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- PDB-4xt0: Crystal Structure of Beta-etherase LigF from Sphingobium sp. stra... -

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Basic information

Entry
Database: PDB / ID: 4xt0
TitleCrystal Structure of Beta-etherase LigF from Sphingobium sp. strain SYK-6
ComponentsProtein LigF
KeywordsTRANSFERASE / beta-etherase / lignase / LigF / thioredoxin / glutathione / GST
Function / homology
Function and homology information


lignin catabolic process
Similarity search - Function
Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase, C-terminal / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily / Thioredoxin-like superfamily
Similarity search - Domain/homology
GLUTATHIONE / Protein LigF
Similarity search - Component
Biological speciesSphingobium sp. SYK-6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.07 Å
AuthorsHelmich, K.E. / Bingman, C.A. / Donohue, T.J. / Phillips Jr., G.N.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-FC02-07ER64494 United States
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Structural Basis of Stereospecificity in the Bacterial Enzymatic Cleavage of beta-Aryl Ether Bonds in Lignin.
Authors: Helmich, K.E. / Pereira, J.H. / Gall, D.L. / Heins, R.A. / McAndrew, R.P. / Bingman, C. / Deng, K. / Holland, K.C. / Noguera, D.R. / Simmons, B.A. / Sale, K.L. / Ralph, J. / Donohue, T.J. / ...Authors: Helmich, K.E. / Pereira, J.H. / Gall, D.L. / Heins, R.A. / McAndrew, R.P. / Bingman, C. / Deng, K. / Holland, K.C. / Noguera, D.R. / Simmons, B.A. / Sale, K.L. / Ralph, J. / Donohue, T.J. / Adams, P.D. / Phillips, G.N.
History
DepositionJan 22, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2016Group: Database references / Source and taxonomy
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
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: Protein LigF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9604
Polymers28,2921
Non-polymers6683
Water4,720262
1
A: Protein LigF
hetero molecules

A: Protein LigF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,9208
Polymers56,5842
Non-polymers1,3356
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_657-x+y+1,y,-z+5/21
Buried area2180 Å2
ΔGint-10 kcal/mol
Surface area21540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.708, 123.708, 66.416
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-419-

HOH

21A-468-

HOH

31A-470-

HOH

DetailsThe biological unit is a dimer, generated from the monomer in the asymmetric unit by the operation -x+y+1, y, -z+5/2.

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Components

#1: Protein Protein LigF


Mass: 28292.068 Da / Num. of mol.: 1 / Fragment: UNP residues 1-243
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingobium sp. SYK-6 (bacteria) / Gene: ligF / Plasmid: pVP67K / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P30347
#2: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 262 / 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: 2.59 Å3/Da / Density % sol: 52.56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 1 uL protein solution (10mM HEPES pH 7.5, 50mM NaCl, 0.5mM TCEP, 1mM glutathione) mixed with 0.8 uL of the well solution (25% MEPEG 2000, 0.2M TMAO, 0.1M BTP pH 9) and 0.2 uL of a suspension ...Details: 1 uL protein solution (10mM HEPES pH 7.5, 50mM NaCl, 0.5mM TCEP, 1mM glutathione) mixed with 0.8 uL of the well solution (25% MEPEG 2000, 0.2M TMAO, 0.1M BTP pH 9) and 0.2 uL of a suspension of LigF micro-crystals (0.2M Magnesium formate, 30% PEG 3350, 1mM glutathione) Cryoprotected with 30% MEPEG 2000, 0.2M TMAO, 0.1M Tris pH 8.5, 1mM glutathione

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.07→40.493 Å / Num. obs: 18884 / % possible obs: 99.8 % / Redundancy: 17.3 % / Biso Wilson estimate: 24.29 Å2 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.019 / Rrim(I) all: 0.079 / Χ2: 1.003 / Net I/av σ(I): 32.714 / Net I/σ(I): 11.9 / Num. measured all: 326246
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.07-2.1112.90.6378990.9220.1810.6630.74798.3
2.11-2.1414.50.6099210.9530.1620.6310.74299.1
2.14-2.1915.70.4989080.970.1280.5140.77100
2.19-2.2317.20.4089330.9820.0990.420.816100
2.23-2.2818.10.3239220.9910.0770.3330.838100
2.28-2.3318.10.2639210.9920.0630.2710.878100
2.33-2.3918.10.2479560.9920.0590.2540.9100
2.39-2.4518.30.2029100.9940.0480.2080.953100
2.45-2.5318.10.189420.9950.0430.1850.982100
2.53-2.6118.20.1639280.9950.0390.1680.99100
2.61-2.718.20.1439420.9960.0340.1471.093100
2.7-2.8118.20.139290.9960.0310.1341.196100
2.81-2.9418.10.1179540.9970.0280.121.307100
2.94-3.0918.10.1059340.9970.0250.1081.389100
3.09-3.29180.099450.9980.0220.0931.374100
3.29-3.5417.90.0789580.9980.0190.081.2899.9
3.54-3.917.70.0699600.9990.0170.0711.20699.8
3.9-4.4617.40.0649700.9990.0160.0661.08799.9
4.46-5.6217.20.0519920.9990.0130.0530.80699.9
5.62-5015.50.03810600.9980.010.0390.49298.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.06 Å45.26 Å
Translation2.06 Å45.26 Å

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHASER2.5.5phasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
HKL-2000data scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.07→40.493 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2143 963 5.28 %
Rwork0.1581 17269 -
obs0.161 18232 96.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 126.79 Å2 / Biso mean: 40.8004 Å2 / Biso min: 7.81 Å2
Refinement stepCycle: final / Resolution: 2.07→40.493 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1975 0 44 262 2281
Biso mean--41.09 45.94 -
Num. residues----243
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082080
X-RAY DIFFRACTIONf_angle_d1.0222808
X-RAY DIFFRACTIONf_chiral_restr0.042284
X-RAY DIFFRACTIONf_plane_restr0.005365
X-RAY DIFFRACTIONf_dihedral_angle_d14.593779
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.07-2.17310.26311090.18212010211981
2.1731-2.30920.2321260.17442377250395
2.3092-2.48750.22741560.163524982654100
2.4875-2.73780.27171350.173525402675100
2.7378-3.13380.23661280.172225542682100
3.1338-3.94780.19811590.147225702729100
3.9478-40.50070.18251500.14372720287099
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)
13.18760.3269-0.13143.404-1.33642.8604-0.05240.78430.3031-0.39710.13450.06020.05180.1279-0.01920.1722-0.02950.01280.27790.06390.111966.027956.231167.341
22.73451.7471-1.49512.58160.37291.51810.2970.4121.01770.00590.10360.5025-0.93390.0443-0.03540.4203-0.01680.06710.19080.12810.482767.774773.720575.5928
32.46730.2004-0.88512.98840.17131.6290.08910.14130.37160.0054-0.1434-0.646-0.52880.6965-0.10260.1975-0.13820.00630.34690.09570.333682.301662.031278.907
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 88 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 89 through 178 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 179 through 242 )A0

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