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- PDB-4yag: Crystal structure of LigL in complex with NADH from Sphingobium s... -

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Basic information

Entry
Database: PDB / ID: 4yag
TitleCrystal structure of LigL in complex with NADH 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 / cytosol
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
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / C alpha-dehydrogenase
Similarity search - Component
Biological speciesSphingobium sp. SYK-6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.5 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

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Assembly

Deposited unit
A: C alpha-dehydrogenase
B: C alpha-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,9964
Polymers62,6652
Non-polymers1,3312
Water11,692649
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7120 Å2
ΔGint-51 kcal/mol
Surface area19410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.041, 72.816, 58.972
Angle α, β, γ (deg.)90.00, 105.36, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-614-

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: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 649 / 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: 2.08 Å3/Da / Density % sol: 40.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
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: 1.5→50 Å / Num. obs: 82006 / % possible obs: 100 % / Redundancy: 3.7 % / Net I/σ(I): 21.6

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Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 1.5→50 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 14.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1544 4111 5.01 %
Rwork0.1326 --
obs0.1337 81999 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4114 0 88 649 4851
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094282
X-RAY DIFFRACTIONf_angle_d1.3135812
X-RAY DIFFRACTIONf_dihedral_angle_d12.6711584
X-RAY DIFFRACTIONf_chiral_restr0.071644
X-RAY DIFFRACTIONf_plane_restr0.007766
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5002-1.51790.23851320.22672563X-RAY DIFFRACTION94
1.5179-1.53640.24381470.20732627X-RAY DIFFRACTION100
1.5364-1.55580.24621320.20042724X-RAY DIFFRACTION100
1.5558-1.57630.21281500.18772644X-RAY DIFFRACTION100
1.5763-1.59790.2021310.17652681X-RAY DIFFRACTION100
1.5979-1.62070.19151520.16732700X-RAY DIFFRACTION100
1.6207-1.64490.19361430.16622660X-RAY DIFFRACTION100
1.6449-1.67060.1721340.15822666X-RAY DIFFRACTION100
1.6706-1.6980.21171330.16142694X-RAY DIFFRACTION100
1.698-1.72730.22721520.15852692X-RAY DIFFRACTION100
1.7273-1.75870.18751720.15462631X-RAY DIFFRACTION100
1.7587-1.79250.1781630.14312645X-RAY DIFFRACTION100
1.7925-1.82910.16611360.14132722X-RAY DIFFRACTION100
1.8291-1.86890.18441450.13142681X-RAY DIFFRACTION100
1.8689-1.91240.14861310.13052702X-RAY DIFFRACTION100
1.9124-1.96020.15771460.12422690X-RAY DIFFRACTION100
1.9602-2.01320.1491570.11642646X-RAY DIFFRACTION100
2.0132-2.07250.12621500.11572678X-RAY DIFFRACTION100
2.0725-2.13940.13161450.11192697X-RAY DIFFRACTION100
2.1394-2.21580.13441360.11192701X-RAY DIFFRACTION100
2.2158-2.30450.13731200.11882692X-RAY DIFFRACTION100
2.3045-2.40940.15341270.11572714X-RAY DIFFRACTION100
2.4094-2.53640.16571530.12062694X-RAY DIFFRACTION100
2.5364-2.69530.15461310.12712733X-RAY DIFFRACTION100
2.6953-2.90340.15051530.12822657X-RAY DIFFRACTION100
2.9034-3.19560.15531360.13042711X-RAY DIFFRACTION100
3.1956-3.65780.14191370.12312736X-RAY DIFFRACTION100
3.6578-4.60790.11581470.11612728X-RAY DIFFRACTION100
4.6079-48.43460.15541200.15292779X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 29.0122 Å / Origin y: 60.1402 Å / Origin z: 13.3568 Å
111213212223313233
T0.1001 Å20.0273 Å2-0.0077 Å2-0.0794 Å2-0.0017 Å2--0.0711 Å2
L1.0044 °20.4982 °2-0.0671 °2-0.8253 °2-0.1266 °2--0.5544 °2
S0.0326 Å °0.0124 Å °0.0102 Å °0.0158 Å °-0.005 Å °0.0441 Å °-0.024 Å °-0.0298 Å °-0.0211 Å °
Refinement TLS groupSelection details: all

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