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- PDB-5vn5: Crystal structure of LigY from Sphingobium sp. strain SYK-6 -

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Basic information

Entry
Database: PDB / ID: 5vn5
TitleCrystal structure of LigY from Sphingobium sp. strain SYK-6
Components2,2',3-trihydroxy-3'-methoxy-5,5'-dicarboxybiphenyl meta-cleavage compound hydrolase
KeywordsHYDROLASE / amidohydrolase / lignin degradation / meta-cleavage product hydrolase
Function / homology2-amino-3-carboxymuconate-6-semialdehyde decarboxylase / Amidohydrolase / carboxy-lyase activity / Amidohydrolase-related / Metal-dependent hydrolase / hydrolase activity / 2,2',3-trihydroxy-3'-methoxy-5,5'-dicarboxybiphenyl meta-cleavage compound hydrolase
Function and homology information
Biological speciesSphingobium sp. SYK-6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsKuatsjah, E. / Chan, A.C.K. / Kobylarz, M.J. / Murphy, M.E.P. / Eltis, L.D.
Funding support Canada, 2items
OrganizationGrant numberCountry
Genome Canada2108 Canada
Natural Sciences and Engineering Research Council (NSERC, Canada)171359 Canada
CitationJournal: J. Biol. Chem. / Year: 2017
Title: The bacterialmeta-cleavage hydrolase LigY belongs to the amidohydrolase superfamily, not to the alpha / beta-hydrolase superfamily.
Authors: Kuatsjah, E. / Chan, A.C.K. / Kobylarz, M.J. / Murphy, M.E.P. / Eltis, L.D.
History
DepositionApr 28, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 1, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 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.pdbx_ptnr1_label_alt_id / _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: 2,2',3-trihydroxy-3'-methoxy-5,5'-dicarboxybiphenyl meta-cleavage compound hydrolase
B: 2,2',3-trihydroxy-3'-methoxy-5,5'-dicarboxybiphenyl meta-cleavage compound hydrolase
C: 2,2',3-trihydroxy-3'-methoxy-5,5'-dicarboxybiphenyl meta-cleavage compound hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,5897
Polymers114,3583
Non-polymers2324
Water9,638535
1
A: 2,2',3-trihydroxy-3'-methoxy-5,5'-dicarboxybiphenyl meta-cleavage compound hydrolase
B: 2,2',3-trihydroxy-3'-methoxy-5,5'-dicarboxybiphenyl meta-cleavage compound hydrolase
C: 2,2',3-trihydroxy-3'-methoxy-5,5'-dicarboxybiphenyl meta-cleavage compound hydrolase
hetero molecules

A: 2,2',3-trihydroxy-3'-methoxy-5,5'-dicarboxybiphenyl meta-cleavage compound hydrolase
B: 2,2',3-trihydroxy-3'-methoxy-5,5'-dicarboxybiphenyl meta-cleavage compound hydrolase
C: 2,2',3-trihydroxy-3'-methoxy-5,5'-dicarboxybiphenyl meta-cleavage compound hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)229,17914
Polymers228,7166
Non-polymers4638
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x-1,y,-z-1/21
Buried area19580 Å2
ΔGint-258 kcal/mol
Surface area63960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.020, 195.361, 178.249
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11C-561-

HOH

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Components

#1: Protein 2,2',3-trihydroxy-3'-methoxy-5,5'-dicarboxybiphenyl meta-cleavage compound hydrolase


Mass: 38119.266 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: NBRC 103272 / Source: (gene. exp.) Sphingobium sp. SYK-6 (bacteria) / Gene: ligY, SLG_07750 / Plasmid: pET41b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: G2IN02
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 535 / 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: 2.28 Å3/Da / Density % sol: 46.16 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M Tris-Cl, pH 7.5, 0.2 M lithium sulfate, ~24% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.9795 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Sep 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.9→59.42 Å / Num. obs: 82888 / % possible obs: 100 % / Redundancy: 6.2 % / Biso Wilson estimate: 23.28 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.035 / Rrim(I) all: 0.087 / Net I/σ(I): 13.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
1.9-1.946.10.5150.8250.2260.563100
9.87-59.425.30.0390.9980.0180.04399.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.35 Å48.23 Å
Translation5.35 Å48.23 Å

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Processing

Software
NameVersionClassification
Aimless0.5.14data scaling
PHASER2.5.5phasing
PHENIXrefinement
PDB_EXTRACT3.22data extraction
iMOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→54.614 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.4
RfactorNum. reflection% reflectionSelection details
Rfree0.189 4252 5.13 %Random selection
Rwork0.1624 ---
obs0.1638 82836 99.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 121.58 Å2 / Biso mean: 34.4641 Å2 / Biso min: 12.23 Å2
Refinement stepCycle: final / Resolution: 1.9→54.614 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7838 0 4 535 8377
Biso mean--24.92 34.35 -
Num. residues----998
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088143
X-RAY DIFFRACTIONf_angle_d0.85311073
X-RAY DIFFRACTIONf_chiral_restr0.0521181
X-RAY DIFFRACTIONf_plane_restr0.0061464
X-RAY DIFFRACTIONf_dihedral_angle_d17.4574849
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.9-1.92160.23411480.216425572705
1.9216-1.94420.25661270.207326012728
1.9442-1.96790.2371630.203825622725
1.9679-1.99280.22081310.197926232754
1.9928-2.0190.23121450.18625592704
2.019-2.04670.20441540.193525942748
2.0467-2.07590.21511340.184326052739
2.0759-2.10690.21771370.175325682705
2.1069-2.13990.20541360.177726412777
2.1399-2.17490.20451450.167125632708
2.1749-2.21240.22251390.164126122751
2.2124-2.25270.20091360.162525772713
2.2527-2.2960.14941220.156926502772
2.296-2.34290.19321450.154425802725
2.3429-2.39380.19111590.157626042763
2.3938-2.44950.19281530.160325672720
2.4495-2.51080.19521590.164526262785
2.5108-2.57860.18951170.154626082725
2.5786-2.65450.18691520.16125992751
2.6545-2.74020.21131360.162326412777
2.7402-2.83810.19231500.152226122762
2.8381-2.95180.18441410.157426022743
2.9518-3.08610.17521480.156126322780
3.0861-3.24880.17871330.15926352768
3.2488-3.45230.2091480.157826192767
3.4523-3.71880.17011500.144226502800
3.7188-4.09290.16641490.138326682817
4.0929-4.68490.13811390.134326742813
4.6849-5.90130.16671270.161427172844
5.9013-54.63660.22571290.204628382967
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)
12.2597-0.54941.50382.6028-0.37862.5464-0.1734-0.14310.24450.32230.0146-0.0277-0.56490.08050.11270.2348-0.0427-0.01320.2305-0.00640.1893-11.4979-5.1928-14.0433
21.10990.15470.2431.8516-0.01291.3851-0.01340.06860.01140.0126-0.0133-0.1586-0.14170.2963-0.00210.0905-0.0295-0.00060.24150.02980.1682-7.551-16.7553-25.4315
32.78960.13630.5682.83730.60351.98460.10740.0525-0.3837-0.01210.0116-0.24050.35930.2794-0.15630.13280.05-0.03890.20260.06150.2628-10.2041-36.1348-18.0446
42.0605-0.38010.43442.53050.39591.4061-0.0492-0.3473-0.15050.5030.06-0.22250.13910.3358-0.03710.22530.0086-0.07250.31830.05160.2017-6.0338-24.6694-4.7321
50.92350.2636-0.73042.387-1.22991.04390.37170.0574-0.3791-0.44240.1590.26950.7641-0.4822-0.1850.448-0.1184-0.19630.28920.10230.4202-35.4105-47.4694-37.9681
60.1763-0.07-0.10161.7017-1.08150.83370.3344-0.0161-0.5619-0.14020.00010.18060.9762-0.5299-0.1280.6345-0.2092-0.26570.14340.13570.4882-33.2825-50.6206-31.8459
70.90090.32050.36760.6716-0.21331.10180.1475-0.2042-0.133-0.10880.17420.21360.3535-0.70.02080.0338-0.0967-0.0250.42070.14470.3323-36.9313-34.4647-24.0454
82.12870.8347-0.14233.81150.64833.2320.1676-0.4264-0.05930.3369-0.04850.13070.0547-0.2635-0.11690.1468-0.03370.01410.27710.06970.161-25.7649-32.1871-9.3762
90.85080.805-0.12080.96370.46373.18820.3395-0.3797-0.44810.11930.20470.15350.8894-0.09450.66360.4689-0.1013-0.11880.29960.21690.3905-25.5204-49.7312-12.5454
101.0129-0.4281-0.10492.79081.26551.481-0.1145-0.1490.05450.3935-0.0045-0.3422-0.30690.2257-0.05840.4508-0.0261-0.09650.1854-0.00770.2173-26.388210.726-18.2047
110.967-0.2072-0.0491.3031-0.09541.6832-0.0603-0.0119-0.02070.1269-0.04490.183-0.2034-0.15530.11130.24420.0225-0.03030.124-0.02590.1748-39.13978.7301-28.916
121.2514-0.5614-0.86811.9424-0.19141.2573-0.0265-0.01560.14580.2391-0.11040.0095-0.8078-0.09690.09720.57590.0455-0.1140.1657-0.0160.2487-35.568127.0634-34.8235
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 82 )A1 - 82
2X-RAY DIFFRACTION2chain 'A' and (resid 83 through 225 )A83 - 225
3X-RAY DIFFRACTION3chain 'A' and (resid 226 through 272 )A226 - 272
4X-RAY DIFFRACTION4chain 'A' and (resid 273 through 332 )A273 - 332
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 37 )B1 - 37
6X-RAY DIFFRACTION6chain 'B' and (resid 38 through 103 )B38 - 103
7X-RAY DIFFRACTION7chain 'B' and (resid 104 through 225 )B104 - 225
8X-RAY DIFFRACTION8chain 'B' and (resid 226 through 272 )B226 - 272
9X-RAY DIFFRACTION9chain 'B' and (resid 273 through 332 )B273 - 332
10X-RAY DIFFRACTION10chain 'C' and (resid 1 through 82 )C1 - 82
11X-RAY DIFFRACTION11chain 'C' and (resid 83 through 225 )C83 - 225
12X-RAY DIFFRACTION12chain 'C' and (resid 226 through 334 )C226 - 334

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