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- PDB-3mcr: Crystal structure of NADH dehydrogenase subunit C (Tfu_2693) from... -

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Basic information

Entry
Database: PDB / ID: 3mcr
TitleCrystal structure of NADH dehydrogenase subunit C (Tfu_2693) from THERMOBIFIDA FUSCA YX-ER1 at 2.65 A resolution
ComponentsNADH dehydrogenase, subunit C
KeywordsOXIDOREDUCTASE / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / NADH dehydrogenase (ubiquinone) activity / quinone binding / plasma membrane
Similarity search - Function
NADH:ubiquinone oxidoreductase Nqo5 subunit / NADH dehydrogenase, subunit C / NADH:ubiquinone oxidoreductase, 30kDa subunit / NADH:ubiquinone oxidoreductase, 30kDa subunit superfamily / Respiratory-chain NADH dehydrogenase, 30 Kd subunit / Beta Polymerase; domain 2 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / HEXANE-1,6-DIOL / NADH-quinone oxidoreductase subunit C
Similarity search - Component
Biological speciesThermobifida fusca (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 2.65 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of NADH dehydrogenase subunit C (Tfu_2693) from THERMOBIFIDA FUSCA YX-ER1 at 2.65 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMar 29, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 17, 2019Group: Data collection / Refinement description / Category: software
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
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NADH dehydrogenase, subunit C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1823
Polymers24,0051
Non-polymers1772
Water1086
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: NADH dehydrogenase, subunit C
hetero molecules

A: NADH dehydrogenase, subunit C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3646
Polymers48,0092
Non-polymers3544
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area2240 Å2
ΔGint-29 kcal/mol
Surface area14900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.264, 69.264, 114.210
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-213-

CO

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Components

#1: Protein NADH dehydrogenase, subunit C


Mass: 24004.711 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Genomic DNA from the protease deficient ER1 strain derived form Thermobifida fusca YX was a gift from David B. Wilson at Cornell University.
Source: (gene. exp.) Thermobifida fusca (bacteria) / Strain: YX / Gene: Tfu_2693 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q47LE6
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-HEZ / HEXANE-1,6-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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 RESIDUES 1-212 OF THE FULL LENGTH (252 AMINO ACID) TARGET SEQUENCE.

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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: 2.85 Å3/Da / Density % sol: 56.89 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 1.0000M 1,6-Hexanediol, 0.0100M CoCl2, 0.1M Acetate pH 4.6, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97922
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 10, 2008 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97922 Å / Relative weight: 1
ReflectionResolution: 2.65→48.97 Å / Num. obs: 8611 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 6.95 % / Biso Wilson estimate: 82.093 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 25.89
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.65-2.740.812.156877941100
2.74-2.850.4533.860428431100
2.85-2.980.3274.959608361100
2.98-3.140.2167.861458641100
3.14-3.340.13213.260838581100
3.34-3.590.07222.258008261100
3.59-3.950.04931.95999853199.6
3.95-4.520.0348.260168701100
4.52-5.670.02655.15973883199.9
5.67-48.970.02260.76108986199.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0102refinement
PHENIXrefinement
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: molecular replacement
Starting model: 2fug

2fug


Resolution: 2.65→48.97 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.923 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 22.045 / SU ML: 0.206 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.352 / ESU R Free: 0.273 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY 3.COBALT (CO) AND 1,6-HEXANEDIOL (HEZ) FROM THE CRYSTALLIZATION SOLUTION WERE MODELED INTO ...Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY 3.COBALT (CO) AND 1,6-HEXANEDIOL (HEZ) FROM THE CRYSTALLIZATION SOLUTION WERE MODELED INTO THE STRUCTURE. THE MODELING OF COBALT IS SUPPORTED BY ANOMALOUS DIFFERENCE MAPS. 4. THE ELECTRON DENSITY CORRESPONDING TO THE N-TERMINAL 59 RESIDUES WAS DISORDERED AND THIS REGION COULD NOT BE MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.259 402 4.7 %RANDOM
Rwork0.207 ---
obs0.21 8568 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 74.72 Å2 / Biso mean: 40.196 Å2 / Biso min: 19.26 Å2
Baniso -1Baniso -2Baniso -3
1-1.75 Å20 Å20 Å2
2--1.75 Å20 Å2
3----3.51 Å2
Refinement stepCycle: LAST / Resolution: 2.65→48.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1222 0 9 6 1237
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0211283
X-RAY DIFFRACTIONr_bond_other_d0.0020.02853
X-RAY DIFFRACTIONr_angle_refined_deg1.411.9471758
X-RAY DIFFRACTIONr_angle_other_deg0.96732061
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.9875157
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.20923.23568
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.55815179
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.8951511
X-RAY DIFFRACTIONr_chiral_restr0.0710.2191
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211457
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02276
X-RAY DIFFRACTIONr_mcbond_it1.0873780
X-RAY DIFFRACTIONr_mcbond_other0.1743307
X-RAY DIFFRACTIONr_mcangle_it2.12651269
X-RAY DIFFRACTIONr_scbond_it3.6058503
X-RAY DIFFRACTIONr_scangle_it5.75411487
LS refinement shellResolution: 2.65→2.719 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.435 35 -
Rwork0.371 585 -
all-620 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 53.536 Å / Origin y: 41.0403 Å / Origin z: 31.0986 Å
111213212223313233
T0.3335 Å20.0136 Å2-0.004 Å2-0.2358 Å2-0.0439 Å2--0.2211 Å2
L2.9653 °21.0644 °20.7181 °2-1.907 °21.2701 °2--2.7202 °2
S-0.0534 Å °-0.0611 Å °0.2599 Å °-0.1365 Å °0.0924 Å °-0.0751 Å °-0.1782 Å °0.1546 Å °-0.039 Å °

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