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- PDB-3lwx: Crystal structure of Na(+)-translocating NADH-quinone reductase s... -

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Basic information

Entry
Database: PDB / ID: 3lwx
TitleCrystal structure of Na(+)-translocating NADH-quinone reductase subunit C (YP_001302508.1) from Parabacteroides distasonis ATCC 8503 at 1.10 A resolution
ComponentsNADH:ubiquinone oxidoreductase, Na translocating, C subunit
KeywordsOXIDOREDUCTASE / Na(+)-translocating NADH-quinone reductase subunit C / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / Transport / Ubiquinone
Function / homology
Function and homology information


NADH:ubiquinone reductase (Na+-transporting) / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / sodium ion transport / FMN binding / membrane => GO:0016020 / iron ion binding / plasma membrane
Similarity search - Function
Na(+)-translocating NADH-quinone reductase subunit C / FMN-binding / FMN-binding domain / FMN_bind / Rubredoxin-like domain / Rubredoxin-like domain profile.
Similarity search - Domain/homology
Na(+)-translocating NADH-quinone reductase subunit C
Similarity search - Component
Biological speciesParabacteroides distasonis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.1 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Na(+)-translocating NADH-quinone reductase subunit C (YP_001302508.1) from Parabacteroides distasonis ATCC 8503 at 1.10 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionFeb 24, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 31, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NADH:ubiquinone oxidoreductase, Na translocating, C subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0974
Polymers21,8211
Non-polymers2763
Water6,666370
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.444, 60.693, 82.758
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein NADH:ubiquinone oxidoreductase, Na translocating, C subunit


Mass: 21820.781 Da / Num. of mol.: 1 / Fragment: sequence database residues 73-270
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Parabacteroides distasonis (bacteria) / Strain: ATCC 8503 / DSM 20701 / NCTC 11152 / Gene: BDI_1123 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: A6LB22
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 370 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. THE CLONED CONSTRUCT CONTAINS RESIDUES 73-270 OF THE FULL LENGTH PROTEIN.

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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: 2.15 Å3/Da / Density % sol: 42.92 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 15.0000% Glycerol, 0.1700M NaOAc, 25.5000% PEG-4000, 0.1M TRIS pH 8.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97861
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 25, 2010 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97861 Å / Relative weight: 1
ReflectionResolution: 1.1→29.739 Å / Num. obs: 74185 / % possible obs: 95.2 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 7.951 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 14.69
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.1-1.140.5342.2337551351589.9
1.14-1.180.4052.8305311205892.6
1.18-1.240.3423.3395221552093.4
1.24-1.30.2684.3329941293394.6
1.3-1.390.1945.7395541542594.8
1.39-1.490.1357.8338711321195.7
1.49-1.640.0811.8369071434096.4
1.64-1.880.05418.6441791463297.3
1.88-2.370.03235.5626721461298.4
2.37-29.7390.02550.9647691468899.1

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0102refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.1→29.739 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.978 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 0.806 / SU ML: 0.017 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.028 / ESU R Free: 0.028
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. GLYCEROL (GOL) FROM THE CRYSTALLIZATION SOLUTION WERE MODELED INTO THE STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.138 3700 5 %RANDOM
Rwork0.116 ---
obs0.117 74143 96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 45.59 Å2 / Biso mean: 13.424 Å2 / Biso min: 5.82 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20 Å20 Å2
2--0.34 Å20 Å2
3----0.55 Å2
Refinement stepCycle: LAST / Resolution: 1.1→29.739 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1803 0 24 411 2238
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221905
X-RAY DIFFRACTIONr_bond_other_d0.0010.021320
X-RAY DIFFRACTIONr_angle_refined_deg1.4741.9652638
X-RAY DIFFRACTIONr_angle_other_deg1.64733308
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2495286
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.2126.27986
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.88615355
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.216154
X-RAY DIFFRACTIONr_chiral_restr0.070.2290
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022241
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02365
X-RAY DIFFRACTIONr_mcbond_it1.47421173
X-RAY DIFFRACTIONr_mcbond_other0.8592478
X-RAY DIFFRACTIONr_mcangle_it2.35641944
X-RAY DIFFRACTIONr_scbond_it3.716732
X-RAY DIFFRACTIONr_scangle_it5.3548654
X-RAY DIFFRACTIONr_rigid_bond_restr1.15933225
LS refinement shellResolution: 1.1→1.129 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.197 256 -
Rwork0.193 4887 -
all-5143 -
obs--91.53 %

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