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- PDB-4yap: Crystal structure of LigG-apo form from Sphingobium sp. strain SYK-6 -

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Basic information

Entry
Database: PDB / ID: 4yap
TitleCrystal structure of LigG-apo form from Sphingobium sp. strain SYK-6
ComponentsGlutathione S-transferase homolog
KeywordsTRANSFERASE / GSH-lyase GSH-dependent
Function / homology
Function and homology information


transferase activity
Similarity search - Function
Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal domain / Glutaredoxin domain profile. / Glutathione transferase family / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, C-terminal-like ...Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal domain / Glutaredoxin domain profile. / Glutathione transferase family / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / 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 / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Glutathione S-transferase / Glutathione S-transferase homolog
Similarity search - Component
Biological speciesSphingobium sp. SYK-6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.111 Å
AuthorsPereira, J.H. / McAndrew, R.P. / Heins, R.A. / Sale, K.L. / Simmons, B.A. / Adams, P.D.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Structural and Biochemical Characterization of the Early and Late Enzymes in the Lignin beta-Aryl Ether Cleavage Pathway from Sphingobium sp. SYK-6.
Authors: Pereira, J.H. / Heins, R.A. / Gall, D.L. / McAndrew, R.P. / Deng, K. / Holland, K.C. / Donohue, T.J. / Noguera, D.R. / Simmons, B.A. / Sale, K.L. / Ralph, J. / Adams, P.D.
History
DepositionFeb 17, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2016Group: Database references
Revision 1.2Jun 1, 2016Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutathione S-transferase homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4152
Polymers30,3181
Non-polymers961
Water7,945441
1
A: Glutathione S-transferase homolog
hetero molecules

A: Glutathione S-transferase homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,8294
Polymers60,6372
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_675x-y+1,-y+2,-z+1/31
Buried area2820 Å2
ΔGint-43 kcal/mol
Surface area22620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.664, 64.664, 120.731
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Glutathione S-transferase homolog


Mass: 30318.486 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingobium sp. SYK-6 (bacteria) / Gene: ligG / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WXJ9, UniProt: G2IN94*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 441 / 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: 2.4 Å3/Da / Density % sol: 48.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Bis-Tris propane pH 7.0, 1.5 M Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.99996 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 30, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99996 Å / Relative weight: 1
ReflectionResolution: 1.11→50 Å / Num. obs: 115374 / % possible obs: 99.8 % / Redundancy: 9.1 % / Net I/σ(I): 24

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Processing

Software
NameVersionClassification
PHENIXdev_1839refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 1.111→41.055 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1822 5784 5.02 %
Rwork0.1678 --
obs0.1685 115285 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.111→41.055 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2113 0 5 441 2559
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0192258
X-RAY DIFFRACTIONf_angle_d1.8373062
X-RAY DIFFRACTIONf_dihedral_angle_d12.947856
X-RAY DIFFRACTIONf_chiral_restr0.103311
X-RAY DIFFRACTIONf_plane_restr0.014403
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1112-1.12380.2721880.2663541X-RAY DIFFRACTION99
1.1238-1.1370.26961970.24743630X-RAY DIFFRACTION100
1.137-1.15090.2441740.22843648X-RAY DIFFRACTION100
1.1509-1.16540.22711820.21443578X-RAY DIFFRACTION100
1.1654-1.18080.22372030.20523627X-RAY DIFFRACTION100
1.1808-1.1970.21271860.19853621X-RAY DIFFRACTION100
1.197-1.21410.17991880.19143620X-RAY DIFFRACTION100
1.2141-1.23220.20971990.19683618X-RAY DIFFRACTION100
1.2322-1.25140.19641950.19883590X-RAY DIFFRACTION100
1.2514-1.2720.22312010.18553627X-RAY DIFFRACTION100
1.272-1.29390.20742050.18763651X-RAY DIFFRACTION100
1.2939-1.31740.20881770.18683658X-RAY DIFFRACTION100
1.3174-1.34280.20061790.18473604X-RAY DIFFRACTION100
1.3428-1.37020.21791920.18323654X-RAY DIFFRACTION100
1.3702-1.40.21351990.17793610X-RAY DIFFRACTION100
1.4-1.43250.19481910.17623620X-RAY DIFFRACTION100
1.4325-1.46840.17521940.17333666X-RAY DIFFRACTION100
1.4684-1.50810.20011990.17433609X-RAY DIFFRACTION100
1.5081-1.55240.19282040.16583655X-RAY DIFFRACTION100
1.5524-1.60260.17152160.1613610X-RAY DIFFRACTION100
1.6026-1.65980.15911880.16043663X-RAY DIFFRACTION100
1.6598-1.72630.18021830.15763661X-RAY DIFFRACTION100
1.7263-1.80490.18661700.16473724X-RAY DIFFRACTION100
1.8049-1.90.17181860.16013661X-RAY DIFFRACTION100
1.9-2.01910.17741810.15773702X-RAY DIFFRACTION100
2.0191-2.17490.17771860.15363684X-RAY DIFFRACTION100
2.1749-2.39380.17092210.14913686X-RAY DIFFRACTION100
2.3938-2.74010.18261930.16013729X-RAY DIFFRACTION100
2.7401-3.4520.1762090.16063746X-RAY DIFFRACTION100
3.452-41.08290.15791980.16253808X-RAY DIFFRACTION97
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)
11.20560.7118-0.5641.4032-0.33661.2734-0.05910.19270.066-0.15570.0385-0.0351-0.0669-0.07410.0090.11660.0236-0.0060.1112-0.00510.0816-15.39354.22080.3615
20.99340.1768-1.91385.7623-0.33853.7484-0.01620.02780.15310.04650.0297-0.1438-0.16850.09640.06290.14280.0563-0.00650.11280.00220.0849-15.155163.28065.7921
30.847-0.0546-0.66660.33880.03681.07490.08420.0365-0.0145-0.0131-0.0340.0563-0.0727-0.1259-0.05340.0941-0.003-0.00630.0576-0.00260.0711-17.297949.257217.148
44.77080.5349-1.7310.9056-0.62091.9828-0.0122-0.20470.00550.0103-0.0156-0.09930.01550.3104-0.0030.0777-0.0006-0.01690.10020.00380.07040.035839.06421.7193
51.0948-0.0636-0.67140.22650.03071.11810.01650.0222-0.0917-0.0399-0.03180.01950.0338-0.00440.01870.0869-0.0027-0.01290.0476-0.00150.0866-9.713638.178911.5801
62.55080.13580.38361.3736-0.73993.53-0.01230.0153-0.0128-0.046-0.0062-0.0836-0.00270.14980.02030.09180.01110.00950.0715-0.01280.08285.1743.4041-3.8007
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 48 )
2X-RAY DIFFRACTION2chain 'A' and (resid 49 through 70 )
3X-RAY DIFFRACTION3chain 'A' and (resid 71 through 117 )
4X-RAY DIFFRACTION4chain 'A' and (resid 118 through 145 )
5X-RAY DIFFRACTION5chain 'A' and (resid 146 through 219 )
6X-RAY DIFFRACTION6chain 'A' and (resid 220 through 265 )

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