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

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Basic information

Entry
Database: PDB / ID: 4yae
TitleCrystal structure of LigL-apo form from Sphingobium sp. strain SYK-6
ComponentsC alpha-dehydrogenase
KeywordsOXIDOREDUCTASE / Short Chain Dehydrogenase/reductase SDR family
Function / homology
Function and homology information


oxidoreductase activity / nucleotide binding
Similarity search - Function
short chain dehydrogenase / PKS_KR / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
C alpha-dehydrogenase
Similarity search - Component
Biological speciesSphingobium sp. SYK-6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.602 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: C alpha-dehydrogenase
B: C alpha-dehydrogenase


Theoretical massNumber of molelcules
Total (without water)62,6652
Polymers62,6652
Non-polymers00
Water9,746541
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4840 Å2
ΔGint-38 kcal/mol
Surface area17770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.645, 74.929, 56.283
Angle α, β, γ (deg.)90.00, 104.53, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-319-

HOH

21A-385-

HOH

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Components

#1: Protein C alpha-dehydrogenase / Calpha-dehydrogenase


Mass: 31332.443 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingobium sp. SYK-6 (bacteria) / Gene: ligL, SLG_33660 / Production host: Escherichia coli (E. coli) / References: UniProt: C0SUJ9
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 541 / 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: 2.06 Å3/Da / Density % sol: 40.37 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Magnesium Chloride, 0.1 M Hepes pH 7.5, 25% PEG 3,350
PH range: 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.99999 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 29, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 66935 / % possible obs: 100 % / Redundancy: 3.7 % / Net I/σ(I): 17.2

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Processing

Software
NameVersionClassification
PHENIXdev_1839refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 1.602→50 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1654 2000 2.99 %
Rwork0.1498 --
obs0.1503 66929 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.602→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3520 0 0 541 4061
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063580
X-RAY DIFFRACTIONf_angle_d1.0514850
X-RAY DIFFRACTIONf_dihedral_angle_d12.31310
X-RAY DIFFRACTIONf_chiral_restr0.039548
X-RAY DIFFRACTIONf_plane_restr0.006646
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.602-1.64160.23331410.22074577X-RAY DIFFRACTION100
1.6416-1.6860.20241420.20674595X-RAY DIFFRACTION100
1.686-1.73560.23821420.19714639X-RAY DIFFRACTION100
1.7356-1.79160.20331430.18314645X-RAY DIFFRACTION100
1.7916-1.85570.19181420.18274594X-RAY DIFFRACTION100
1.8557-1.92990.20011430.16184646X-RAY DIFFRACTION100
1.9299-2.01780.17411420.14244609X-RAY DIFFRACTION100
2.0178-2.12420.15691420.13424624X-RAY DIFFRACTION100
2.1242-2.25730.15071440.13614669X-RAY DIFFRACTION100
2.2573-2.43150.14021430.13174623X-RAY DIFFRACTION100
2.4315-2.67620.1641430.14124663X-RAY DIFFRACTION100
2.6762-3.06340.18241430.15224645X-RAY DIFFRACTION100
3.0634-3.85930.14981440.144659X-RAY DIFFRACTION100
3.8593-47.01440.14761460.14524741X-RAY DIFFRACTION100
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)
12.49430.8028-0.47782.0297-0.05832.27580.05340.0491-0.0656-0.06630.003-0.0328-0.00890.185-0.01470.1053-0.0142-0.0070.1498-0.0030.126253.696969.665411.4421
24.11280.9059-2.44722.8213-1.51565.5456-0.1962-0.4151-0.90460.0307-0.1111-0.28090.25220.4560.05640.11040.01260.00970.23520.03610.266662.013561.664516.536
33.06510.8257-0.48621.3757-0.05251.00480.0333-0.0334-0.11030.0723-0.0486-0.1421-0.05560.003-0.00750.1347-0.0272-0.0240.17130.01760.140652.659569.9622.1308
41.0050.7925-0.02211.05210.09170.85510.02520.0115-0.09260.05430.0044-0.05270.0389-0.0107-0.00710.1132-0.0057-0.01190.11050.00630.136438.428863.549314.8339
51.74061.53710.03144.0178-0.90110.95990.01760.0758-0.1041-0.051-0.0453-0.08750.05610.0843-0.00350.0977-0.01480.00410.1253-0.01270.120332.977859.63679.104
62.40460.75780.05931.78650.52042.001-0.06250.1839-0.0855-0.01890.09560.0893-0.02150.04390.00610.1205-0.01840.00130.12740.01930.094140.002771.90936.2372
72.02491.20120.29250.81060.05270.3881-0.08340.4622-0.105-0.14940.1624-0.020.08190.0177-0.02540.1871-0.0109-0.0040.2029-0.01420.121837.057664.5855-2.7801
82.63610.52570.48131.84850.14982.15840.02370.070.06540.0681-0.0560.1834-0.0566-0.16430.05140.1249-0.02250.03360.1505-0.01680.1664.65553.292815.4496
97.21181.8753.6382.14521.92744.8989-0.0677-0.38390.59520.3756-0.21130.6279-0.047-0.52850.06290.22810.0180.07410.2343-0.06690.3329-2.520359.454923.6779
103.69881.5252-0.52021.61560.20510.48690.0528-0.130.05880.2891-0.13740.16840.0344-0.09060.0550.1943-0.03830.03540.1725-0.00350.16078.902150.163525.8456
110.7840.60070.10551.20890.33510.6071-0.00160.0260.05810.06320.00550.05910.0011-0.00580.01340.1102-0.00920.00510.11870.00170.122520.289758.283213.4967
121.87070.8326-0.31991.2288-0.12560.4737-0.10110.39990.1866-0.14460.12260.1467-0.0839-0.0776-0.01060.1763-0.009-0.03350.22120.0250.13117.679261.8918-0.7557
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 38 )
2X-RAY DIFFRACTION2chain 'A' and (resid 39 through 51 )
3X-RAY DIFFRACTION3chain 'A' and (resid 52 through 82 )
4X-RAY DIFFRACTION4chain 'A' and (resid 83 through 152 )
5X-RAY DIFFRACTION5chain 'A' and (resid 153 through 171 )
6X-RAY DIFFRACTION6chain 'A' and (resid 172 through 230 )
7X-RAY DIFFRACTION7chain 'A' and (resid 231 through 271 )
8X-RAY DIFFRACTION8chain 'B' and (resid 1 through 38 )
9X-RAY DIFFRACTION9chain 'B' and (resid 39 through 52 )
10X-RAY DIFFRACTION10chain 'B' and (resid 53 through 82 )
11X-RAY DIFFRACTION11chain 'B' and (resid 83 through 230 )
12X-RAY DIFFRACTION12chain 'B' and (resid 231 through 271 )

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