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- PDB-5jwa: the structure of malaria PfNDH2 -

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Basic information

Entry
Database: PDB / ID: 5jwa
Titlethe structure of malaria PfNDH2
ComponentsNADH dehydrogenase, putative
KeywordsMEMBRANE PROTEIN/INHIBITOR / PfNDH2 / FAD / MEMBRANE PROTEIN-INHIBITOR complex
Function / homology
Function and homology information


NADH:quinone reductase (non-electrogenic) / NADPH:quinone reductase activity / NADH oxidation / NADH:ubiquinone reductase (non-electrogenic) activity / oxidoreductase activity / nucleotide binding / mitochondrion / metal ion binding
Similarity search - Function
PfNDH2 helical insertion domain / Alternative NADH dehydrogenase / NDH2 C-terminal domain / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
ACETATE ION / FLAVIN-ADENINE DINUCLEOTIDE / NADH:ubiquinone reductase (non-electrogenic)
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.162 Å
AuthorsYu, Y. / Yang, Y.Q. / Li, X.L. / Yu, J. / Ge, J.P. / Li, J. / Rao, Y. / Yang, M.J.
CitationJournal: J. Med. Chem. / Year: 2017
Title: Target Elucidation by Cocrystal Structures of NADH-Ubiquinone Oxidoreductase of Plasmodium falciparum (PfNDH2) with Small Molecule To Eliminate Drug-Resistant Malaria
Authors: Yang, Y. / Yu, Y. / Li, X. / Li, J. / Wu, Y. / Yu, J. / Ge, J. / Huang, Z. / Jiang, L. / Rao, Y. / Yang, M.
History
DepositionMay 11, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NADH dehydrogenase, putative
H: NADH dehydrogenase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,18830
Polymers120,5982
Non-polymers4,58928
Water5,386299
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13790 Å2
ΔGint-107 kcal/mol
Surface area42780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)191.670, 191.670, 91.388
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41

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Components

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Protein , 1 types, 2 molecules AH

#1: Protein NADH dehydrogenase, putative


Mass: 60299.215 Da / Num. of mol.: 2 / Fragment: UNP residues 25-533
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / Gene: PFI0735c
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
References: UniProt: Q8I302, NADH dehydrogenase

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Non-polymers , 5 types, 327 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-TRT / FRAGMENT OF TRITON X-100 / 1-{2-[2-(2-METHOXYETHOXY)ETHOXY]ETHOXY}-4-(1,1,3,3-TETRAMETHYLBUTYL)BENZENE


Mass: 352.508 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H36O4 / Comment: detergent*YM
#5: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 299 / 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: 3.67 Å3/Da / Density % sol: 66.47 %
Description: the entry contains friedel pairs in F_Plus/Minus columns
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: protein(10mg/ml) reservoir solution (2.7M sodium acetate trihydrate, pH screen kit from Hampoton Research at 4.8 or 10.0 to 10.0 to 10.6)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 20, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.16→50 Å / Num. obs: 87149 / % possible obs: 98.4 % / Redundancy: 6.2 % / Biso Wilson estimate: 38.14 Å2 / Rmerge(I) obs: 0.08 / Net I/av σ(I): 30.286 / Net I/σ(I): 11.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.16-2.260.837196.7
2.2-2.2460.711197.9
2.24-2.286.10.619196.8
2.28-2.336.10.56198
2.33-2.386.10.465198.1
2.38-2.436.10.431198.2
2.43-2.496.10.369198.1
2.49-2.566.20.307198.2
2.56-2.646.20.39198.3
2.64-2.726.20.214198.4
2.72-2.826.30.169198.7
2.82-2.936.40.133198.4
2.93-3.066.40.104198.8
3.06-3.236.40.085199.3
3.23-3.436.40.065198.8
3.43-3.696.40.056199.1
3.69-4.066.40.049199.3
4.06-4.656.20.045199.4
4.65-5.8660.041199.4
5.86-506.30.04198.2

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIXphenix.refine: 1.8.4_1496refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHASphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4G6G

4g6g


Resolution: 2.162→45.177 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.08
RfactorNum. reflection% reflection
Rfree0.2284 4380 5.03 %
Rwork0.1881 --
obs0.1902 87114 98.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 101.01 Å2 / Biso mean: 41.2 Å2 / Biso min: 21.25 Å2
Refinement stepCycle: final / Resolution: 2.162→45.177 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8093 0 279 299 8671
Biso mean--44.73 43.29 -
Num. residues----990
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088558
X-RAY DIFFRACTIONf_angle_d1.1611583
X-RAY DIFFRACTIONf_chiral_restr0.0491252
X-RAY DIFFRACTIONf_plane_restr0.0041425
X-RAY DIFFRACTIONf_dihedral_angle_d16.8223199
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1617-2.18630.29911650.25222674283996
2.1863-2.2120.25681450.24462703284897
2.212-2.2390.26741430.23162757290098
2.239-2.26730.27861350.2222692282797
2.2673-2.29720.26311440.23212700284498
2.2972-2.32860.2581380.23172762290097
2.3286-2.36190.28641510.22472697284899
2.3619-2.39720.24071520.22032729288197
2.3972-2.43460.27191590.21122754291399
2.4346-2.47450.2671410.21492734287597
2.4745-2.51720.25431300.21112742287298
2.5172-2.5630.23741500.20882762291299
2.563-2.61220.30561550.25932680283597
2.6122-2.66560.25421360.22362755289199
2.6656-2.72350.25071450.2112771291699
2.7235-2.78690.28551450.22122762290798
2.7869-2.85650.27431470.20672747289498
2.8565-2.93380.25741290.21862759288899
2.9338-3.02010.27991440.21262784292899
3.0201-3.11750.26891650.20492774293999
3.1175-3.22890.22111390.19842780291999
3.2289-3.35820.25651480.18542767291599
3.3582-3.51090.19931480.18062764291299
3.5109-3.6960.22721470.18152804295199
3.696-3.92740.18831310.16432802293399
3.9274-4.23040.20911440.15592800294499
4.2304-4.65580.16681620.15112800296299
4.6558-5.32860.16941440.155128222966100
5.3286-6.70990.25181530.18852813296699
6.7099-45.18690.20591450.16782844298997

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