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- PDB-5tr3: 2.5 Angstrom Resolution Crystal Structure of Dihydrolipoyl Dehydr... -

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Basic information

Entry
Database: PDB / ID: 5tr3
Title2.5 Angstrom Resolution Crystal Structure of Dihydrolipoyl Dehydrogenase from Pseudomonas putida in Complex with FAD.
ComponentsDihydrolipoyl dehydrogenaseDihydrolipoamide dehydrogenase
KeywordsHYDROLASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / dihydrolipoyl dehydrogenase
Function / homology
Function and homology information


dihydrolipoyl dehydrogenase / dihydrolipoyl dehydrogenase activity / flavin adenine dinucleotide binding / cytoplasm
Similarity search - Function
Dihydrolipoamide dehydrogenase / Pyridine nucleotide-disulphide oxidoreductase / FAD binding domain / Pyridine nucleotide-disulphide oxidoreductase, class I / FAD/NAD-linked reductase, C-terminal dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, class I, active site / Pyridine nucleotide-disulphide oxidoreductases class-I active site. / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily ...Dihydrolipoamide dehydrogenase / Pyridine nucleotide-disulphide oxidoreductase / FAD binding domain / Pyridine nucleotide-disulphide oxidoreductase, class I / FAD/NAD-linked reductase, C-terminal dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, class I, active site / Pyridine nucleotide-disulphide oxidoreductases class-I active site. / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / Enolase-like; domain 1 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Dihydrolipoyl dehydrogenase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMinasov, G. / Wawrzak, Z. / Shuvalova, L. / Kiryukhina, O. / Dubrovska, I. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: 2.5 Angstrom Resolution Crystal Structure of Dihydrolipoyl Dehydrogenase from Pseudomonas putida in Complex with FAD.
Authors: Minasov, G. / Wawrzak, Z. / Shuvalova, L. / Kiryukhina, O. / Dubrovska, I. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionOct 25, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_oper_list / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dihydrolipoyl dehydrogenase
B: Dihydrolipoyl dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,2686
Polymers100,4832
Non-polymers1,7854
Water4,522251
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10310 Å2
ΔGint-63 kcal/mol
Surface area35960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.886, 132.113, 158.132
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: 0 / Auth seq-ID: 1 - 474 / Label seq-ID: 4 - 477

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Dihydrolipoyl dehydrogenase / Dihydrolipoamide dehydrogenase


Mass: 50241.492 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (strain ATCC 47054 / DSM 6125 / NCIMB 11950 / KT2440) (bacteria)
Strain: ATCC 47054 / DSM 6125 / NCIMB 11950 / KT2440 / Gene: lpdG, PP_4187 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) magic / References: UniProt: Q88FB1, dihydrolipoyl dehydrogenase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 251 / 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: 2.75 Å3/Da / Density % sol: 55.2 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Protein: 13.7 mg/ml, 0.5M Sodium chloride, 0.01M Tris HCl (pH 8.3), 1mM FAD; Screen: Classics II(F10), 0.2M Sodim chloride, 0.01M Tris HCl (pH 6.5), 25% (w/v) PEG 3350.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 5, 2016 / Details: C(111)
RadiationMonochromator: beryllium lenses / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 42116 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Biso Wilson estimate: 51.2 Å2 / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 20.1
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.632 / Mean I/σ(I) obs: 2.6 / CC1/2: 0.837 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LAD

3lad


Resolution: 2.5→29.42 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.926 / SU B: 25.441 / SU ML: 0.279 / Cross valid method: THROUGHOUT / ESU R: 0.474 / ESU R Free: 0.288 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26422 2044 4.9 %RANDOM
Rwork0.2254 ---
obs0.22729 40007 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 60.399 Å2
Baniso -1Baniso -2Baniso -3
1--1.47 Å20 Å20 Å2
2--7.17 Å20 Å2
3----5.69 Å2
Refinement stepCycle: 1 / Resolution: 2.5→29.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6924 0 120 251 7295
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0197180
X-RAY DIFFRACTIONr_bond_other_d0.0010.027046
X-RAY DIFFRACTIONr_angle_refined_deg1.4591.9839749
X-RAY DIFFRACTIONr_angle_other_deg0.877316225
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.9985952
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.20125.494253
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.771151200
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2041524
X-RAY DIFFRACTIONr_chiral_restr0.0810.21161
X-RAY DIFFRACTIONr_gen_planes_refined0.0230.028102
X-RAY DIFFRACTIONr_gen_planes_other0.020.021448
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7333.5433806
X-RAY DIFFRACTIONr_mcbond_other1.7323.5413804
X-RAY DIFFRACTIONr_mcangle_it2.7635.3074758
X-RAY DIFFRACTIONr_mcangle_other2.7635.3084759
X-RAY DIFFRACTIONr_scbond_it1.7583.7963374
X-RAY DIFFRACTIONr_scbond_other1.7543.7963374
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.8225.6184992
X-RAY DIFFRACTIONr_long_range_B_refined5.66543.258010
X-RAY DIFFRACTIONr_long_range_B_other5.65143.1567991
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 27492 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 142 -
Rwork0.359 2897 -
obs--99.22 %
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)
13.24190.01521.27093.13921.11550.96210.01570.07020.07730.03570.0228-0.1474-0.05190.1585-0.03850.089-0.1050.02820.23590.00380.051942.7649101.844825.6594
21.07710.5484-0.6311.2166-0.75540.8412-0.0505-0.16080.0596-0.16460.05470.13660.16520.2592-0.00420.30450.023-0.02870.23950.03970.294732.583893.130925.4844
31.6123-1.1282-0.5781.0743-0.16662.32470.0687-0.19420.0159-0.25220.05660.21150.27080.4933-0.12540.47060.0869-0.03470.13180.05880.369927.922478.162113.8844
41.9514-0.52041.32681.686-0.91833.103-0.09870.1938-0.3247-0.23420.16970.08430.50820.0083-0.07110.5520.08410.02020.1088-0.00770.358628.97670.32510.5168
52.93721.0974-0.77073.3119-1.08130.4831-0.0610.0408-0.1473-0.2205-0.1092-0.53070.13630.16280.17020.09080.15670.0480.33710.0550.128252.001489.823721.5536
63.6714-0.4174-0.12130.7981-0.05641.00520.12860.2125-0.0473-0.1859-0.221-0.2710.0189-0.09710.09230.34070.16270.03940.11990.07790.308744.575466.063638.1023
72.9289-0.7899-0.25112.48120.10141.05350.15430.29630.0395-0.0279-0.144-0.07110.12690.0233-0.01030.43250.2023-0.03770.1146-0.02110.320235.734449.764958.3665
80.9228-0.55730.81141.6674-0.61360.73960.07420.1017-0.048-0.01130.04930.06960.06530.0759-0.12350.39580.18030.04140.09530.03830.406726.408458.179754.0519
90.3318-0.04950.99181.5118-0.21433.10650.14780.0954-0.09540.31740.13740.38420.29460.2509-0.28520.42250.130.09460.05880.0620.473617.419972.704463.1895
103.78290.145-1.51390.5321-0.39892.60530.0873-0.10060.36010.41410.12710.3127-0.2010.0909-0.21440.40090.12090.1470.04770.05260.362716.935180.483766.4398
113.0519-0.32210.97951.9513-1.04553.28090.16630.08220.2660.3025-0.0412-0.0879-0.27760.2589-0.12510.39290.1446-0.02720.1037-0.02070.275242.577359.294668.1012
121.40350.00110.11281.9019-0.0221.02480.09560.0436-0.1380.1577-0.0622-0.2336-0.04980.1457-0.03330.10970.04340.00790.09740.08260.14742.220484.113149.1185
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 55
2X-RAY DIFFRACTION2A56 - 154
3X-RAY DIFFRACTION3A155 - 218
4X-RAY DIFFRACTION4A219 - 278
5X-RAY DIFFRACTION5A279 - 359
6X-RAY DIFFRACTION6A360 - 474
7X-RAY DIFFRACTION7B1 - 55
8X-RAY DIFFRACTION8B56 - 153
9X-RAY DIFFRACTION9B154 - 218
10X-RAY DIFFRACTION10B219 - 279
11X-RAY DIFFRACTION11B280 - 344
12X-RAY DIFFRACTION12B345 - 474

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