[English] 日本語
Yorodumi
- PDB-8ew9: Crystal structure of Saccharomyces cerevisiae Altered Inheritance... -

+
Open data


ID or keywords:

Loading...

-
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 / 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
Similarity search - Domain/homology
2-OXOGLUTARIC ACID / Altered inheritance of mitochondria protein 46, mitochondrial
Similarity search - Component
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more