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- PDB-3qwb: Crystal structure of Saccharomyces cerevisiae Zeta-crystallin-lik... -

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Basic information

Entry
Database: PDB / ID: 3qwb
TitleCrystal structure of Saccharomyces cerevisiae Zeta-crystallin-like quinone oxidoreductase Zta1 complexed with NADPH
ComponentsProbable quinone oxidoreductase
KeywordsOXIDOREDUCTASE / Rossmann Fold / quinone oxidoreductases / NADPH / cytoplasm and nucleus
Function / homology
Function and homology information


NADPH:quinone reductase / 2-alkenal reductase [NAD(P)+] activity / NADPH:quinone reductase activity / mRNA 3'-UTR AU-rich region binding / NADPH binding / cellular response to oxidative stress / zinc ion binding / nucleus / cytoplasm / cytosol
Similarity search - Function
: / Quinone oxidoreductase/zeta-crystallin, conserved site / Quinone oxidoreductase / zeta-crystallin signature. / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain ...: / Quinone oxidoreductase/zeta-crystallin, conserved site / Quinone oxidoreductase / zeta-crystallin signature. / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase / GroES-like superfamily / 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
Chem-NDP / Probable quinone oxidoreductase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsGuo, P.C. / Ma, X.X. / Bao, Z.Z. / Chen, Y.X. / Zhou, C.Z.
CitationJournal: J.Struct.Biol. / Year: 2011
Title: Structural insights into the cofactor-assisted substrate recognition of yeast quinone oxidoreductase Zta1
Authors: Guo, P.C. / Ma, X.X. / Bao, Z.Z. / Ma, J.D. / Chen, Y. / Zhou, C.Z.
History
DepositionFeb 28, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 8, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Probable quinone oxidoreductase
B: Probable quinone oxidoreductase
C: Probable quinone oxidoreductase
D: Probable quinone oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,69613
Polymers148,2544
Non-polymers3,4429
Water29,3101627
1
A: Probable quinone oxidoreductase
B: Probable quinone oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,8947
Polymers74,1272
Non-polymers1,7675
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2450 Å2
ΔGint-7 kcal/mol
Surface area27220 Å2
MethodPISA
2
C: Probable quinone oxidoreductase
D: Probable quinone oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,8026
Polymers74,1272
Non-polymers1,6754
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2430 Å2
ΔGint-7 kcal/mol
Surface area26970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.961, 75.362, 182.833
Angle α, β, γ (deg.)90.00, 92.11, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Probable quinone oxidoreductase / NADPH:quinone reductase / NADPH-dependent quinone reductase


Mass: 37063.566 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: S288C / Gene: YBR0421, YBR046C, ZTA1 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P38230, NADPH:quinone reductase
#2: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1627 / 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: 2.51 Å3/Da / Density % sol: 50.91 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 25% polyethylene glycol 3350, 0.1M Tris-HCl pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 289.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 8, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.59→50 Å / Num. obs: 190318 / % possible obs: 97.2 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.106 / Net I/σ(I): 8.67
Reflection shellResolution: 1.59→1.61 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.157 / Mean I/σ(I) obs: 6.05 / Num. unique all: 8502 / % possible all: 87.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0072refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QOR

1qor


Resolution: 1.59→35.5 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.939 / SU B: 3.186 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21133 9637 5.1 %RANDOM
Rwork0.18774 ---
obs0.18894 180675 97.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.774 Å2
Baniso -1Baniso -2Baniso -3
1-0.61 Å20 Å20 Å2
2---0.2 Å20 Å2
3----0.42 Å2
Refinement stepCycle: LAST / Resolution: 1.59→35.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10340 0 222 1627 12189
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02210781
X-RAY DIFFRACTIONr_angle_refined_deg1.282.01214605
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.72451316
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.71224.766428
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.326151900
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0071536
X-RAY DIFFRACTIONr_chiral_restr0.0850.21636
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217884
X-RAY DIFFRACTIONr_mcbond_it0.671.56548
X-RAY DIFFRACTIONr_mcangle_it1.107210564
X-RAY DIFFRACTIONr_scbond_it1.32334233
X-RAY DIFFRACTIONr_scangle_it2.2674.54041
LS refinement shellResolution: 1.593→1.634 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 654 -
Rwork0.23 12496 -
obs--91.78 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.07170.0451-0.05650.1355-0.05430.11080.00070.00470.0036-0.01090.00910.01570.0083-0.007-0.00980.0019-0.0008-0.00190.00070.00120.002419.29860.232866.6273
20.5238-0.5744-0.23170.63470.24670.3644-0.00270.00130.04910.00490.0041-0.04980.025-0.0122-0.00130.00340.00130.00320.00550.00380.011427.6447-1.753466.7536
30.08640.042-0.03650.0624-0.01830.0748-0.003-0.0040.0001-0.0055-0.0011-0.0008-0.00270.00380.00410.0008-0.00010.00010.00030.00010.002535.62538.52272.793
40.4898-0.3031-0.46030.29930.2970.7927-0.02210.00150.01840.00660.015-0.00250.0337-0.0150.00710.0023-0.00160.00030.0030.00050.005333.6836.45580.869
50.094-0.07740.05210.0872-0.05810.1367-0.0042-0.003-0.00810.00660.00360.0074-0.0129-0.01080.00060.0077-0.00020.00020.0011-0.00020.00118.794126.518524.4121
60.08760.12790.22960.59610.39610.6124-0.0077-0.0063-0.0035-0.01010.0154-0.0026-0.0247-0.0117-0.00770.0108-0.0024-0.00130.00280.00090.000427.095428.432225.3639
70.0749-0.04440.0340.0426-0.05230.2026-0.00040-0.00660.0006-0.00560.00740.01160.02430.0060.00180.00110.00170.00340.00050.003436.679-11.54319.448
80.18160.03530.02850.12080.43861.65110.0021-0.0014-0.0129-0.0204-0.0044-0.0015-0.0802-0.01830.00230.01140.0022-0.00090.0007-0.00010.00136.023-9.18911.204
90.0007-0.00280.00150.0183-0.0140.01370.0011-0.0003-0.001-0.00470.0010.00380.0015-0.0003-0.00210.0028-0.0003-0.00110.00040.00080.00226.82414.65448.118
1029.7406-24.5485-20.642520.271517.036114.3284-0.0113-0.2520.2407-0.01010.1892-0.19680.00420.1775-0.17790.02020.0069-0.00330.01710.00090.008223.534324.043318.6994
110.81224.4318-1.176424.1825-6.41921.7040.00780.01020.04220.04690.05380.2292-0.0125-0.0145-0.06160.0007-0.0008-0.00150.00950.00550.00938.38931.7675.207
1221.902121.76213.754321.622913.66648.6377-0.05510.1641-0.106-0.03450.142-0.1062-0.02180.1019-0.08690.0081-0.0044-0.0010.01830.0110.009123.34582.806672.7665
1315.5672-17.6997-0.89520.1261.01890.05250.16040.1126-0.225-0.2111-0.1480.2496-0.015-0.006-0.01240.0405-0.01230.01520.0204-0.00180.036226.4582-18.757663.0063
140.70111.42535.03882.897610.243736.2136-0.02620.01040.0001-0.05740.02320.0003-0.20320.07430.00290.00540.00590.00360.0117-0.00030.018739.828-4.36317.177
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 334
2X-RAY DIFFRACTION2A335
3X-RAY DIFFRACTION3B5 - 334
4X-RAY DIFFRACTION4B335
5X-RAY DIFFRACTION5C5 - 334
6X-RAY DIFFRACTION6C335
7X-RAY DIFFRACTION7D5 - 334
8X-RAY DIFFRACTION8D335
9X-RAY DIFFRACTION9A338 - 1627
10X-RAY DIFFRACTION9B337 - 1624
11X-RAY DIFFRACTION9C337 - 1623
12X-RAY DIFFRACTION9D337 - 1626
13X-RAY DIFFRACTION10C336
14X-RAY DIFFRACTION11B336
15X-RAY DIFFRACTION12A336
16X-RAY DIFFRACTION13A337
17X-RAY DIFFRACTION14D336

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