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- PDB-4di9: CRYSTAL STRUCTURE OF THE D248A mutant of 2-PYRONE-4,6-DICARBOXYLI... -

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Basic information

Entry
Database: PDB / ID: 4di9
TitleCRYSTAL STRUCTURE OF THE D248A mutant of 2-PYRONE-4,6-DICARBOXYLIC ACID HYDROLASE FROM SPHINGOMONAS PAUCIMOBILIS complexed with substrate at pH 6.5
Components2-pyrone-4,6-dicarbaxylate hydrolase
KeywordsHYDROLASE
Function / homology
Function and homology information


2-pyrone-4,6-dicarboxylate lactonase / 2-pyrone-4,6-dicarboxylate lactonase activity / 3,4-dihydroxybenzoate catabolic process / lignin catabolic process
Similarity search - Function
: / Amidohydrolase / Amidohydrolase-related / Metal-dependent hydrolases / Metal-dependent hydrolase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-0GY / ACETATE ION / 2-pyrone-4,6-dicarboxylate hydrolase
Similarity search - Component
Biological speciesSphingomonas paucimobilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.35 Å
AuthorsMalashkevich, V.N. / Toro, R. / Hobbs, M.E. / Raushel, F.M. / Almo, S.C.
CitationJournal: Biochemistry / Year: 2012
Title: Structure and Catalytic Mechanism of LigI: Insight into the Amidohydrolase Enzymes of cog3618 and Lignin Degradation.
Authors: Hobbs, M.E. / Malashkevich, V. / Williams, H.J. / Xu, C. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / Raushel, F.M.
History
DepositionJan 11, 2012Deposition site: RCSB / Processing site: RCSB
SupersessionOct 3, 2012ID: 4D9A
Revision 1.0Oct 3, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 9, 2013Group: Database references
Revision 1.2Jan 23, 2013Group: Database references
Revision 1.3Feb 20, 2013Group: Database references
Revision 1.4Feb 10, 2021Group: Database references / Derived calculations
Category: citation_author / struct_ref_seq_dif / struct_site
Item: _citation_author.identifier_ORCID / _struct_ref_seq_dif.details ..._citation_author.identifier_ORCID / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2-pyrone-4,6-dicarbaxylate hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2483
Polymers33,9871
Non-polymers2612
Water7,746430
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.552, 50.952, 73.346
Angle α, β, γ (deg.)90.00, 91.86, 90.00
Int Tables number5
Space group name H-MC121
Detailsmonomer

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Components

#1: Protein 2-pyrone-4,6-dicarbaxylate hydrolase / 2-pyrone-4 / 6-dicarboxylic acid hydrolase


Mass: 33986.762 Da / Num. of mol.: 1 / Mutation: D246A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingomonas paucimobilis (bacteria) / Strain: SYK-6 / Gene: ligI / Plasmid: BC-PSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CODON+RIL / References: UniProt: O87170
#2: Chemical ChemComp-0GY / (1E,3Z)-4-hydroxybuta-1,3-diene-1,2,4-tricarboxylic acid


Mass: 202.118 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O7
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 430 / 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: 2.02 Å3/Da / Density % sol: 39.13 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M Na-chloride, 0.1 M Bis-Tris pH 6.5, 25% peg 3350, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 23, 2010
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. obs: 56051 / % possible obs: 84 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.057 / Χ2: 1.252 / Net I/σ(I): 11.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.3-1.321.30.5547130.628121.4
1.32-1.351.50.51611240.693133.8
1.35-1.371.80.48215350.651146.6
1.37-1.42.30.43918680.644156
1.4-1.432.70.42421760.693166.1
1.43-1.462.90.37525300.722175.6
1.46-1.53.10.32229610.733189.4
1.5-1.543.70.26933120.791198.4
1.54-1.593.70.22132290.82198.4
1.59-1.643.80.18732820.852198.5
1.64-1.73.80.16232890.905198.8
1.7-1.763.70.12932810.972199
1.76-1.843.80.10333011.07199
1.84-1.943.70.07933161.123199.3
1.94-2.063.80.06533101.321199.5
2.06-2.223.70.05533571.47199.6
2.22-2.453.70.05133121.618199.8
2.45-2.83.70.05233752.221199.9
2.8-3.533.60.04333592.295199.9
3.53-503.60.03534211.989199.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 32.55 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å36.08 Å
Translation2.5 Å36.08 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.35→19.17 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.965 / WRfactor Rfree: 0.1791 / WRfactor Rwork: 0.1555 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8998 / SU B: 1.967 / SU ML: 0.036 / SU R Cruickshank DPI: 0.0596 / SU Rfree: 0.0605 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.06 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.1833 2785 5.2 %RANDOM
Rwork0.1598 ---
obs0.161 54012 90.61 %-
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 max: 47.89 Å2 / Biso mean: 16.0036 Å2 / Biso min: 6.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.35→19.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2304 0 18 430 2752
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222408
X-RAY DIFFRACTIONr_angle_refined_deg1.2611.9673289
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8825298
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.16222.982114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.61715368
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.461523
X-RAY DIFFRACTIONr_chiral_restr0.0840.2347
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0221915
X-RAY DIFFRACTIONr_mcbond_it0.683.51488
X-RAY DIFFRACTIONr_mcangle_it1.973502407
X-RAY DIFFRACTIONr_scbond_it3.8650920
X-RAY DIFFRACTIONr_scangle_it1.0274.5879
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 102 -
Rwork0.317 2056 -
all-2158 -
obs--49.48 %
Refinement TLS params.Method: refined / Origin x: 18.5811 Å / Origin y: -11.4159 Å / Origin z: 18.7965 Å
111213212223313233
T0.013 Å2-0.0073 Å20.0014 Å2-0.0085 Å20.0021 Å2--0.0145 Å2
L0.2367 °2-0.0935 °20.0806 °2-0.5052 °2-0.2676 °2--0.9369 °2
S0.0098 Å °0.0105 Å °0.0058 Å °-0.0608 Å °0.0128 Å °0.0093 Å °0.0916 Å °-0.0763 Å °-0.0227 Å °

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