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- PDB-3w91: crystal structure of SeMet-labeled yeast N-acetyltransferase Mpr1... -

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Basic information

Entry
Database: PDB / ID: 3w91
Titlecrystal structure of SeMet-labeled yeast N-acetyltransferase Mpr1 L87M mutant
ComponentsMPR1 protein
KeywordsTRANSFERASE / antioxidant enzyme / N-acetyltransferase
Function / homology
Function and homology information


L-glutamate-5-semialdehyde N-acetyltransferase / azetidine-2-carboxylic acid acetyltransferase activity / L-proline catabolic process / L-arginine biosynthetic process / mitochondrion / nucleus / cytosol
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
N-acetyltransferase MPR1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsNasuno, R. / Hirano, Y. / Itoh, T. / Hakoshima, T. / Hibi, T. / Takagi, H.
CitationJournal: 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.
History
DepositionMar 23, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 17, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2013Group: Database references
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)80,0163
Polymers80,0163
Non-polymers00
Water3,567198
1
A: MPR1 protein

A: MPR1 protein


Theoretical massNumber of molelcules
Total (without water)53,3442
Polymers53,3442
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_566x,x-y+1,-z+11
Buried area2540 Å2
ΔGint-20 kcal/mol
Surface area19230 Å2
MethodPISA
2
B: MPR1 protein
C: MPR1 protein


Theoretical massNumber of molelcules
Total (without water)53,3442
Polymers53,3442
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2580 Å2
ΔGint-20 kcal/mol
Surface area19010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.558, 83.558, 192.424
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number151
Space group name H-MP3112

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Components

#1: Protein MPR1 protein


Mass: 26671.906 Da / Num. of mol.: 3 / Mutation: L87M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: MPR1 / Plasmid: pQE2 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 (DE3) / References: UniProt: E9P8D2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.42 Å3/Da / Density % sol: 49.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 20.5% PEG3350, 0.1M Bistris-HCl (pH 5.5), 0.24M magnesium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9792 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Apr 21, 2012 / Details: mirrors
RadiationMonochromator: Rotated-inclined double-crystal monochromator , Si (111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 45346 / Num. obs: 45346 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.1 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 42.5
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 10 % / Rmerge(I) obs: 0.214 / Mean I/σ(I) obs: 9.9 / % possible all: 96.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.917 / SU B: 11.52 / SU ML: 0.138 / Cross valid method: THROUGHOUT / ESU R: 0.232 / ESU R Free: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24568 2273 5 %RANDOM
Rwork0.20259 ---
obs0.2047 42768 99.47 %-
all-45346 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.219 Å2
Baniso -1Baniso -2Baniso -3
1-0.65 Å20.32 Å2-0 Å2
2--0.65 Å2-0 Å2
3----0.97 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5474 0 0 198 5672
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.025673
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1841.947736
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5965681
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.88624.613271
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.50415863
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.7161513
X-RAY DIFFRACTIONr_chiral_restr0.0810.2831
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214401
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7541.53401
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.55425500
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.35232273
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.0264.52238
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 158 -
Rwork0.225 3012 -
obs--98.48 %
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)
10.648-0.1026-0.35770.74060.33392.3577-0.06390.0008-0.0753-0.02770.0512-0.04730.08970.27360.01270.0182-0.02150.00640.13250.00760.097548.397264.432382.5416
20.801-0.2165-0.530.81520.52433.294-0.02020.26320.0854-0.1707-0.18090.1019-0.4599-0.89720.20110.10340.1211-0.09410.4795-0.08070.19719.182871.010572.979
30.93190.1402-0.10710.56990.61243.35860.01160.1029-0.03250.0119-0.2770.1108-0.2575-1.1970.26540.02840.084-0.00070.6101-0.17230.2391-0.768873.5195105.3798
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 229
2X-RAY DIFFRACTION1A301 - 405
3X-RAY DIFFRACTION2B5 - 228
4X-RAY DIFFRACTION2B301 - 335
5X-RAY DIFFRACTION3C1 - 228
6X-RAY DIFFRACTION3C301 - 357

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