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- PDB-4di8: CRYSTAL STRUCTURE OF THE D248A mutant of 2-PYRONE-4,6-DICARBOXYLI... -

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Basic information

Entry
Database: PDB / ID: 4di8
TitleCRYSTAL STRUCTURE OF THE D248A mutant of 2-PYRONE-4,6-DICARBOXYLIC ACID HYDROLASE FROM SPHINGOMONAS PAUCIMOBILIS complexed with substrate at pH 8.5
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 / 2-oxo-2H-pyran-4,6-dicarboxylic acid / ACETATE ION / 2-pyrone-4,6-dicarboxylate hydrolase
Similarity search - Component
Biological speciesSphingomonas paucimobilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.81 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: 4D95
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 / pdbx_struct_conn_angle ...citation_author / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _citation_author.identifier_ORCID / _pdbx_struct_conn_angle.ptnr1_auth_seq_id ..._citation_author.identifier_ORCID / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_seq_id / _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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)68,91310
Polymers67,9742
Non-polymers9398
Water12,160675
1
A: 2-pyrone-4,6-dicarbaxylate hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4324
Polymers33,9871
Non-polymers4453
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 2-pyrone-4,6-dicarbaxylate hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4816
Polymers33,9871
Non-polymers4945
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.348, 52.131, 76.539
Angle α, β, γ (deg.)90.00, 93.73, 90.00
Int Tables number4
Space group name H-MP1211
Detailsmonomer

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 33986.762 Da / Num. of mol.: 2 / 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

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Non-polymers , 5 types, 683 molecules

#2: Chemical ChemComp-0GZ / 2-oxo-2H-pyran-4,6-dicarboxylic acid


Mass: 184.103 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H4O6
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-0GY / (1E,3Z)-4-hydroxybuta-1,3-diene-1,2,4-tricarboxylic acid


Mass: 202.118 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6O7
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 675 / 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: 2.17 Å3/Da / Density % sol: 43.44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 30% peg 4000, 0.1 M Tris HCl pH 8.5, 0.2 M Na-acetate, VAPOR DIFFUSION, SITTING 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: Sep 23, 2010
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.81→50 Å / Num. obs: 53516 / % possible obs: 99.8 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.073 / Χ2: 1.509 / Net I/σ(I): 10.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.81-1.843.50.33225920.953198.7
1.84-1.873.60.28926821.051199.8
1.87-1.913.60.25726411.0841100
1.91-1.953.60.22826651.1581100
1.95-1.993.60.18526631.18199.8
1.99-2.043.60.17326401.202199.7
2.04-2.093.60.15426661.269199.9
2.09-2.153.60.1426771.36199.9
2.15-2.213.60.11726611.373199.6
2.21-2.283.70.11326661.433199.9
2.28-2.363.70.10526741.497199.9
2.36-2.463.70.09426791.525199.6
2.46-2.573.70.08226721.545199.8
2.57-2.73.70.07626601.637199.7
2.7-2.873.70.0726861.7011100
2.87-3.093.70.06226831.796199.8
3.09-3.413.60.0626872.356199.8
3.41-3.93.60.05127022.4281100
3.9-4.913.50.04127271.893199.9
4.91-503.70.0427931.609199.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 45.19 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å43.06 Å
Translation2.5 Å43.06 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: 1.81→19.8 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.957 / WRfactor Rfree: 0.1756 / WRfactor Rwork: 0.1489 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.864 / SU B: 5.003 / SU ML: 0.071 / SU R Cruickshank DPI: 0.1242 / SU Rfree: 0.1123 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.124 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES: WITH TLS ADDED. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.1868 2718 5.1 %RANDOM
Rwork0.1566 ---
obs0.1582 53460 99.8 %-
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 max: 57.5 Å2 / Biso mean: 17.2451 Å2 / Biso min: 6.36 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.81→19.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4620 0 64 675 5359
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0224868
X-RAY DIFFRACTIONr_angle_refined_deg1.2311.9746648
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8025600
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.43423.114228
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.1715748
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2431544
X-RAY DIFFRACTIONr_chiral_restr0.0860.2695
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0223894
X-RAY DIFFRACTIONr_mcbond_it0.6813.52989
X-RAY DIFFRACTIONr_mcangle_it2.278504836
X-RAY DIFFRACTIONr_scbond_it4.844501879
X-RAY DIFFRACTIONr_scangle_it0.8854.51805
LS refinement shellResolution: 1.81→1.857 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 187 -
Rwork0.213 3692 -
all-3879 -
obs--99.23 %
Refinement TLS params.

T12: 0.0012 Å2 / 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)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8560.01140.07640.64590.00010.6230.01250.0513-0.0133-0.0056-0.03640.0874-0.0169-0.09510.02390.00920.0050.0222-0.01210.018519.328111.27790.0848
20.7422-0.1104-0.0160.658-0.06490.42350.0230.0216-0.0095-0.0587-0.03550.06860.0005-0.08330.01250.0173-0.00170.021-0.00890.009921.8515-13.4698-37.7757
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 295
2X-RAY DIFFRACTION2B2 - 295

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