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- PDB-4dia: CRYSTAL STRUCTURE OF THE D248N mutant of 2-PYRONE-4,6-DICARBOXYLI... -

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Basic information

Entry
Database: PDB / ID: 4dia
TitleCRYSTAL STRUCTURE OF THE D248N mutant of 2-PYRONE-4,6-DICARBOXYLIC ACID HYDROLASE FROM SPHINGOMONAS PAUCIMOBILIS complexed with substrate at pH 4.6
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
2-pyrone-4,6-dicarboxylate hydrolase
Similarity search - Component
Biological speciesSphingomonas paucimobilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 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: 4D9D
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 / Category: citation_author / struct_ref_seq_dif
Item: _citation_author.identifier_ORCID / _struct_ref_seq_dif.details
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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)34,0301
Polymers34,0301
Non-polymers00
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.269, 54.058, 96.316
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsmonomer

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Components

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


Mass: 34029.785 Da / Num. of mol.: 1 / Mutation: D246N
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / 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 Å3/Da / Density % sol: 38.48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 30% peg4000, 0.1 M Na-acetate pH 4.6, 0.2 M ammonium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 29, 2010
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.94→50 Å / Num. obs: 20448 / % possible obs: 98.1 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.093 / Χ2: 1.594 / Net I/σ(I): 8.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.94-1.9760.6489851.064198
1.97-2.016.60.58810060.984197.8
2.01-2.056.80.51710071.072199.9
2.05-2.096.90.48610341.1181100
2.09-2.1470.43910221.1521100
2.14-2.1870.36510231.1151100
2.18-2.247.10.31110181.1981100
2.24-2.37.10.27710481.271100
2.3-2.3770.24110241.2911100
2.37-2.447.10.22910341.3011100
2.44-2.5370.17710131.5161100
2.53-2.6370.15410421.5341100
2.63-2.7570.13710461.6891100
2.75-2.970.11310411.7561100
2.9-3.086.90.09510441.9171100
3.08-3.326.90.0810492.1731100
3.32-3.656.80.07110462.6691100
3.65-4.185.60.0618583.052179.4
4.18-5.266.40.0479512.425187.6
5.26-506.30.03911572.08199.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 42.82 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å48.16 Å
Translation2.5 Å48.16 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: 2→19.23 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.942 / WRfactor Rfree: 0.2074 / WRfactor Rwork: 0.167 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8459 / SU B: 8.431 / SU ML: 0.117 / SU R Cruickshank DPI: 0.2006 / SU Rfree: 0.1711 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.201 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2269 950 5.1 %RANDOM
Rwork0.1804 ---
obs0.1828 18573 97.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 87.44 Å2 / Biso mean: 35.4497 Å2 / Biso min: 19.19 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2→19.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2240 0 0 122 2362
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192328
X-RAY DIFFRACTIONr_angle_refined_deg1.3811.9593180
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9225290
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.923.182110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.02115357
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1371521
X-RAY DIFFRACTIONr_chiral_restr0.090.2337
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0221840
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 58 -
Rwork0.229 1159 -
all-1217 -
obs--99.35 %
Refinement TLS params.Method: refined / Origin x: 12.5703 Å / Origin y: -1.099 Å / Origin z: -13.3149 Å
111213212223313233
T0.0483 Å20.0387 Å20.0006 Å2-0.0533 Å20.0168 Å2--0.0471 Å2
L0.5317 °20.1066 °2-0.5118 °2-0.9602 °2-0.4556 °2--1.8542 °2
S-0.008 Å °0.0476 Å °0.0036 Å °0.0634 Å °0.0871 Å °0.0149 Å °-0.2375 Å °-0.2618 Å °-0.0792 Å °

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