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- PDB-4g9q: Crystal structure of a 4-carboxymuconolactone decarboxylase -

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Basic information

Entry
Database: PDB / ID: 4g9q
TitleCrystal structure of a 4-carboxymuconolactone decarboxylase
Components4-carboxymuconolactone decarboxylase
KeywordsLYASE / PSI-biology / nysgrc / Structural Genomics / New York Structural Genomics Research Consortium / All alpha structure / trimer / Benzoate degradation
Function / homology
Function and homology information


peroxiredoxin activity
Similarity search - Function
: / AhpD-like / Carboxymuconolactone decarboxylase-like / AhpD-like / Carboxymuconolactone decarboxylase family / AhpD-like / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
4-carboxymuconolactone decarboxylase
Similarity search - Component
Biological speciesSinorhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.77 Å
AuthorsHickey, H.D. / Mcgillick, B.E. / Eswaramoorthy, S. / Chamala, S. / Evans, B. / Foti, R. / Gizzi, A. / Hillerich, B. / Kar, A. / Lafleur, J. ...Hickey, H.D. / Mcgillick, B.E. / Eswaramoorthy, S. / Chamala, S. / Evans, B. / Foti, R. / Gizzi, A. / Hillerich, B. / Kar, A. / Lafleur, J. / Seidel, R. / Villigas, G. / Zencheck, W. / Almo, S.C. / Swaminathan, S. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: Crystal structure of a 4-carboxymuconolactone decarboxylase
Authors: Hickey, H.D. / Mcgillick, B.E. / Eswaramoorthy, S. / Almo, S.C. / Swaminathan, S.
History
DepositionJul 24, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2012Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 4-carboxymuconolactone decarboxylase


Theoretical massNumber of molelcules
Total (without water)29,7821
Polymers29,7821
Non-polymers00
Water2,774154
1
A: 4-carboxymuconolactone decarboxylase

A: 4-carboxymuconolactone decarboxylase

A: 4-carboxymuconolactone decarboxylase


Theoretical massNumber of molelcules
Total (without water)89,3453
Polymers89,3453
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area11020 Å2
ΔGint-77 kcal/mol
Surface area26340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.345, 104.345, 63.191
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein 4-carboxymuconolactone decarboxylase


Mass: 29781.504 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Strain: 1021 / Gene: RA0292, SMa0559 / Plasmid: PET3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q930A6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 2.22 Å3/Da / Density % sol: 44.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 15% PEG3350; 0.1M Magnesium formate, sodium Iodide, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 16, 2012
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.77→50 Å / Num. all: 24950 / Num. obs: 24950 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.3 % / Biso Wilson estimate: 14.19 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 28.4
Reflection shellResolution: 1.77→1.82 Å / Redundancy: 11.3 % / Rmerge(I) obs: 0.104 / Num. unique all: 2075 / % possible all: 100

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Processing

Software
NameVersionClassification
CBASSdata collection
SHELXSphasing
REFMAC5.5.0110refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.77→50 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.937 / SU B: 1.697 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.112 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19218 1272 5.1 %RANDOM
Rwork0.17464 ---
all0.175 23678 --
obs0.17554 23678 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.681 Å2
Baniso -1Baniso -2Baniso -3
1--0.41 Å2-0.21 Å20 Å2
2---0.41 Å20 Å2
3---0.62 Å2
Refinement stepCycle: LAST / Resolution: 1.77→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1844 0 0 154 1998
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0221884
X-RAY DIFFRACTIONr_angle_refined_deg0.9951.9562567
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3715237
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.25623.66790
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.73615295
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6711517
X-RAY DIFFRACTIONr_chiral_restr0.0770.2285
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211468
X-RAY DIFFRACTIONr_mcbond_it0.4081.51186
X-RAY DIFFRACTIONr_mcangle_it0.83621901
X-RAY DIFFRACTIONr_scbond_it1.6943698
X-RAY DIFFRACTIONr_scangle_it2.8114.5666
LS refinement shellResolution: 1.77→1.816 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.21 97 -
Rwork0.199 1739 -
obs-1836 100 %

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