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- PDB-8ew8: Crystal structure of Saccharomyces cerevisiae Altered Inheritance... -

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Basic information

Entry
Database: PDB / ID: 8ew8
TitleCrystal structure of Saccharomyces cerevisiae Altered Inheritance rate of Mitochondria protein 18 (AIM18p) R123A mutant
ComponentsAltered inheritance of mitochondria protein 18, mitochondrial
KeywordsUNKNOWN FUNCTION / Altered inheritance of mitochondria protein 18 / mitochondrial protein / YHR198C / FMP22
Function / homology
Function and homology information


intramolecular lyase activity / mitochondrial inner membrane / heme binding / mitochondrion
Similarity search - Function
Chalcone isomerase like / Chalcone isomerase / Chalcone isomerase, 3-layer sandwich / Chalcone isomerase superfamily / Chalcone isomerase - #10 / Chalcone isomerase / 3-Layer(bba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Altered inheritance of mitochondria protein 18, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.15 Å
AuthorsBingman, C.A. / Schmitz, J.M. / Smith, R.W. / Pagliarini, D.J.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM131795 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM008505 United States
National Science Foundation (NSF, United States)DGE-1747503 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 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Altered inheritance of mitochondria protein 18, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7857
Polymers28,2081
Non-polymers5766
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)127.390, 127.390, 54.270
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-542-

HOH

21A-622-

HOH

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Components

#1: Protein Altered inheritance of mitochondria protein 18, mitochondrial / Found in mitochondrial proteome protein 22


Mass: 28208.270 Da / Num. of mol.: 1 / Mutation: R123A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c / Gene: AIM18, FMP22, YHR198C / Production host: Escherichia coli (E. coli) / References: UniProt: P38884
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#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 interestN
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: 4.5 Å3/Da / Density % sol: 72.71 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Crystals for data collection were obtained by mixing 200 nL of protein soiution (15.1 mg/mL Nd70 R123A Aim18p, 20 mM HEPES buffer, pH 7.5, 200 mM NaCl, 2 mM TCEP) with 150 nL of reservoir ...Details: Crystals for data collection were obtained by mixing 200 nL of protein soiution (15.1 mg/mL Nd70 R123A Aim18p, 20 mM HEPES buffer, pH 7.5, 200 mM NaCl, 2 mM TCEP) with 150 nL of reservoir solution (26% PEG 3350, 200 mM Li2SO4, 100 mM HEPES pH 7.5) in a SD2 crystallization tray with a TTP Labtech Mosquito crystallization robot. Crystals were cryoprotected with reservoir solution supplemented to 30% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.964370, 0.979370, 0.979610
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 7, 2018
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.964371
20.979371
30.979611
ReflectionResolution: 2.15→48.7 Å / Num. obs: 27153 / % possible obs: 97.59 % / Redundancy: 18.8 % / Biso Wilson estimate: 40.56 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.09783 / Rpim(I) all: 0.02266 / Rrim(I) all: 0.1005 / Net I/σ(I): 21.8
Reflection shellResolution: 2.15→2.227 Å / Redundancy: 12.3 % / Rmerge(I) obs: 0.9956 / Mean I/σ(I) obs: 2.38 / Num. unique obs: 2241 / CC1/2: 0.702 / CC star: 0.908 / Rpim(I) all: 0.2836 / Rrim(I) all: 1.039 / % possible all: 81.11

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Coot0.9.5model building
XDSVERSION Nov 11, 2017 BUILT=20171111data reduction
XSCALEVERSION Nov 11, 2017 BUILT=20171111data scaling
PHASER2.8.0phasing
AutoSolphasing
RefinementMethod to determine structure: MAD / Resolution: 2.15→48.7 Å / SU ML: 0.265 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.8387
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2116 1990 7.33 %
Rwork0.1784 25161 -
obs0.1808 27151 97.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.38 Å2
Refinement stepCycle: LAST / Resolution: 2.15→48.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1885 0 30 122 2037
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00691968
X-RAY DIFFRACTIONf_angle_d0.79832667
X-RAY DIFFRACTIONf_chiral_restr0.0461305
X-RAY DIFFRACTIONf_plane_restr0.0054339
X-RAY DIFFRACTIONf_dihedral_angle_d11.3426729
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.20.27331160.24281439X-RAY DIFFRACTION78.93
2.2-2.260.27111260.21951612X-RAY DIFFRACTION88.31
2.26-2.330.25821430.21631793X-RAY DIFFRACTION99.59
2.33-2.410.23881440.20571819X-RAY DIFFRACTION99.34
2.41-2.490.27111490.22481829X-RAY DIFFRACTION100
2.49-2.590.25051410.23711832X-RAY DIFFRACTION100
2.59-2.710.25711480.21921843X-RAY DIFFRACTION100
2.71-2.850.23441420.19651809X-RAY DIFFRACTION100
2.85-3.030.23441450.21411855X-RAY DIFFRACTION99.95
3.03-3.260.24181430.20531808X-RAY DIFFRACTION100
3.26-3.590.1921450.17231853X-RAY DIFFRACTION100
3.59-4.110.19171520.14741854X-RAY DIFFRACTION100
4.11-5.180.15631430.12971873X-RAY DIFFRACTION100
5.18-48.70.2071530.17381942X-RAY DIFFRACTION100
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)
12.463991801860.1199599912080.2928220852772.434397036770.4949179982483.761172707230.0254211543545-0.249765399766-0.4741881526890.127446901119-0.0392582421615-0.126617492720.2058082662750.101132862580.03846386833640.24298606066-0.0256550884649-0.003302405519420.2967305255220.08015553232530.32462480035779.383257691136.517006903-2.96313033515
26.986502939810.2676713724482.18268710532.43768800371-0.5220505960956.14330979668-0.198434319332-0.9891719792030.5172524047470.261389975012-0.1653609553980.145160271572-0.720735631773-0.3001413972740.4041026554810.508694031699-0.127604967549-0.05620185811580.666692219871-0.08139313636680.40910976935683.342449691456.543267497114.230606389
32.070699190352.609534156190.6034348498824.444984964380.5281445360241.38734449145-0.0662585400559-0.08646729898460.220523114821-0.129962705742-0.1040591981780.130413414851-0.1734037738010.113906749770.1652829775940.241793667384-0.02714840442140.01189189600290.3856571425870.007832778904890.33400519406181.887854228851.2722117356-11.7225732212
48.26325587533.433922587133.230205571394.271155796570.5331688443995.165015290770.004833535893260.729319465554-0.262007131561-0.1091732605490.13095347531-0.419565282001-0.2626488040280.86249867189-0.09009661997080.222053768272-0.009943089734840.04889419955270.35061398772-0.005618345496960.30469504833682.394130250940.807808995-16.2606993827
54.145569146172.3184061201-0.7624998888244.508001466990.7295331047284.049925277510.0360850445701-0.0154749258796-0.0748462112833-0.182368891750.0277452735041-0.281284016649-0.1606156142620.269321959514-0.1069800137630.1990626894460.00649648366806-0.05357392555980.3147513064810.08285487158270.28615664622782.936721937844.9611397329-11.6717856186
63.92179522331-2.867579103265.682315129276.77196985501-2.660622427968.764042624190.506573468996-1.00674745716-0.3549814250520.366574719639-0.200755913820.246432772980.413346460666-0.733611853738-0.2074916295160.316691418326-0.1147794133890.007230028250170.5325331870570.06776387408830.26692498384477.640176316544.39231829836.3725391752
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 83 through 150 )83 - 1501 - 68
22chain 'A' and (resid 151 through 188 )151 - 18869 - 106
33chain 'A' and (resid 189 through 244 )189 - 244107 - 162
44chain 'A' and (resid 245 through 266 )245 - 266163 - 184
55chain 'A' and (resid 267 through 306 )267 - 306185 - 224
66chain 'A' and (resid 307 through 321 )307 - 321225 - 239

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