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- PDB-3w6s: yeast N-acetyltransferase Mpr1 involved in oxidative stress toler... -

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Basic information

Entry
Database: PDB / ID: 3w6s
Titleyeast N-acetyltransferase Mpr1 involved in oxidative stress tolerance via proline metabolism
ComponentsMPR1 protein
KeywordsTRANSFERASE / detoxification of L-azetidine-2-carboxylate / antioxidant enzyme
Function / homologyL-glutamate-5-semialdehyde N-acetyltransferase / acyltransferase activity / Gcn5-related N-acetyltransferase (GNAT) / Acyl-CoA N-acyltransferase / Aminopeptidase / mitochondrion / 3-Layer(aba) Sandwich / Alpha Beta / N-acetyltransferase MPR1
Function and homology information
Biological speciesSaccharomyces cerevisiae (baker's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsNasuno, R. / Hirano, Y. / Itoh, T. / Hakoshima, T. / Hibi, T. / Takagi, H.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Structural and functional analysis of the yeast N-acetyltransferase Mpr1 involved in oxidative stress tolerance via proline metabolism
Authors: Nasuno, R. / Hirano, Y. / Itoh, T. / Hakoshima, T. / Hibi, T. / Takagi, H.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2009
Title: Crystallization and preliminary crystallographic analysis of N-acetyltransferase Mpr1 from Saccharomyces cerevisiae.
Authors: Hibi, T. / Yamamoto, H. / Nakamura, G. / Takagi, H.
History
DepositionFeb 21, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 17, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MPR1 protein
B: MPR1 protein
C: MPR1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,7007
Polymers83,8293
Non-polymers8714
Water4,107228
1
A: MPR1 protein
hetero molecules

A: MPR1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4996
Polymers55,8862
Non-polymers6134
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_655-x+y+1,y,-z+1/31
Buried area3500 Å2
ΔGint-11 kcal/mol
Surface area18450 Å2
MethodPISA
2
B: MPR1 protein
C: MPR1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4504
Polymers55,8862
Non-polymers5652
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3340 Å2
ΔGint-10 kcal/mol
Surface area17840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.862, 83.862, 193.819
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number151
Space group name H-MP3112
Components on special symmetry positions
IDModelComponents
11A-302-

MG

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Components

#1: Protein MPR1 protein


Mass: 27942.863 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (baker's yeast)
Strain: sigma1278b / Gene: MPR1 / Plasmid: pQE2 / Production host: Escherichia coli (E. coli) / Strain (production host): SG13009
References: UniProt: E9P8D2, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 282.331 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 228 / 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: 2.35 Å3/Da / Density % sol: 47.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 22, 2008
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
Reflection twinOperator: -h,-k,l / Fraction: 0.27
ReflectionResolution: 1.9→48.3 Å / Num. obs: 61875 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.9 % / Biso Wilson estimate: 33.5 Å2 / Rmerge(I) obs: 0.06
Reflection shellResolution: 1.9→2 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.287 / Mean I/σ(I) obs: 2.4 / Num. unique all: 8966 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3W91
Resolution: 1.9→48.271 Å / Occupancy max: 1 / Occupancy min: 0.05 / FOM work R set: 0.817 / σ(F): 1.35 / Phase error: 25.7 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.1872 3088 5 %random
Rwork0.1657 ---
all0.1706 61875 --
obs0.1706 61806 99.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 75.24 Å2 / Biso mean: 30.373 Å2 / Biso min: 9.46 Å2
Refine analyzeLuzzati coordinate error obs: 0.3107 Å
Refinement stepCycle: LAST / Resolution: 1.9→48.271 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5257 0 43 228 5528
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085508
X-RAY DIFFRACTIONf_angle_d1.0157515
X-RAY DIFFRACTIONf_dihedral_angle_d13.5321901
X-RAY DIFFRACTIONf_chiral_restr0.053825
X-RAY DIFFRACTIONf_plane_restr0.004952
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20 / % reflection obs: 95 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.9001-1.93290.25511520.23052878
1.9329-1.9680.25021560.21812893
1.968-2.00590.24481540.20522928
2.0059-2.04680.2281520.21012937
2.0468-2.09130.19991540.20732907
2.0913-2.140.1981530.20172896
2.14-2.19350.23581510.19912913
2.1935-2.25280.21811490.19472920
2.2528-2.31910.21971530.19742927
2.3191-2.39390.18421540.20042950
2.3939-2.47950.22171510.1952908
2.4795-2.57870.17551550.19382903
2.5787-2.69610.21221590.1912932
2.6961-2.83820.19421530.18782920
2.8382-3.0160.22221540.18112962
3.016-3.24870.19461560.17482934
3.2487-3.57550.16021540.15492945
3.5755-4.09250.19011610.13182972
4.0925-5.15450.13861500.11172993
5.1545-40.99250.21321650.16073071
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.0055-0.00230.00630.0056-0.00570.02070.0046-0.0047-0.01570.04560.0127-0.0072-0.03210.027500.0978-0.0040.00030.10280.00420.096936.0179-27.428155.7108
20.00240.00280.0014-0.000200.00090.00430.0311-0.00180.0123-0.0130.0030.0016-0.020900.0718-0.01430.00510.1386-0.01460.097323.1814-31.431440.3391
3-0.00130.005-0.00420.0022-0.0010.00330.01970.07060.00590.00130.0115-0.0110.0181-0.026800.0533-0.02240.00280.0369-0.00260.082330.6447-29.656339.1668
40.00080.001-0.00120.0001-0.00050.001-0.004-0.00040.00250.01230.00280.00510.0125-0.0131-00.19620.00280.04990.15330.00270.163222.0093-31.320358.8341
50.0012-0.00080.00520.0035-0.00060.0099-0.03390.0006-0.0062-0.0231-0.01390.0268-0.04520.003700.068-0.00540.01110.0778-0.00140.082336.4174-24.392744.4237
6-0.0036-0.0048-0.00510.00420.00550.0060.0987-0.03460.0325-0.03430.0381-0.0026-0.0752-0.0307-00.02290.19990.0628-0.3157-0.04480.141231.9099-17.465945.6932
7-0.0028-0.0019-0.00160.0023-0.0022-0.00180.0139-0.01330.0054-0.01450.0245-0.017-0.0244-0.0005-00.24450.16870.0673-0.17020.03270.120832.4332-8.338440.7013
80.00090.00040.0010.0003-0.00020.0001-0.00190.00670.007-0.0057-0.00020.00030.0036-0.020500.13140.1931-0.00290.12480.10090.117226.7358-14.205424.3828
9-0.001-0.00260.00180.00120.00110.00010.0215-0.02750.0319-0.0047-0.0178-0.0237-0.005-0.014800.1691-0.0050.02510.0692-0.01210.152637.054-10.229249.4161
100.0035-0.0012-0.0005-0.0003-0.0005-0.0005-0.061-0.0294-0.0009-0.0061-0.0616-0.01310.0120.0497-00.08440.26490.15940.09560.00210.187926.410421.207317.0022
11-0.0005-0.004-0.00280.0018-0.00280.0004-0.01930.00860.0196-0.0032-0.04480.01430.03750.003500.36670.18250.1185-0.0071-0.02390.196713.234712.415817.4228
12-0.0031-0.0068-0.00760.0038-0.002-0.00360.0022-0.0106-0.0086-0.0032-0.0197-0.00530.0353-0.006300.29320.3750.29-0.0498-0.09610.096112.279911.937826.0568
13-0.0009-0.00560.00010.00120.0030.0002-0.02970.0025-0.02450.00560.0058-0.00940.0278-0.0049-00.43580.22250.20090.0986-0.03050.145518.078810.929110.4702
14-0.0006-0.00130.00170-00.00030.0019-0.00880.0001-0.00140.00230.00060.01110.015700.25210.21510.07250.28930.08170.221224.677120.806434.7551
15-0.0007-0.00090.00080.0008-0.0002-0.0003-0.00490.0146-0.0022-0.00390.01650.00010.0053-0.016400.30410.09620.06910.12510.05350.239320.52371.067917.8618
16-0.0003-00.00040.00090.0003-0.00010.001-0.0075-0.0042-0.00090-0.00360.01470.0124-00.2960.26110.10340.23220.06350.255429.759812.413820.745
170.0007-0.0013-0.00190.0007-0.002-0.0027-0.0068-0.00570.00340.0113-0.0034-0.00470.03220.018400.30560.16420.10890.26160.07630.291925.93329.393733.0814
180.0002-0.0098-0.00090.0061-0.0036-0.0030.00020.0075-0.0150.00290.0066-0.00420.01470.0005-00.44280.34220.1480.1970.1360.326225.12770.576435.5826
19-0.0003-0.0027-0.00050.00230.0003-0.0005-0.00590.0105-0.00360.0078-0.0088-0.00230.00280.0027-00.29230.13560.08730.26570.04490.298534.896510.684527.6737
20-0.0052-0.00190.00440.0067-0.00970.0008-0.0421-0.03820.0017-0.0396-0.0091-0.02880.04630.0377-00.45270.19850.11210.07950.20050.11156.185213.474360.0195
210.0005-0.0024-0.00030.00020.00120.0006-0.0182-0.00170.0007-0.01520.01330.00750.01890.009900.27390.08770.02670.1760.02650.20123.758422.045359.4536
220.00040.0002-0.00110.00120.00030.0013-0.0040.00470.0014-0.00130.0057-0.0115-0.00740.0115-00.2160.06440.01510.18490.02330.17512.881832.613252.7102
230.0014-0.01230.0019-0.0017-0.00160.0005-0.03960.0023-0.01240.0104-0.0115-0.03860.01710.0255-00.15230.39290.07860.03560.01180.144310.556426.788354.5293
24-0.0053-0.00610.00410.0021-0.00610.0049-0.064-0.0357-0.0185-0.0181-0.0642-0.03830.03150.0204-00.27690.3980.05840.00570.13230.157513.061717.251751.3727
25-0.0009-0.00120.00160.0006-0.00140.0013-0.034-0.0175-00.0118-0.0216-0.01320.01730.0295-00.30670.389-0.00370.21070.1520.159417.404218.247560.2033
260.0009-0.00080.0002-0.0001-0.0017-0.003-0.0019-0.0073-0.00420.00990.02590.00370.01070.0283-00.29560.16380.02040.25680.05870.248223.291314.450750.1708
270.0001-0.00270.00070.0002-0.00040.00020.0067-0.0056-0.0133-0.004-0.0023-0.00690.0014-0.002200.30090.2129-0.01480.36190.08370.308928.678812.038553.926
280.0003-0.00040.00050.00130.0003-0.0005-0.0028-0.0051-0.00010.0001-0.0035-0.0029-0.00250.004300.26380.0749-0.00140.36750.03590.303534.098625.626242.3263
290.0008-0.006-0.00240.0016-0.0016-0.0010.0172-0.0075-0.01480.0107-0.0097-0.01540.01580.0028-00.3310.20350.06140.26370.08590.278522.11748.024958.5512
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 5:54 )
2X-RAY DIFFRACTION2chain 'A' and (resseq 55:71 )
3X-RAY DIFFRACTION3chain 'A' and (resseq 72:99 )
4X-RAY DIFFRACTION4chain 'A' and (resseq 100:111 )
5X-RAY DIFFRACTION5chain 'A' and (resseq 112:133 )
6X-RAY DIFFRACTION6chain 'A' and (resseq 134:179 )
7X-RAY DIFFRACTION7chain 'A' and (resseq 180:196 )
8X-RAY DIFFRACTION8chain 'A' and (resseq 197:210 )
9X-RAY DIFFRACTION9chain 'A' and (resseq 211:229 )
10X-RAY DIFFRACTION10chain 'B' and (resseq 5:40 )
11X-RAY DIFFRACTION11chain 'B' and (resseq 41:71 )
12X-RAY DIFFRACTION12chain 'B' and (resseq 72:99 )
13X-RAY DIFFRACTION13chain 'B' and (resseq 100:122 )
14X-RAY DIFFRACTION14chain 'B' and (resseq 123:137 )
15X-RAY DIFFRACTION15chain 'B' and (resseq 138:148 )
16X-RAY DIFFRACTION16chain 'B' and (resseq 149:164 )
17X-RAY DIFFRACTION17chain 'B' and (resseq 165:179 )
18X-RAY DIFFRACTION18chain 'B' and (resseq 180:210 )
19X-RAY DIFFRACTION19chain 'B' and (resseq 211:228 )
20X-RAY DIFFRACTION20chain 'C' and (resseq 5:40 )
21X-RAY DIFFRACTION21chain 'C' and (resseq 41:54 )
22X-RAY DIFFRACTION22chain 'C' and (resseq 55:71 )
23X-RAY DIFFRACTION23chain 'C' and (resseq 72:111 )
24X-RAY DIFFRACTION24chain 'C' and (resseq 112:133 )
25X-RAY DIFFRACTION25chain 'C' and (resseq 134:164 )
26X-RAY DIFFRACTION26chain 'C' and (resseq 165:180 )
27X-RAY DIFFRACTION27chain 'C' and (resseq 181:196 )
28X-RAY DIFFRACTION28chain 'C' and (resseq 197:210 )
29X-RAY DIFFRACTION29chain 'C' and (resseq 211:228 )

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