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- PDB-5jwb: Structure of NDH2 from plasmodium falciparum in complex with NADH -

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Basic information

Entry
Database: PDB / ID: 5jwb
TitleStructure of NDH2 from plasmodium falciparum in complex with NADH
ComponentsType II NADH:ubiquinone oxidoreductase
KeywordsMEMBRANE PROTEIN/INHIBITOR / PfNDH2 / NADH / MEMBRANE PROTEIN-INHIBITOR complex
Function / homology
Function and homology information


NADH:quinone reductase (non-electrogenic) / quinone reductase (NADPH) activity / NADH dehydrogenase (quinone) (non-electrogenic) activity / oxidoreductase activity / nucleotide binding / mitochondrion / metal ion binding
Similarity search - Function
: / PfNDH2 helical insertion domain / : / NDH2 C-terminal domain / Alternative NADH dehydrogenase / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
ACETATE ION / FLAVIN-ADENINE DINUCLEOTIDE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NADH:ubiquinone reductase (non-electrogenic)
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsYu, Y. / Li, X.L.
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 12, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 29, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_Rpim_I_all / _reflns.pdbx_Rrim_I_all ..._reflns.pdbx_Rpim_I_all / _reflns.pdbx_Rrim_I_all / _reflns_shell.number_unique_all / _reflns_shell.number_unique_obs / _reflns_shell.pdbx_Rpim_I_all / _reflns_shell.pdbx_Rrim_I_all
Revision 1.2Nov 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_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Type II NADH:ubiquinone oxidoreductase
H: Type II NADH:ubiquinone oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,66229
Polymers120,5982
Non-polymers6,06327
Water50428
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16440 Å2
ΔGint-91 kcal/mol
Surface area41330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)191.530, 191.530, 91.258
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 Type II NADH:ubiquinone oxidoreductase


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: PF3D7_0915000 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: Q8I302, NADH:ubiquinone reductase (H+-translocating)

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Non-polymers , 7 types, 55 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-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#6: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical ChemComp-CXS / 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID


Mass: 221.317 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H19NO3S / Comment: pH buffer*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 3.65 Å3/Da / Density % sol: 66.32 %
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)

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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: 2.7→50 Å / Num. obs: 45452 / % possible obs: 99.9 % / Redundancy: 7.4 % / Biso Wilson estimate: 50.94 Å2 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.099 / Rrim(I) all: 0.036 / Χ2: 1.316 / Net I/σ(I): 9.7 / Num. measured all: 337713
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.743 / Num. unique obs: 4672 / CC1/2: 1 / Rpim(I) all: 1.1 / Χ2: 1.133 / % possible all: 99.8

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Processing

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

4g6g


Resolution: 2.7→45.91 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.34
RfactorNum. reflection% reflection
Rfree0.226 2294 5.05 %
Rwork0.18 43137 -
obs0.183 45431 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 102.33 Å2 / Biso mean: 46.32 Å2 / Biso min: 19.96 Å2
Refinement stepCycle: final / Resolution: 2.7→45.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8053 0 375 28 8456
Biso mean--50.45 42.89 -
Num. residues----985
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7006-2.75930.38011320.275326782810100
2.7593-2.82340.28611440.255726732817100
2.8234-2.8940.28281440.221926582802100
2.894-2.97230.2951510.219326942845100
2.9723-3.05970.26741390.213426762815100
3.0597-3.15850.26881320.216727152847100
3.1585-3.27130.261660.195526612827100
3.2713-3.40230.26661460.178127062852100
3.4023-3.5570.22911520.173526372789100
3.557-3.74450.2281470.178226982845100
3.7445-3.9790.19931530.165226912844100
3.979-4.2860.20351190.154627092828100
4.286-4.71690.16961420.138527152857100
4.7169-5.39850.1671510.158326952846100
5.3985-6.79810.24011340.189127682902100
6.7981-45.9160.2221420.1812763290599

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