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- PDB-6dxq: Crystal structure of the LigJ Hydratase product complex with 4-ca... -

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Basic information

Entry
Database: PDB / ID: 6dxq
TitleCrystal structure of the LigJ Hydratase product complex with 4-carboxy-4-hydroxy-2-oxoadipate
Components4-oxalomesaconate hydratase
KeywordsLYASE / Hydratase / lignin degradation
Function / homology
Function and homology information


Lyases; Carbon-oxygen lyases; Hydro-lyases / lignin catabolic process / carboxy-lyase activity / hydrolase activity / metal ion binding
Similarity search - Function
2-amino-3-carboxymuconate-6-semialdehyde decarboxylase / Amidohydrolase / Amidohydrolase-related / Metal-dependent hydrolase
Similarity search - Domain/homology
Chem-7QD / 2-keto-4-carboxy-3-hexenedioate hydratase
Similarity search - Component
Biological speciesSphingobium sp. SYK-6 (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.02 Å
AuthorsMabanglo, M.F. / Raushel, F.M.
Funding support United States, 1items
OrganizationGrant numberCountry
Robert A. Welch FoundationA-840 United States
CitationJournal: Biochemistry / Year: 2018
Title: Structure and Reaction Mechanism of the LigJ Hydratase: An Enzyme Critical for the Bacterial Degradation of Lignin in the Protocatechuate 4,5-Cleavage Pathway.
Authors: Hogancamp, T.N. / Mabanglo, M.F. / Raushel, F.M.
History
DepositionJun 29, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2018Group: 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_author.identifier_ORCID
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 4-oxalomesaconate hydratase
B: 4-oxalomesaconate hydratase
C: 4-oxalomesaconate hydratase
D: 4-oxalomesaconate hydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,99112
Polymers151,8494
Non-polymers1,1428
Water20,1591119
1
A: 4-oxalomesaconate hydratase
hetero molecules

C: 4-oxalomesaconate hydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,4966
Polymers75,9242
Non-polymers5714
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
Buried area4520 Å2
ΔGint-22 kcal/mol
Surface area23490 Å2
MethodPISA
2
B: 4-oxalomesaconate hydratase
hetero molecules

D: 4-oxalomesaconate hydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,4966
Polymers75,9242
Non-polymers5714
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_747-x+2,y-1/2,-z+21
Buried area4470 Å2
ΔGint-29 kcal/mol
Surface area23610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.521, 78.301, 135.637
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
4-oxalomesaconate hydratase


Mass: 37962.215 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingobium sp. SYK-6 (bacteria) / Gene: ligJ, SLG_12520 / Production host: Escherichia coli (E. coli) / References: UniProt: G2IQQ5, 4-oxalomesaconate hydratase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-7QD / (2S)-2-hydroxy-4-oxobutane-1,2,4-tricarboxylic acid


Mass: 220.134 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H8O8 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1119 / 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: 2.91 Å3/Da / Density % sol: 57.7 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.1 M sodium malonate 12% (w/v) polyethyleneglycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.5
ReflectionResolution: 2.02→27.8 Å / Num. obs: 112743 / % possible obs: 99.4 % / Redundancy: 3.4 % / Net I/σ(I): 10.7
Reflection shellResolution: 2.02→2.09 Å

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIXdev_1108refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementResolution: 2.02→27.8 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 25.4
RfactorNum. reflection% reflection
Rfree0.2156 2013 1.79 %
Rwork0.176 --
obs0.1923 112725 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 92.93 Å2 / Biso mean: 46.95 Å2 / Biso min: 28.85 Å2
Refinement stepCycle: final / Resolution: 2.02→27.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10539 0 84 1119 11742
Biso mean--54.9 51.02 -
Num. residues----1342
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00610883
X-RAY DIFFRACTIONf_angle_d1.04614790
X-RAY DIFFRACTIONf_chiral_restr0.0721577
X-RAY DIFFRACTIONf_plane_restr0.0051966
X-RAY DIFFRACTIONf_dihedral_angle_d14.5543990
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 (%)
2.0215-2.0720.3351410.29547698783995
2.072-2.1280.34451370.26397743788097
2.128-2.19060.30831530.24787813796697
2.1906-2.26130.2651410.2377899804098
2.2613-2.3420.33941280.2247918804698
2.342-2.43570.22791490.21577929807898
2.4357-2.54650.31231460.20317868801498
2.5465-2.68060.26581340.19297964809898
2.6806-2.84840.2331400.18877933807398
2.8484-3.0680.25711430.17377918806198
3.068-3.37620.20561470.1717944809198
3.3762-3.86330.22031460.15717919806598
3.8633-4.86210.14441490.14717986813598
4.8621-25.95430.19851520.18658094824698
Refinement TLS params.Method: refined / Origin x: 76.7385 Å / Origin y: 49.1307 Å / Origin z: 106.997 Å
111213212223313233
T0.3429 Å2-0.0047 Å2-0.0104 Å2-0.34 Å2-0.005 Å2--0.4163 Å2
L-0.005 °2-0.002 °2-0.0047 °2-0.0005 °2-0.0076 °2--0.0037 °2
S-0.0055 Å °0.0012 Å °0.0077 Å °-0.0006 Å °0.0029 Å °-0.0083 Å °-0.0026 Å °-0.0005 Å °-0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA4 - 341
2X-RAY DIFFRACTION1allB2 - 341
3X-RAY DIFFRACTION1allC2 - 341
4X-RAY DIFFRACTION1allD3 - 341
5X-RAY DIFFRACTION1allE5 - 8
6X-RAY DIFFRACTION1allG1 - 4
7X-RAY DIFFRACTION1allS1 - 1332

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