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- PDB-8ew9: Crystal structure of Saccharomyces cerevisiae Altered Inheritance... -

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Basic information

Entry
Database: PDB / ID: 8ew9
TitleCrystal structure of Saccharomyces cerevisiae Altered Inheritance rate of Mitochondria protein 46 (AIM46p)
ComponentsAltered inheritance of mitochondria protein 46, mitochondrial
KeywordsUNKNOWN FUNCTION / Altered inheritance of mitochondria protein 46 / mitochondrial protein / YHR199C / FMP34 / Structural Genomics / PSI-2 / Protein Structure Initiative / Mitochondrial Protein Partnership / MPP
Function / homologyChalcone isomerase like / intramolecular lyase activity / Chalcone isomerase, 3-layer sandwich / Chalcone isomerase / Chalcone isomerase superfamily / mitochondrion / 2-OXOGLUTARIC ACID / Altered inheritance of mitochondria protein 46, mitochondrial
Function and homology information
Biological speciesSaccharomyces cerevisiae S288C (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBingman, C.A. / Schmitz, J.M. / Smith, R.W. / Pagliarini, D.J. / Mitochondrial Protein Partnership (MPP)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: J.Biol.Chem. / Year: 2023
Title: Aim18p and Aim46p are chalcone isomerase domain-containing mitochondrial hemoproteins in Saccharomyces cerevisiae.
Authors: Schmitz, J.M. / Wolters, J.F. / Murray, N.H. / Guerra, R.M. / Bingman, C.A. / Hittinger, C.T. / Pagliarini, D.J.
History
DepositionOct 21, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Altered inheritance of mitochondria protein 46, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3732
Polymers27,2271
Non-polymers1461
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.870, 71.350, 40.220
Angle α, β, γ (deg.)90.000, 95.165, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Altered inheritance of mitochondria protein 46, mitochondrial / Found in mitochondrial proteome protein 34


Mass: 27227.098 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c / Gene: AIM46, FMP34, YHR199C / Production host: Escherichia coli (E. coli) / References: UniProt: P38885
#2: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.16 Å3/Da / Density % sol: 42.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Crystals grew from 180 nL 31.4 mg/mL Aim46p Nd62, 20 nL microseeds in 30% PEG 2000, 0.1 M MES buffer, pH 6.0, mixed with 300 nL reservoir solution composed of 18% PEG 2000, 100 mM MES ...Details: Crystals grew from 180 nL 31.4 mg/mL Aim46p Nd62, 20 nL microseeds in 30% PEG 2000, 0.1 M MES buffer, pH 6.0, mixed with 300 nL reservoir solution composed of 18% PEG 2000, 100 mM MES buffer, pH 6.5. Microseeded crystallization plates were set with a Mosquito crystallization robot in a MRC SD2 crystallization plate. Crystals were cryopreserved with reservoir solution supplemented with 30% PEG 2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03321 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 8, 2018
Details: double crystal monochromator and K-B pair of bimorph mirrors for vertical and horizontal focusing
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03321 Å / Relative weight: 1
ReflectionResolution: 2→40.06 Å / Num. obs: 15174 / % possible obs: 99.61 % / Redundancy: 6.8 % / Biso Wilson estimate: 30.63 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.1234 / Rpim(I) all: 0.05099 / Rrim(I) all: 0.1337 / Net I/σ(I): 11.51
Reflection shellResolution: 2→2.072 Å / Redundancy: 6.9 % / Rmerge(I) obs: 1.159 / Mean I/σ(I) obs: 1.36 / Num. unique obs: 1471 / CC1/2: 0.718 / CC star: 0.914 / Rpim(I) all: 0.4731 / Rrim(I) all: 1.253 / % possible all: 98.92

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Processing

Software
NameVersionClassification
Coot0.9.5model building
PHENIX1.19.2_4158refinement
XDSVERSION Jan 26, 2018 BUILT=20180409data reduction
XSCALEVERSION Jan 26, 2018 BUILT=20180409data scaling
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7RSG

7rsg
PDB Unreleased entry


Resolution: 2→40.06 Å / SU ML: 0.2873 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.7237
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2335 1521 10.04 %
Rwork0.1672 13631 -
obs0.1736 15152 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.56 Å2
Refinement stepCycle: LAST / Resolution: 2→40.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1857 0 10 122 1989
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00681928
X-RAY DIFFRACTIONf_angle_d0.77322614
X-RAY DIFFRACTIONf_chiral_restr0.048294
X-RAY DIFFRACTIONf_plane_restr0.0058344
X-RAY DIFFRACTIONf_dihedral_angle_d12.9045726
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.060.37851350.28891191X-RAY DIFFRACTION98.66
2.06-2.140.31571370.24581228X-RAY DIFFRACTION99.2
2.14-2.220.32451390.21671251X-RAY DIFFRACTION99.36
2.22-2.320.26461400.1911220X-RAY DIFFRACTION99.42
2.33-2.450.25871380.18861237X-RAY DIFFRACTION99.78
2.45-2.60.26571420.18861230X-RAY DIFFRACTION99.64
2.6-2.80.25061410.19861244X-RAY DIFFRACTION99.64
2.8-3.080.25091370.18451264X-RAY DIFFRACTION99.93
3.08-3.530.24781390.16661225X-RAY DIFFRACTION100
3.53-4.440.19681360.12221264X-RAY DIFFRACTION99.93
4.45-40.060.16461370.13671277X-RAY DIFFRACTION99.93
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)
15.70068262948-2.917904115162.193109635022.91083324872-1.750214187695.875796624910.0664659557984-0.04564264949090.767167842665-0.0108323273948-0.0537801898242-0.447272741406-0.2566584176940.268577671302-0.03487329887020.230091382067-0.0255590071750.01467424865520.2677967997-0.02944841748110.3828883202548.5094093132158.47543061659.4171478328
27.61134322307-2.74552595306-0.9721646196355.15809568835-0.1486013603142.66110028106-0.0246953761012-0.3992852944140.5943367639520.194095659024-0.120062479621-0.478497166536-0.08901071381620.2058124959090.1695253139870.220239597892-0.0733403609206-0.02244896023080.2918705866-0.04430893373860.1683550023263.6564590350352.466664013916.3420838334
33.62778407064-0.919127821178-1.40155050276.836861791791.389928350594.87004179964-0.0465679483891-0.1359583114460.05748909444650.4107742523630.1611939997790.170050229962-0.129841381083-0.221819427811-0.1003460542310.2304969427470.04067748437290.006122217701170.366337146207-0.01461486209190.242547765616-11.243509523451.924886235229.4662565766
46.43697950023-1.58147051215-1.208619696353.36957071249-0.5928587684892.733573265350.01732235211970.204519631001-0.167800639592-0.115922913425-0.193016047227-0.05615794619910.1473415517410.07998971541410.1810532587080.233731552891-0.0109218654186-0.03172544939890.257884241213-0.049574034050.2196409433657.141176082545.426376886910.5856637206
57.136788550185.035622271922.976232789479.05127449174-1.327887908653.601179666860.0147284848367-0.240707416072-0.3281414752910.352132394765-0.03677872914920.1738472426860.393891743073-0.427861908610.06488554747120.3204506604180.0766717795546-0.007500866406310.261455464271-0.07795162386670.322632656018-0.49523284449734.28393760879.73849455967
66.73933602081.55861394513-1.997237412182.66071979319-0.6049126372152.46400473397-0.110717346930.209004564324-0.0307337385575-0.08960224265350.115356517701-0.0144547247681-0.0545342487005-0.02331308988750.01412776988410.2158225381510.0420885027335-0.01646658302420.225539991715-0.05160966254860.2073142243623.8130395419146.4415843727.03657593075
78.40148667428-4.87149637388-1.958647661186.162462711630.1507444422595.51605017387-0.289574846244-0.9118761804711.018883534950.2456368886150.613222564579-0.7424061643770.1889129147460.724740373438-0.265800588430.2940003885730.0366809117816-0.05931909590130.461278189182-0.1208387554730.3209822919090.97003112365355.809501457823.4500609986
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 70 through 107 )70 - 1071 - 38
22chain 'A' and (resid 108 through 134 )108 - 13439 - 65
33chain 'A' and (resid 135 through 179 )135 - 17966 - 110
44chain 'A' and (resid 180 through 202 )180 - 202111 - 133
55chain 'A' and (resid 203 through 239 )203 - 239134 - 170
66chain 'A' and (resid 240 through 295 )240 - 295171 - 226
77chain 'A' and (resid 296 through 310 )296 - 310227 - 241

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