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- PDB-3fet: Crystal Structure of the Electron Transfer Flavoprotein Subunit A... -

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Basic information

Entry
Database: PDB / ID: 3fet
TitleCrystal Structure of the Electron Transfer Flavoprotein Subunit Alpha related Protein Ta0212 from Thermoplasma acidophilum
ComponentsElectron transfer flavoprotein subunit alpha related protein
KeywordsELECTRON TRANSPORT / alpha-beta-alpha sandwich / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


fatty acid beta-oxidation using acyl-CoA dehydrogenase / flavin adenine dinucleotide binding / electron transfer activity
Similarity search - Function
Electron transfer flavoprotein alpha subunit/FixB / Electron transfer flavoprotein, alpha/beta-subunit, N-terminal / Electron transfer flavoprotein, alpha subunit, C-terminal / Electron transfer flavoprotein FAD-binding domain / Electron transfer flavoprotein domain / DHS-like NAD/FAD-binding domain superfamily / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Electron transfer flavoprotein subunit alpha related protein
Similarity search - Component
Biological speciesThermoplasma acidophilum (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.05 Å
AuthorsKim, Y. / Tesar, C. / Souvong, K. / Moy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of the Electron Transfer Flavoprotein Subunit Alpha related Protein Ta0212 from Thermoplasma acidophilum
Authors: Kim, Y. / Tesar, C. / Souvong, K. / Moy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
History
DepositionDec 1, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Jul 18, 2012Group: Database references
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Electron transfer flavoprotein subunit alpha related protein
B: Electron transfer flavoprotein subunit alpha related protein
C: Electron transfer flavoprotein subunit alpha related protein
D: Electron transfer flavoprotein subunit alpha related protein


Theoretical massNumber of molelcules
Total (without water)72,8894
Polymers72,8894
Non-polymers00
Water6,125340
1
A: Electron transfer flavoprotein subunit alpha related protein
C: Electron transfer flavoprotein subunit alpha related protein


Theoretical massNumber of molelcules
Total (without water)36,4452
Polymers36,4452
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2530 Å2
ΔGint-11 kcal/mol
Surface area15390 Å2
MethodPISA
2
B: Electron transfer flavoprotein subunit alpha related protein
D: Electron transfer flavoprotein subunit alpha related protein


Theoretical massNumber of molelcules
Total (without water)36,4452
Polymers36,4452
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-10 kcal/mol
Surface area15060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.696, 115.358, 63.462
Angle α, β, γ (deg.)90.00, 109.79, 90.00
Int Tables number4
Space group name H-MP1211
Detailstwo dimers in the asymmetric unit

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Components

#1: Protein
Electron transfer flavoprotein subunit alpha related protein


Mass: 18222.260 Da / Num. of mol.: 4 / Fragment: residues 1-163
Source method: isolated from a genetically manipulated source
Details: N-terminal 6-His tag with TEV protease cut site / Source: (gene. exp.) Thermoplasma acidophilum (acidophilic) / Strain: DSM1728 / Gene: Ta0212 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: Q9HLL5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 340 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.3 Å3/Da / Density % sol: 46.55 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.1 M Na Citrate pH 5.6 20% iso-Propanol, 20% PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 6, 2008 / Details: mirrors
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. all: 39380 / Num. obs: 39380 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 27.7 Å2 / Rmerge(I) obs: 0.104 / Net I/σ(I): 6.9
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.1 / Num. unique all: 1352 / % possible all: 67.6

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
MLPHAREphasing
DMmodel building
SHELXDphasing
RESOLVEmodel building
Cootmodel building
REFMAC5.5.0053refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.05→41.49 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.932 / SU B: 10.337 / SU ML: 0.126 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.226 / ESU R Free: 0.188 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.232 1978 5 %RANDOM
Rwork0.179 ---
all0.181 37345 --
obs0.181 37345 95.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.389 Å2
Baniso -1Baniso -2Baniso -3
1-2.74 Å20 Å21.04 Å2
2---2.99 Å20 Å2
3---0.96 Å2
Refinement stepCycle: LAST / Resolution: 2.05→41.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5026 0 0 340 5366
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0225239
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.581.977051
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2975677
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.97324.253221
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.03115963
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5351529
X-RAY DIFFRACTIONr_chiral_restr0.1180.2789
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023896
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.8681.53289
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.5825284
X-RAY DIFFRACTIONr_scbond_it2.86531950
X-RAY DIFFRACTIONr_scangle_it4.9274.51767
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 93 -
Rwork0.247 1903 -
obs-1996 66.27 %
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)
11.31720.05880.45661.4210.27641.7510.02550.06790.03430.1244-0.05380.0134-0.0941-0.04950.02840.1174-0.02870.00750.05870.00360.002310.264254.493958.8933
22.4302-1.0886-0.37951.70150.29080.91020.04020.069-0.4245-0.0667-0.01830.29160.0823-0.0975-0.02190.0153-0.006-0.02660.0155-0.00690.10332.798438.701625.3013
31.67520.505-0.44952.33850.07571.13190.0436-0.0758-0.03910.2519-0.11560.07450.1144-0.01580.07190.1179-0.02050.03220.0323-0.0030.01148.631829.466852.5861
40.9145-0.46450.04842.5475-0.16260.8548-0.0018-0.02710.08680.0913-0.0181-0.0683-0.11250.02630.01990.02630.00280.00020.0190.010.017516.730859.340230.5272
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 162
2X-RAY DIFFRACTION2B0 - 162
3X-RAY DIFFRACTION3C0 - 162
4X-RAY DIFFRACTION4D-1 - 162

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