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- PDB-4y9d: Crystal structure of LigD in complex with NADH from Sphingobium s... -

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Basic information

Entry
Database: PDB / ID: 4y9d
TitleCrystal structure of LigD 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
Similarity search - Function
short chain dehydrogenase / 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: 2.012 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: Source and taxonomy
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0442
Polymers32,3791
Non-polymers6651
Water21612
1
A: C alpha-dehydrogenase
hetero molecules

A: C alpha-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,0884
Polymers64,7572
Non-polymers1,3312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-2/31
Buried area6090 Å2
ΔGint-36 kcal/mol
Surface area18100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.762, 61.762, 134.713
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein C alpha-dehydrogenase


Mass: 32378.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingobium sp. SYK-6 (bacteria) / Gene: ligD / Production host: Escherichia coli (E. coli) / References: UniProt: G2IN91
#2: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH / Nicotinamide adenine dinucleotide


Mass: 665.441 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C21H29N7O14P2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 2.29 Å3/Da / Density % sol: 46.31 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.1M Hepes pH7.5, 1.5 M Lithium Sulfate / PH range: 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 3, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.01→50 Å / Num. obs: 19774 / % possible obs: 96.5 % / Redundancy: 10.6 % / Net I/σ(I): 26.1

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Processing

Software
NameVersionClassification
PHENIXdev_1839refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 2.012→49.712 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 0.13 / Phase error: 34.2 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2485 1620 10.12 %
Rwork0.2109 --
obs0.2147 16006 78.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.012→49.712 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1724 0 27 12 1763
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081783
X-RAY DIFFRACTIONf_angle_d1.0032421
X-RAY DIFFRACTIONf_dihedral_angle_d15.903634
X-RAY DIFFRACTIONf_chiral_restr0.041273
X-RAY DIFFRACTIONf_plane_restr0.005315
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.012-2.07120.37771020.3749851X-RAY DIFFRACTION57
2.0712-2.13810.44051100.3448973X-RAY DIFFRACTION65
2.1381-2.21450.35361310.33671081X-RAY DIFFRACTION73
2.2145-2.30310.31481150.27331071X-RAY DIFFRACTION71
2.3031-2.4080.30851210.24231061X-RAY DIFFRACTION70
2.408-2.53490.28251200.24151070X-RAY DIFFRACTION71
2.5349-2.69370.30011260.23881146X-RAY DIFFRACTION74
2.6937-2.90170.30151360.25751164X-RAY DIFFRACTION77
2.9017-3.19360.29711460.25821284X-RAY DIFFRACTION85
3.1936-3.65560.23371600.21411531X-RAY DIFFRACTION98
3.6556-4.60520.20041680.16781506X-RAY DIFFRACTION97
4.6052-49.72750.20221850.17131648X-RAY DIFFRACTION99
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)
10.2358-0.08870.08160.4704-0.20310.2468-0.0607-0.40840.0407-0.095-0.08930.00670.15840.2119-0.00030.49220.09990.06410.57120.0820.4212-21.892416.7667-20.9088
20.20420.9263-0.6314-0.018-0.49692.4624-0.236-0.19510.1529-0.2233-0.0248-0.01540.50190.1458-0.00030.46050.07740.03910.35690.02860.4535-19.358420.5416-36.6995
30.44760.2875-0.19470.33160.10080.43280.1063-0.35120.26250.0564-0.155-0.0415-0.2308-0.4336-0.00750.44670.14880.00140.4499-0.03470.5652-24.414736.7752-34.7395
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 66 )
2X-RAY DIFFRACTION2chain 'A' and (resid 67 through 178 )
3X-RAY DIFFRACTION3chain 'A' and (resid 179 through 272 )

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