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- PDB-3dg9: Crystal Structure of Malonate Decarboxylase from Bordatella bronc... -

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Basic information

Entry
Database: PDB / ID: 3dg9
TitleCrystal Structure of Malonate Decarboxylase from Bordatella bronchiseptica
ComponentsArylmalonate decarboxylase
KeywordsLYASE / Malonate decarboxylase AMDase / 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
PHOSPHATE ION / Arylmalonate decarboxylase
Similarity search - Component
Biological speciesBordetella bronchiseptica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.5 Å
AuthorsOkrasa, K. / Levy, C. / Baudendistel, N. / Leys, D. / Micklefield, J.
CitationJournal: Chemistry / Year: 2008
Title: Structure and Mechanism of an Unusual Malonate Decarboxylase and Related Racemases.
Authors: Okrasa, K. / Levy, C. / Hauer, B. / Baudendistel, N. / Leys, D. / Micklefield, J.
History
DepositionJun 13, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type
Revision 1.3Feb 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)25,9212
Polymers25,8271
Non-polymers951
Water5,945330
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.666, 65.849, 42.209
Angle α, β, γ (deg.)90.00, 110.82, 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) / References: UniProt: Q05115, arylmalonate decarboxylase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 330 / 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: 2.03 Å3/Da / Density % sol: 39.38 %
Crystal growMethod: vapor diffusion, sitting drop
Details: well solution 0.1M Tris pH8.0 and 30% Peg 10K, Protein 10-15mg/ml in Tris pH7.5, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1 Å
DetectorDetector: CCD / Date: Mar 13, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 30804 / % possible obs: 97.2 % / Redundancy: 3.3 % / Biso Wilson estimate: 10.42 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 8.5
Reflection shellHighest resolution: 1.5 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.292 / Mean I/σ(I) obs: 2.7

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Phasing

PhasingMethod: MIR

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
REFMACrefinement
PDB_EXTRACT3.006data extraction
XDSdata reduction
XDSdata scaling
MLPHAREphasing
RefinementResolution: 1.5→39.453 Å / Occupancy max: 1 / Occupancy min: 0.99 / SU ML: 0.17 / σ(F): 1.38 / Phase error: 18.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.188 1561 5.07 %
Rwork0.155 29214 -
obs0.157 30775 97.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.836 Å2 / ksol: 0.442 e/Å3
Displacement parametersBiso max: 46.88 Å2 / Biso mean: 11.346 Å2 / Biso min: 2.33 Å2
Baniso -1Baniso -2Baniso -3
1--2.137 Å2-0 Å2-0.507 Å2
2---1.174 Å2-0 Å2
3---0.346 Å2
Refinement stepCycle: LAST / Resolution: 1.5→39.453 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1671 0 5 330 2006
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013405
X-RAY DIFFRACTIONf_angle_d1.1476172
X-RAY DIFFRACTIONf_dihedral_angle_d12.318852
X-RAY DIFFRACTIONf_chiral_restr0.089279
X-RAY DIFFRACTIONf_plane_restr0.006525
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.5480.2621180.1862466258491
1.548-1.6040.2111330.1712647278097
1.604-1.6680.2121300.1562635276596
1.668-1.7440.2031470.1482622276997
1.744-1.8360.1851460.1492687283397
1.836-1.9510.191430.1452642278598
1.951-2.1020.191550.1422674282998
2.102-2.3130.181430.1342688283199
2.313-2.6480.1631340.1372726286099
2.648-3.3350.1711570.1462714287199
3.335-39.4670.1781550.1572713286898

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