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- PDB-2zcv: Crystal structure of NADPH-dependent quinone oxidoreductase QOR2 ... -

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Basic information

Entry
Database: PDB / ID: 2zcv
TitleCrystal structure of NADPH-dependent quinone oxidoreductase QOR2 complexed with NADPH from escherichia coli
ComponentsUncharacterized oxidoreductase ytfG
KeywordsOXIDOREDUCTASE / ALPHA-BETA SANDWICH / COMPLEX WITH NADPH
Function / homology
Function and homology information


NADPH dehydrogenase (quinone) activity / NAD(P)H dehydrogenase (quinone) / NADH:ubiquinone reductase (non-electrogenic) activity / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / cytosol
Similarity search - Function
NmrA-like domain / NmrA-like family / UDP-galactose 4-epimerase, domain 1 / UDP-galactose 4-epimerase; domain 1 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
COPPER (II) ION / Chem-NDP / Quinone oxidoreductase 2
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKim, I.K. / Yim, H.S. / Kim, M.K. / Kim, D.W. / Kim, Y.M. / Cha, S.S. / Kang, S.O.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Crystal structure of a new type of NADPH-dependent quinone oxidoreductase (QOR2) from Escherichia coli
Authors: Kim, I.K. / Yim, H.S. / Kim, M.K. / Kim, D.W. / Kim, Y.M. / Cha, S.S. / Kang, S.O.
History
DepositionNov 13, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 27, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 20, 2013Group: Non-polymer description
Revision 1.3Nov 1, 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 / pdbx_struct_conn_angle / struct_conn / 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_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

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized oxidoreductase ytfG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7635
Polymers29,7621
Non-polymers1,0014
Water4,017223
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.284, 81.284, 77.506
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Uncharacterized oxidoreductase ytfG / hypothetical protein YTFG / YTFG gene product / NADPH-dependent quinone oxidoreductase


Mass: 29762.406 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: strain K12 / Plasmid: PET3A / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P39315, NADPH:quinone reductase
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / 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: 2.38 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 285 K / Method: evaporation / pH: 7.5
Details: PEG 4000, COPPER CHLRORIDE, HEPES, AMMONIUM SULFATE, pH 7.50, EVAPORATION, temperature 285K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6B / Wavelength: 1.12714
DetectorType: BRUKER PROTEUM 300 / Detector: CCD / Date: May 10, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12714 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 13535 / % possible obs: 86.9 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 30.4 Å2
Reflection shellResolution: 2.3→2.4 Å / % possible all: 82

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Processing

Software
NameVersionClassification
CNSrefinement
SMARTdata reduction
SAINT& PROSCALEdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZCU

2zcu


Resolution: 2.3→19.52 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 198248.85 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.298 1135 10.4 %RANDOM
Rwork0.217 ---
obs0.217 10926 86.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 73.43 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 39.9 Å2
Baniso -1Baniso -2Baniso -3
1-8.77 Å29.78 Å20 Å2
2--8.77 Å20 Å2
3----17.54 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.3→19.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2012 0 59 223 2294
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.72
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.371 178 10.9 %
Rwork0.292 1458 -
obs--73.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4NADP9.PARAMNADP9.TOP

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