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- PDB-6p3k: Crystal structure of LigU(C100S) -

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Basic information

Entry
Database: PDB / ID: 6p3k
TitleCrystal structure of LigU(C100S)
Components(4E)-oxalomesaconate Delta-isomerase
KeywordsISOMERASE / Lignin degradation / protocatechuate 4 / 5-cleavage pathway / PrpF superfamily / (4E)-oxalomesaconate isomerase mechanism
Function / homology
Function and homology information


Isomerases; Intramolecular oxidoreductases; Transposing C=C bonds / lignin catabolic process / isomerase activity
Similarity search - Function
: / PrpF protein / PrpF protein / Diaminopimelate Epimerase; Chain A, domain 1 / Diaminopimelate Epimerase; Chain A, domain 1 / Roll / Alpha Beta
Similarity search - Domain/homology
(4E)-oxalomesaconate Delta-isomerase
Similarity search - Component
Biological speciesNovosphingobium sp.
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.88 Å
AuthorsCory, S.A. / Hogancamp, T.N. / Raushel, F.M. / Barondeau, D.P.
Funding support United States, 1items
OrganizationGrant numberCountry
Robert A. Welch FoundationA-840 United States
CitationJournal: Biochemistry / Year: 2019
Title: Structure and Chemical Reaction Mechanism of LigU, an Enzyme That Catalyzes an Allylic Isomerization in the Bacterial Degradation of Lignin.
Authors: Hogancamp, T.N. / Cory, S.A. / Barondeau, D.P. / Raushel, F.M.
History
DepositionMay 23, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Aug 28, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: (4E)-oxalomesaconate Delta-isomerase
B: (4E)-oxalomesaconate Delta-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,1018
Polymers75,8892
Non-polymers2136
Water6,990388
1
A: (4E)-oxalomesaconate Delta-isomerase
hetero molecules

A: (4E)-oxalomesaconate Delta-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,1018
Polymers75,8892
Non-polymers2136
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_456-x-1,y,-z+11
Buried area3680 Å2
ΔGint-78 kcal/mol
Surface area25610 Å2
MethodPISA
2
B: (4E)-oxalomesaconate Delta-isomerase
hetero molecules

B: (4E)-oxalomesaconate Delta-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,1018
Polymers75,8892
Non-polymers2136
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area3850 Å2
ΔGint-77 kcal/mol
Surface area25730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.417, 142.334, 60.350
Angle α, β, γ (deg.)90.000, 111.720, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-516-

HOH

21A-626-

HOH

31A-633-

HOH

41A-663-

HOH

51B-620-

HOH

61B-660-

HOH

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Components

#1: Protein (4E)-oxalomesaconate Delta-isomerase / OMA isomerase / 1 / 3-allylic isomerase LigU


Mass: 37944.250 Da / Num. of mol.: 2 / Mutation: C100S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Novosphingobium sp. (strain KA1) (bacteria)
Strain: KA1 / Gene: ligU, ORF100 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q0KJL4, Isomerases; Intramolecular oxidoreductases; Transposing C=C bonds
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 388 / 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: 2.56 Å3/Da / Density % sol: 51.97 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Well - 200 mM magnesium chloride hexahydrate, 100 mM HEPES/KOH, pH 7.5, 25% (w/v) PEG 3350 Drop - 2 uL enzyme, 2 uL well where the enzyme concentration was 10 mg/mL in 20 mM phosphate buffer pH 7.9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.1271 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1271 Å / Relative weight: 1
ReflectionResolution: 1.88→50 Å / Num. obs: 53939 / % possible obs: 87.3 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.03 / Rrim(I) all: 0.055 / Χ2: 0.761 / Net I/σ(I): 22.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.88-1.911.80.2422.114470.9150.20.3150.4147.1
1.91-1.9520.26118150.9250.2040.3330.45458.8
1.95-1.982.10.24520580.9390.1870.310.48467.1
1.98-2.032.20.21921870.9510.1640.2750.48171.3
2.03-2.072.30.21323750.9530.1580.2670.46977.1
2.07-2.122.70.21928380.9570.1520.2680.48392.6
2.12-2.1730.20129750.9720.1340.2430.49795.9
2.17-2.233.20.17630130.980.1140.2110.52497.5
2.23-2.293.20.1729750.9750.1110.2030.55396.7
2.29-2.373.20.14129510.9830.0910.1690.51996.2
2.37-2.453.20.11429800.9890.0740.1370.55895.8
2.45-2.553.20.09829380.990.0640.1170.5895.5
2.55-2.6730.08629100.9910.0570.1030.63994.2
2.67-2.812.80.06728900.9940.0460.0810.68993.6
2.81-2.982.70.05526560.9950.0390.0680.75286.3
2.98-3.213.20.04629990.9970.030.0550.86997
3.21-3.543.30.03830190.9970.0240.0461.0697.7
3.54-4.053.20.03330340.9980.0220.041.19897.3
4.05-5.12.90.0329510.9970.0210.0371.37595
5.1-503.30.02929280.9980.0190.0351.49693.2

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.88 Å45.25 Å

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-20002.3.10data reduction
HKL-20002.3.10data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3G7K

3g7k


Resolution: 1.88→42.02 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.41 / Phase error: 26.04
RfactorNum. reflection% reflection
Rfree0.215 2597 4.82 %
Rwork0.1731 --
obs0.1752 53866 87.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 115.38 Å2 / Biso mean: 43.0379 Å2 / Biso min: 15.48 Å2
Refinement stepCycle: final / Resolution: 1.88→42.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5061 0 6 388 5455
Biso mean--37.65 41.91 -
Num. residues----705
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0145229
X-RAY DIFFRACTIONf_angle_d1.2497129
X-RAY DIFFRACTIONf_chiral_restr0.072847
X-RAY DIFFRACTIONf_plane_restr0.009952
X-RAY DIFFRACTIONf_dihedral_angle_d9.6194266
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8803-1.91450.2978750.23231453152847
1.9145-1.95130.2777930.23371825191859
1.9513-1.99110.26661040.22092055215968
1.9911-2.03440.26811130.2222215232872
2.0344-2.08180.27281260.21512487261380
2.0818-2.13380.27681620.21072897305994
2.1338-2.19150.24411390.2072972311197
2.1915-2.2560.26371610.20733002316397
2.256-2.32880.27751470.20232993314096
2.3288-2.4120.23451530.19152948310196
2.412-2.50860.26911420.19272951309396
2.5086-2.62270.2371470.19932974312195
2.6227-2.7610.21971470.19782893304095
2.761-2.93390.2491320.20252653278586
2.9339-3.16040.22941460.19722984313096
3.1604-3.47830.22411520.18113057320998
3.4783-3.98130.1951560.15253014317098
3.9813-5.01470.15411510.12222968311995
5.0147-42.03060.1721510.1422928307993
Refinement TLS params.

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)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.40370.3892-0.84341.2752-0.47331.6599-0.0347-0.06940.234-0.00990.1237-0.156-0.03450.24690.04530.1765-0.01060.05790.1669-0.01930.1954-46.4544-14.39327.3812
22.74110.0221-0.24382.27740.56440.9156-0.08660.4427-0.5312-0.14670.151-0.5160.25120.00130.02020.366-0.02930.10490.3482-0.04160.4337-39.2672-30.233215.6709
33.32490.3649-2.09090.6037-0.28921.8989-0.3969-0.4524-0.49130.11630.0598-0.03990.34030.1480.01080.27750.0240.1090.26120.03420.3139-7.4154-2.83349.99
44.3339-1.1898-1.91781.7817-0.1581.9165-0.0750.34460.5420.18310.1180.0038-0.1785-0.31670.00120.2935-0.03220.02730.3159-0.02250.3946-22.700211.36686.9042
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 8:130)A8 - 130
2X-RAY DIFFRACTION2(chain A and resid 131:358)A131 - 358
3X-RAY DIFFRACTION3(chain B and resid 7:122)B7 - 122
4X-RAY DIFFRACTION4(chain B and resid 123:360)B123 - 360

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