0.0617-0.08910.01220.005-0.0571-0.0710.028424.561130.7548156.2553
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 240
2X-RAY DIFFRACTION2B5 - 238
3X-RAY DIFFRACTION3C7 - 240
4X-RAY DIFFRACTION4D5 - 240

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