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- PDB-6p3j: Crystal structure of LigU -

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Basic information

Entry
Database: PDB / ID: 6p3j
TitleCrystal structure of LigU
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: 2.02 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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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)76,34314
Polymers75,9212
Non-polymers42212
Water4,035224
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4870 Å2
ΔGint-129 kcal/mol
Surface area26260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.776, 67.364, 161.072
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 37960.312 Da / Num. of mol.: 2
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


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / 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: 2.34 Å3/Da / Density % sol: 47.36 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Well solution - 200 mM calcium chloride dihydrate, 100 mM HEPES/KOH, pH 6.5, 35% pentaerythritol ethoxylate (15/4 EO/OH) Drop - 2 uL enzyme, 2 uL well solution where enzyme was at 22.3 mg/mL ...Details: Well solution - 200 mM calcium chloride dihydrate, 100 mM HEPES/KOH, pH 6.5, 35% pentaerythritol ethoxylate (15/4 EO/OH) Drop - 2 uL enzyme, 2 uL well solution where enzyme was at 22.3 mg/mL in 20 mM HEPES/KOH, pH 7.5

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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: 2.02→50 Å / Num. obs: 45097 / % possible obs: 97.8 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.026 / Rrim(I) all: 0.062 / Χ2: 1.105 / Net I/σ(I): 30.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.02-2.052.80.5971.119510.5930.3880.7170.4386.5
2.05-2.093.40.56220660.6920.3360.660.47590.7
2.09-2.134.10.46921800.8020.2540.5370.47496.5
2.13-2.184.60.42322450.850.2190.4790.4998.3
2.18-2.224.90.36922290.8940.1850.4150.48499.3
2.22-2.274.90.32722710.8970.1640.3680.5699.5
2.27-2.3350.27822640.9410.1360.3110.53199
2.33-2.394.60.22721870.9470.1160.2560.57996.4
2.39-2.475.60.1922460.9640.0880.210.62798.9
2.47-2.5460.16922730.9740.0770.1860.64799.3
2.54-2.6460.14222860.9850.0640.1560.69499.5
2.64-2.745.80.11623020.9890.0530.1280.78199.8
2.74-2.875.90.09422830.990.0430.1040.85799.7
2.87-3.025.80.08422820.9930.0390.0931.02999.4
3.02-3.215.60.06822870.9950.0310.0751.25399
3.21-3.454.90.05822530.9960.0280.0651.6697.4
3.45-3.86.20.05223120.9970.0230.0571.9999.3
3.8-4.356.10.04523390.9980.020.052.27699.5
4.35-5.485.90.04323420.9980.0190.0472.32398.3
5.48-505.60.03624990.9990.0160.0392.0999

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.02 Å41.99 Å
Translation2.02 Å41.99 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
Coot0.8.9.2 ELmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6P3K

6p3k


Resolution: 2.02→41.986 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 22.19
RfactorNum. reflection% reflection
Rfree0.2116 2003 4.48 %
Rwork0.1863 --
obs0.1875 44713 97.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 161.69 Å2 / Biso mean: 61.3809 Å2 / Biso min: 28.42 Å2
Refinement stepCycle: final / Resolution: 2.02→41.986 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5086 0 12 224 5322
Biso mean--59.87 49.95 -
Num. residues----705
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035232
X-RAY DIFFRACTIONf_angle_d0.5967130
X-RAY DIFFRACTIONf_chiral_restr0.045847
X-RAY DIFFRACTIONf_plane_restr0.004951
X-RAY DIFFRACTIONr_dihedral_angle_d15.1643179
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.02-2.07050.31121210.30072707282888
2.0705-2.12650.29391310.25442943307495
2.1265-2.18910.27851500.22473029317999
2.1891-2.25970.33241480.21453042319099
2.2597-2.34050.21441330.20813024315799
2.3405-2.43420.24111490.20193006315597
2.4342-2.5450.24551360.20130673203100
2.545-2.67910.26131520.193330763228100
2.6791-2.84690.23661460.202230943240100
2.8469-3.06670.26051450.2083091323699
3.0667-3.37520.22821510.19753065321698
3.3752-3.86330.18511390.1763117325699
3.8633-4.86620.18031500.15023150330099
4.8662-41.99530.17141520.18023299345199
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)
13.61360.4542-0.27162.9186-0.76842.03660.2276-0.9081-0.97960.1639-0.29550.08450.23520.02190.03530.2976-0.0603-0.09920.51610.06780.4828-27.101-11.749427.992
21.5439-0.23650.48871.4454-0.34142.6003-0.05750.3464-0.2032-0.44760.2292-0.4394-0.20150.3651-0.02440.3812-0.06220.160.4538-0.15160.4331-11.4013-0.7767-4.4016
32.34660.37491.53461.31760.52772.1294-0.34950.4257-0.4242-0.49510.336-0.0415-0.42730.22110.07560.5819-0.12870.21710.4352-0.06730.3613-28.08133.4155-17.3432
41.839-0.06720.93231.7786-0.38332.78170.0085-0.2455-0.32610.20420.1569-0.2578-0.2089-0.1152-0.15820.28250.0447-0.01830.35340.02140.333-17.20790.2821.9874
59.4059-0.40761.05874.5871-0.46222.85490.2112-0.98150.6249-0.292-0.14661.4049-0.1407-0.2885-0.05080.59980.0646-0.09420.9004-0.21571.2041-42.5951-6.976429.4928
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain B and resid 284:361)B284 - 361
2X-RAY DIFFRACTION2(chain A and resid 8:148)A8 - 148
3X-RAY DIFFRACTION3(chain A and resid 149:360)A149 - 360
4X-RAY DIFFRACTION4(chain B and resid 2:170)B2 - 170
5X-RAY DIFFRACTION5(chain B and resid 171:283)B171 - 283

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