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- PDB-2vlb: Structure of unliganded arylmalonate decarboxylase -

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Basic information

Entry
Database: PDB / ID: 2vlb
TitleStructure of unliganded arylmalonate decarboxylase
ComponentsARYLMALONATE DECARBOXYLASE
KeywordsLYASE / PROTEIN DYNAMICS / AMDASE / DECARBOXYLASE / DECARBOXYLATION
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 / PHOSPHATE ION / Arylmalonate decarboxylase
Similarity search - Component
Biological speciesBORDETELLA BRONCHISEPTICA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.92 Å
AuthorsKuettner, E.B. / Keim, A. / Kircher, M. / Rosmus, S. / Strater, N.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Active Site Mobility Revealed by the Crystal Structure of Arylmalonate Decarboxylase from Bordetella Bronchiseptica
Authors: Kuettner, E.B. / Keim, A. / Kircher, M. / Rosmus, S. / Strater, N.
History
DepositionJan 11, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3May 29, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / struct_biol / Item: _exptl_crystal_grow.method
Revision 1.4Apr 9, 2025Group: Data collection / Database references ...Data collection / Database references / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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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)105,42123
Polymers103,8824
Non-polymers1,53819
Water8,035446
1
A: ARYLMALONATE DECARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2224
Polymers25,9711
Non-polymers2513
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: ARYLMALONATE DECARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3796
Polymers25,9711
Non-polymers4085
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: ARYLMALONATE DECARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3796
Polymers25,9711
Non-polymers4085
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: ARYLMALONATE DECARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4417
Polymers25,9711
Non-polymers4706
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)83.214, 100.988, 139.548
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: 25970.602 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: IN ALL PROTEIN CHAINS, C148 AND C188 ARE LINKED TO BETA-MERCAPTO ETHANOL
Source: (gene. exp.) BORDETELLA BRONCHISEPTICA (bacteria) / Description: ALCALIGENES BRONCHISEPTICUS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TOP10 (DH10B) (INVITROGEN) / References: UniProt: Q05115, arylmalonate decarboxylase
#2: Chemical
ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6OS
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 446 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN
Nonpolymer details1,2-ETHANEDIOL (EDO): ORIGINATES FROM CRYSTAL CRYO PROTECTION SOLUTION. BETA-MERCAPTOETHANOL (BME): ...1,2-ETHANEDIOL (EDO): ORIGINATES FROM CRYSTAL CRYO PROTECTION SOLUTION. BETA-MERCAPTOETHANOL (BME): BME IS DISULFID BONDED TO C148 AND C188 IN ALL PROTEIN CHAINS.

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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: 2.8 Å3/Da / Density % sol: 56 % / Description: NONE
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: HANGING-DROP VAPOUR-DIFFUSION SETUP WITH 0.5 ML RESERVOIR SOLUTION AT 292 K. DROPS COMPOSED OF 1 MICROLITER OF PROTEIN AND RESERVOIR SOLUTIONS EACH. PROTEIN SOLUTION CONTAINS 7-8 MG/ML ...Details: HANGING-DROP VAPOUR-DIFFUSION SETUP WITH 0.5 ML RESERVOIR SOLUTION AT 292 K. DROPS COMPOSED OF 1 MICROLITER OF PROTEIN AND RESERVOIR SOLUTIONS EACH. PROTEIN SOLUTION CONTAINS 7-8 MG/ML AMDASE, 20 MM TRIS-HCL PH 8 AND 0.5 MM BETA-MERCAPTO ETHANOL. RESERVOIR SOLUTION CONTAINS 1.4-1.8 M NA/K PHOSPHATE PH 5.8-6.4.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 15, 2006 / Details: TOROIDAL MIRROR
RadiationMonochromator: DIAMOND(111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 1.92→30 Å / Num. obs: 89247 / % possible obs: 98.9 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.3
Reflection shellResolution: 1.92→2.02 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.2 / % possible all: 93.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XDSdata scaling
Auto-Rickshawphasing
MLPHAREphasing
DMphasing
RefinementMethod to determine structure: SIRAS
Starting model: NONE

Resolution: 1.92→29.64 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.955 / SU B: 7.529 / SU ML: 0.106 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.207 1324 1.5 %RANDOM
Rwork0.178 ---
obs0.178 87922 98.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 44.86 Å2
Baniso -1Baniso -2Baniso -3
1-3.59 Å20 Å20 Å2
2---2.23 Å20 Å2
3----1.37 Å2
Refinement stepCycle: LAST / Resolution: 1.92→29.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6633 0 83 446 7162
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0226869
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.40329317
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5925911
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.56121.626246
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.31151035
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0361575
X-RAY DIFFRACTIONr_chiral_restr0.0850.21107
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025115
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2070.23079
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2970.24756
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.2345
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1880.2117
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1390.244
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.58734659
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.22947236
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.95562455
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.8592081
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.92→1.97 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.356 86
Rwork0.282 5888
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)
12.7631.29511.68098.56891.17684.2139-0.0474-0.0444-0.1925-0.04930.06230.00440.2187-0.1006-0.015-0.1985-0.0370.0432-0.17220.0459-0.217185.706341.546917.6045
22.682-0.0798-0.853.05730.19351.4488-0.1013-0.0976-0.0738-0.32920.1342-0.14030.19540.1431-0.0329-0.1192-0.07270.037-0.19180.0202-0.271486.768449.08213.7922
32.59170.1552-0.18562.99370.08061.9396-0.04820.0798-0.0715-0.31880.16510.49040.1711-0.2909-0.117-0.0975-0.1054-0.1228-0.13660.0774-0.092465.494443.008712.03
412.8077.1558-0.37167.56361.90881.2671-0.6651.4981-0.2888-1.02010.550.29460.1325-0.24670.1150.3274-0.1982-0.03160.016-0.0551-0.11776.789637.2249-0.0368
55.9380.762-1.50915.25240.44917.2962-0.2718-0.0383-0.66950.31340.20890.45191.02490.01180.06290.0638-0.00890.2272-0.19440.0006-0.0646102.268146.949-1.2008
61.3334-2.1075-1.7596.44254.182510.08290.04180.1579-0.0628-0.20080.12720.11070.52870.377-0.169-0.13770.04290.1505-0.1192-0.0181-0.0949109.545952.8245-12.1861
71.7187-2.01281.665112.2362.10998.5240.18710.4562-0.946-0.11820.34841.77031.23530.2419-0.53550.24040.10540.082-0.0425-0.06020.3732107.625140.7323-24.8662
84.0404-1.9654-0.67839.12863.284913.25430.02050.4961-0.46330.09590.3075-0.03992.18831.8565-0.3280.34640.39340.0980.1748-0.09370.0043115.815237.6284-11.6504
92.8917-3.86030.899710.0175-2.06081.5839-0.2084-0.05580.27220.23780.258-0.2769-0.1650.1217-0.0496-0.1226-0.02650.1091-0.1090.0431-0.1362108.160480.5727-8.0787
101.5888-0.1560.17612.4637-1.45284.8042-0.0440.23790.1328-0.06940.16340.47690.122-0.1082-0.1194-0.1872-0.00450.1326-0.15150.0703-0.0468100.226873.824-11.1784
112.61990.5923-0.66783.26690.08572.5093-0.03190.48120.0432-0.16380.20360.55930.0696-0.4241-0.1717-0.16790.0021-0.06290.02950.1258-0.013298.445984.2444-27.1723
123.412-3.95511.01626.905-4.06766.8873-0.3936-0.2647-0.2370.82770.78981.2722-0.5267-0.9957-0.3961-0.14430.1120.19980.02510.18520.206791.452686.497-10.67
132.43210.8705-0.91572.83820.9064.8043-0.1210.16780.245-0.68560.2961-0.1332-0.48530.109-0.1751-0.1592-0.03090.0603-0.1795-0.002-0.215293.493870.485416.0859
143.10340.70910.13924.48072.57342.2723-0.1013-0.21810.01060.07570.0520.27670.2334-0.2640.0493-0.28650.01930.0134-0.0509-0.0185-0.237878.473274.473829.3623
152.2941-0.64221.87073.6650.21435.6335-0.3008-0.02680.3624-0.05010.19070.0897-0.4241-0.23320.11-0.23160.0483-0.0472-0.1076-0.0578-0.196483.07387.378829.6894
162.9686-2.6192-1.779511.35537.27835.1694-0.3775-0.55440.35330.65220.6609-1.04370.10430.8139-0.2835-0.2372-0.0011-0.0154-0.0072-0.0878-0.108299.03778.284330.2843
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 58
2X-RAY DIFFRACTION2A59 - 104
3X-RAY DIFFRACTION3A105 - 217
4X-RAY DIFFRACTION4A218 - 240
5X-RAY DIFFRACTION5B6 - 72
6X-RAY DIFFRACTION6B73 - 121
7X-RAY DIFFRACTION7B122 - 199
8X-RAY DIFFRACTION8B200 - 238
9X-RAY DIFFRACTION9C6 - 58
10X-RAY DIFFRACTION10C59 - 123
11X-RAY DIFFRACTION11C124 - 207
12X-RAY DIFFRACTION12C208 - 240
13X-RAY DIFFRACTION13D7 - 112
14X-RAY DIFFRACTION14D113 - 151
15X-RAY DIFFRACTION15D152 - 211
16X-RAY DIFFRACTION16D212 - 240

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