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- PDB-3dtv: Crystal structure of arylmalonate decarboxylase -

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Basic information

Entry
Database: PDB / ID: 3dtv
TitleCrystal structure of arylmalonate decarboxylase
Components(Arylmalonate ...) x 3
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
BETA-MERCAPTOETHANOL / Arylmalonate decarboxylase
Similarity search - Component
Biological speciesBordetella bronchiseptica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.1 Å
AuthorsNakasako, M. / Obata, R. / Miyamaoto, K. / Ohta, H.
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
DepositionJul 16, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.2Mar 26, 2025Group: 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

Downloads & links

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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)100,65719
Polymers99,2504
Non-polymers1,40715
Water6,539363
1
A: Arylmalonate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2326
Polymers24,7551
Non-polymers4765
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA, PQS
2
B: Arylmalonate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2906
Polymers24,8311
Non-polymers4585
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA, PQS
3
C: Arylmalonate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1164
Polymers24,8311
Non-polymers2843
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA, PQS
4
D: Arylmalonate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0203
Polymers24,8311
Non-polymers1882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA, PQS
5
A: Arylmalonate decarboxylase
hetero molecules

B: Arylmalonate decarboxylase
hetero molecules

D: Arylmalonate decarboxylase
hetero molecules

C: Arylmalonate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,65719
Polymers99,2504
Non-polymers1,40715
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
crystal symmetry operation2_554-x+1/2,-y,z-1/21
crystal symmetry operation3_646-x+1,y-1/2,-z+3/21
Buried area10760 Å2
ΔGint-178 kcal/mol
Surface area31810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.630, 99.321, 140.263
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsTHOUGH FOUR MOLECULES OCCUPIED THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT, SMALL-ANGLE X=RAY SCATTERING MEASUREMENT OF THE ENZYME SOLUTION REVEALED THAT THE FUNCTIONAL UNIT OF THE ENZYME IN SOLUTION WAS MONOMER. THIS POINT IS REPORTED IN REFERENCE 1 OF REMARK 1

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Components

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Arylmalonate ... , 3 types, 4 molecules ABCD

#1: Protein Arylmalonate decarboxylase / AMDase


Mass: 24755.357 Da / Num. of mol.: 1
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: Protein Arylmalonate decarboxylase / AMDase


Mass: 24831.475 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella bronchiseptica (bacteria) / Plasmid: pAMD 101 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha-MCR / References: UniProt: Q05115, arylmalonate decarboxylase
#3: Protein Arylmalonate decarboxylase / AMDase


Mass: 24831.475 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella bronchiseptica (bacteria) / Plasmid: pAMD 101 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha-MCR / References: UniProt: Q05115, arylmalonate decarboxylase

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Non-polymers , 4 types, 378 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 363 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.9 Å3/Da / Density % sol: 57.58 %
Description: DATA WERE COLLECTED USING THE OSCIALLTION METHOD
Crystal growTemperature: 293 K / 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
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: 68279 / % possible obs: 99.7 % / Observed criterion σ(I): 1 / Redundancy: 7.2 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 32.4
Reflection shellResolution: 2.1→2.14 Å / Rmerge(I) obs: 0.327 / Mean I/σ(I) obs: 4.5 / % possible all: 98.2

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Processing

Software
NameVersionClassification
DMmodel building
MLPHAREphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MIR / Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.937 / SU B: 9.949 / SU ML: 0.133 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.64 / ESU R Free: 0.171
RfactorNum. reflection% reflectionSelection details
Rfree0.241 3386 5 %RANDOM
Rwork0.193 ---
obs0.195 64363 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.03 Å2
Baniso -1Baniso -2Baniso -3
1-1.63 Å20 Å20 Å2
2---0.36 Å20 Å2
3----1.27 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6628 0 78 363 7069
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0226798
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5532.0059251
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.775908
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.2421.949236
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.658151007
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8761567
X-RAY DIFFRACTIONr_chiral_restr0.1180.21100
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025059
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2350.33367
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3150.54705
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.5619
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1890.3149
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2280.552
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.96124625
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.17637201
X-RAY DIFFRACTIONr_scbond_it3.64422402
X-RAY DIFFRACTIONr_scangle_it4.85632050
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
Rfree0.278 248 -
Rwork0.225 4618 -
obs--98.66 %
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)
10.61410.22480.10070.94140.75231.0671-0.068-0.02110.0619-0.12720.08730.0958-0.15830.1447-0.01930.0328-0.0302-0.0228-0.04570.0114-0.052224.4885.206983.4397
20.46590.05260.22541.0413-0.35360.2478-0.044-0.0774-0.0496-0.10830.16110.1810.05860.0231-0.11710.0449-0.01570.0093-0.04660.057-0.021733.999541.878982.5875
30.57770.4676-0.24261.1214-0.25440.301-0.12240.17720.0433-0.0510.1680.08040.0358-0.1068-0.04560.0073-0.0242-0.01270.01150.0201-0.075736.121425.5615116.3112
40.4141-0.2854-0.02190.73220.28750.5573-0.0723-0.08910.1179-0.03990.1132-0.2306-0.01530.0447-0.0409-0.0147-0.00640.0039-0.032-0.0570.018524.723330.833156.0455
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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