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- PDB-3w6x: Yeast N-acetyltransferase Mpr1 in complex with CHOP -

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Basic information

Entry
Database: PDB / ID: 3w6x
TitleYeast N-acetyltransferase Mpr1 in complex with CHOP
ComponentsMPR1 protein
KeywordsTRANSFERASE / detoxification of L-azetidine-2-carboxylate / antioxidant enzyme
Function / homology
Function and homology information


L-glutamate-5-semialdehyde N-acetyltransferase / acyltransferase activity, transferring groups other than amino-acyl groups / mitochondrion
Similarity search - Function
Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
(4S)-4-hydroxy-L-proline / N-acetyltransferase MPR1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.299 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 25, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 7, 2013Provider: 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_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
Revision 1.2Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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
D: MPR1 protein
E: MPR1 protein
F: MPR1 protein
G: MPR1 protein
H: MPR1 protein
I: MPR1 protein
J: MPR1 protein
K: MPR1 protein
L: MPR1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)319,13732
Polymers315,08312
Non-polymers4,05420
Water10,845602
1
A: MPR1 protein
B: MPR1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,3416
Polymers52,5142
Non-polymers8274
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3440 Å2
ΔGint-9 kcal/mol
Surface area18780 Å2
MethodPISA
2
C: MPR1 protein
D: MPR1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2456
Polymers52,5142
Non-polymers7314
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint-23 kcal/mol
Surface area18560 Å2
MethodPISA
3
E: MPR1 protein
F: MPR1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2456
Polymers52,5142
Non-polymers7314
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3730 Å2
ΔGint-25 kcal/mol
Surface area18810 Å2
MethodPISA
4
G: MPR1 protein
H: MPR1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1496
Polymers52,5142
Non-polymers6364
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3890 Å2
ΔGint-37 kcal/mol
Surface area18870 Å2
MethodPISA
5
I: MPR1 protein
J: MPR1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0794
Polymers52,5142
Non-polymers5652
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3570 Å2
ΔGint-12 kcal/mol
Surface area18980 Å2
MethodPISA
6
K: MPR1 protein
L: MPR1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0794
Polymers52,5142
Non-polymers5652
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3560 Å2
ΔGint-12 kcal/mol
Surface area18880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.345, 229.340, 84.755
Angle α, β, γ (deg.)90.00, 90.94, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
MPR1 protein


Mass: 26256.924 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer'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-HZP / (4S)-4-hydroxy-L-proline


Type: L-peptide linking / Mass: 131.130 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H9NO3
#3: Chemical
ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 282.331 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 602 / 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: 2.48 Å3/Da / Density % sol: 50.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 23%(w/v) PEG 3350, 0.1M bis-tris, 0.2M MgCl2, 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-17A / Wavelength: 0.98508 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 1, 2010
RadiationMonochromator: Si(111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98508 Å / Relative weight: 1
ReflectionResolution: 2.299→56.945 Å / Num. obs: 134196 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 42.2 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 8
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.453 / Mean I/σ(I) obs: 2.5 / Num. unique all: 19509 / % possible all: 98.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIX(autosol)model building
PHENIX(phenix.refine: 1.8.1_1168)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIX(autosol)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3W91

3w91


Resolution: 2.299→56.945 Å / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.855 / SU ML: 0.24 / Isotropic thermal model: Isotropic / σ(F): 1.35 / Phase error: 22.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2145 6742 5.03 %RANDOM
Rwork0.1658 ---
obs0.1683 134101 98.89 %-
all-134139 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 91.32 Å2 / Biso mean: 38.2042 Å2 / Biso min: 15.04 Å2
Refine analyzeLuzzati coordinate error obs: 0.2645 Å
Refinement stepCycle: LAST / Resolution: 2.299→56.945 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21763 0 203 602 22568
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01422651
X-RAY DIFFRACTIONf_angle_d1.36130813
X-RAY DIFFRACTIONf_dihedral_angle_d13.9077991
X-RAY DIFFRACTIONf_chiral_restr0.0783316
X-RAY DIFFRACTIONf_plane_restr0.0073897
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2987-2.32480.29622420.2257404696
2.3248-2.35210.27122310.238427599
2.3521-2.38080.27752190.2247417099
2.3808-2.4110.29872250.2139427399
2.411-2.44270.25662350.2065422599
2.4427-2.47610.27472120.2065421299
2.4761-2.51150.27162270.2101428299
2.5115-2.5490.23982410.2034418899
2.549-2.58880.28132100.2004425099
2.5888-2.63130.26762400.1982423299
2.6313-2.67670.2652120.1959427899
2.6767-2.72530.24032170.1939420699
2.7253-2.77770.23512290.194426699
2.7777-2.83440.26052180.1809424999
2.8344-2.89610.27192120.1889427699
2.8961-2.96340.26522160.1912429199
2.9634-3.03750.2062300.1849421899
3.0375-3.11970.23422130.1894426099
3.1197-3.21140.26812470.1966427899
3.2114-3.31510.23172320.1855422899
3.3151-3.43360.2252100.1701424999
3.4336-3.5710.20982530.1643425399
3.571-3.73350.19162130.1486428699
3.7335-3.93030.17932200.1467427399
3.9303-4.17650.19682300.1362428299
4.1765-4.49880.16512240.115428099
4.4988-4.95130.14472160.111425199
4.9513-5.66720.16442270.1239419698
5.6672-7.13790.18592130.1533426698
7.1379-56.96260.15012280.139432099
Refinement TLS params.Method: refined / Origin x: -3.784 Å / Origin y: 6.815 Å / Origin z: -3.047 Å
111213212223313233
T0.1903 Å2-0.0017 Å2-0.0061 Å2-0.1962 Å20.0007 Å2--0.2108 Å2
L-0.0169 °2-0.0029 °2-0.0256 °2--0.0204 °2-0.0013 °2--0.0589 °2
S0.0209 Å °0.0052 Å °0.0034 Å °-0.0016 Å °-0.0222 Å °-0.0003 Å °-0.0023 Å °0.0004 Å °0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA5 - 229
2X-RAY DIFFRACTION1allA301 - 302
3X-RAY DIFFRACTION1allC5 - 229
4X-RAY DIFFRACTION1allC301 - 302
5X-RAY DIFFRACTION1allB5 - 229
6X-RAY DIFFRACTION1allB301 - 302
7X-RAY DIFFRACTION1allE5 - 229
8X-RAY DIFFRACTION1allE301
9X-RAY DIFFRACTION1allD5 - 228
10X-RAY DIFFRACTION1allD301
11X-RAY DIFFRACTION1allG5 - 229
12X-RAY DIFFRACTION1allG301
13X-RAY DIFFRACTION1allF5 - 228
14X-RAY DIFFRACTION1allF301 - 302
15X-RAY DIFFRACTION1allI5 - 229
16X-RAY DIFFRACTION1allI301
17X-RAY DIFFRACTION1allH5 - 229
18X-RAY DIFFRACTION1allH301
19X-RAY DIFFRACTION1allK5 - 228
20X-RAY DIFFRACTION1allK301
21X-RAY DIFFRACTION1allJ5 - 229
22X-RAY DIFFRACTION1allJ301
23X-RAY DIFFRACTION1allD302
24X-RAY DIFFRACTION1allE302
25X-RAY DIFFRACTION1allG302
26X-RAY DIFFRACTION1allH302
27X-RAY DIFFRACTION1allL5 - 229
28X-RAY DIFFRACTION1allL301
29X-RAY DIFFRACTION1allA401 - 464
30X-RAY DIFFRACTION1allB401 - 476
31X-RAY DIFFRACTION1allC401 - 452
32X-RAY DIFFRACTION1allD401 - 447
33X-RAY DIFFRACTION1allE401 - 456
34X-RAY DIFFRACTION1allF401 - 453
35X-RAY DIFFRACTION1allG401 - 472
36X-RAY DIFFRACTION1allH401 - 438
37X-RAY DIFFRACTION1allI401 - 449
38X-RAY DIFFRACTION1allJ401 - 438
39X-RAY DIFFRACTION1allK401 - 431
40X-RAY DIFFRACTION1allL401 - 426

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