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- PDB-8ud0: Sterile Alpha Motif (SAM) domain from Tric1 from Arabidopsis thal... -

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Basic information

Entry
Database: PDB / ID: 8ud0
TitleSterile Alpha Motif (SAM) domain from Tric1 from Arabidopsis thaliana - G241E mutant
ComponentsChloroplastic import inner membrane translocase subunit HP30-1
KeywordsRNA BINDING PROTEIN / Mitochondria / tRNA import / Tric1 / SAM domain / oligomerization / PRAT domain / sterile alpha motif domain
Function / homology
Function and homology information


protein targeting to chloroplast / chloroplast inner membrane / tRNA import into mitochondrion / protein insertion into mitochondrial inner membrane / chloroplast envelope / plastid / chloroplast / mitochondrion organization / mitochondrion / cytosol
Similarity search - Function
Mitochondrial import inner membrane translocase subunit TIM22 / SAM domain (Sterile alpha motif) / Tim17/Tim22/Tim23/Pmp24 family / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily
Similarity search - Domain/homology
Chloroplastic import inner membrane translocase subunit HP30-1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsOlasz, B. / Vrielink, A. / Smithers, L.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Biol.Chem. / Year: 2024
Title: Structural analysis of the SAM domain of the Arabidopsis mitochondrial tRNA import receptor.
Authors: Olasz, B. / Smithers, L. / Evans, G.L. / Anandan, A. / Murcha, M.W. / Vrielink, A.
History
DepositionSep 27, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2024Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chloroplastic import inner membrane translocase subunit HP30-1
B: Chloroplastic import inner membrane translocase subunit HP30-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9524
Polymers20,4762
Non-polymers4772
Water1,45981
1
A: Chloroplastic import inner membrane translocase subunit HP30-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,4762
Polymers10,2381
Non-polymers2381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Chloroplastic import inner membrane translocase subunit HP30-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,4762
Polymers10,2381
Non-polymers2381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.579, 58.537, 61.949
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
DetailsThe assembly may be hexameric; however, the authors do not know the specific hexameric assembly.

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Components

#1: Protein Chloroplastic import inner membrane translocase subunit HP30-1


Mass: 10237.844 Da / Num. of mol.: 2 / Fragment: SAM domain / Mutation: G241E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: HP30-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 / References: UniProt: Q9SCK3
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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 Å3/Da / Density % sol: 38.48 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.2 / Details: 1.8-2.3 M ammonium sulphate, 0.1 M Tris / PH range: 8.0-8.7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953732 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 6, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953732 Å / Relative weight: 1
ReflectionResolution: 1.89→42.55 Å / Num. obs: 14037 / % possible obs: 99.6 % / Redundancy: 13.1 % / Biso Wilson estimate: 30.12 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.03 / Net I/σ(I): 18.9
Reflection shellResolution: 1.89→1.96 Å / Redundancy: 13 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 2.41 / Num. unique obs: 1355 / CC1/2: 0.0774 / Rpim(I) all: 0.42 / % possible all: 96.1

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.89→42.55 Å / SU ML: 0.2322 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.538
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2368 756 5.41 %
Rwork0.1997 13213 -
obs0.2017 13969 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.78 Å2
Refinement stepCycle: LAST / Resolution: 1.89→42.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1011 0 30 81 1122
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041077
X-RAY DIFFRACTIONf_angle_d0.72991455
X-RAY DIFFRACTIONf_chiral_restr0.0468168
X-RAY DIFFRACTIONf_plane_restr0.0125182
X-RAY DIFFRACTIONf_dihedral_angle_d7.326159
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.89-2.040.30391520.26562519X-RAY DIFFRACTION96.25
2.04-2.240.25511740.21562579X-RAY DIFFRACTION99.89
2.24-2.570.2221300.20822655X-RAY DIFFRACTION99.96
2.57-3.230.25811390.22332678X-RAY DIFFRACTION100
3.23-42.550.21951610.17492782X-RAY DIFFRACTION99.86
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)
13.54860732654-0.4563666883021.537211640648.454246434414.351092988933.13023735349-0.351085122559-1.08486816185-0.8084121160930.7534364392740.4004478063410.4394063433931.18509573426-0.4625237238560.07622527939460.4479087241340.03344775771740.02382821801580.4063985630230.07025542934290.294550009368-8.705-5.51320.38
27.82831323261-5.219620502133.056757919173.74391123564-1.215807507683.95048475412-1.1192334211-1.24791974961-1.236385738020.4871891747050.4534174340340.3930363881311.268856613140.07853386965460.450868255860.6810745542320.1164863329030.2508265681420.3425278420950.1110648207170.392303942799-1.189-15.3220.745
32.76621943823-2.50789561344-0.4806295919695.38428347858-1.454106237292.48353672327-0.340712636381-1.103471423610.2315271281231.220155754840.470894371853-0.06557825820470.5757384825641.06160823648-0.0797711603390.46154746380.14470031586-0.09238521832680.433000278819-0.08093531863670.3624902354026.23-9.91417.184
49.84354602232-4.955383102990.2374632264826.419397778685.575431712638.62260400426-0.436627411273-0.1449469755130.06632005869910.3343748004880.2478025190450.182493515697-0.05230922766110.1066056449490.1634179657360.305376068127-0.004493374379580.02496418986060.1652216174520.00406063686570.199628227397-4.979-7.68612.6
53.2621028889-4.865022228023.187513596297.84335707837-3.697418287388.4395733948-0.01578556326530.6555673842860.0946803440156-0.137675383432-0.205556455386-0.467047565123-0.5313010264440.3715299840880.2559599608780.23083765376-0.02052550931620.05613059001890.194648551329-0.04503842508280.2715556419434.543-10.5636.287
62.90371925068-1.56919903631-3.532383000747.31214667045-1.175901127735.75935164530.2506391941390.102384037157-0.47692070291.59837835441-0.4128370925141.21171029986-0.221763961536-0.7270166051350.07746313069930.4837293603320.003211672012610.1728964818380.268311077906-0.06952274886610.448644688842.03-19.1639.194
71.70365939776-2.56968545402-1.664933409013.87300329032.50936258119.23285606254-0.005322556407030.444209290133-0.5790125487751.13024247029-0.108882788402-0.679314678481.78642801707-0.3230491630670.1133780895190.897713586492-0.2242868574610.03192055256240.9155210713610.3794509506951.425158896121.816-19.0357.571
87.425951324581.030238216744.596757348678.46171482001-0.1130597725753.0691857106-0.3099279225820.04417410222980.8034348017280.240089266494-0.34993576859-0.432146837203-1.106092077380.3563160656960.3805512150590.3398598968580.000668936605193-0.06270877186030.197837442557-0.04078438111480.31365927174-13.1156.6358.948
95.6572495309-0.3341616928252.45805507168.07121390118-2.979279697217.6307977615-0.194570587686-0.8243924540840.4852759857460.266469600679-0.05484370661530.710155735239-0.842397690683-0.8431589100540.06337317930030.2770127920760.055251898257-0.003034473916690.364908256173-0.09408693250930.242759649979-20.7692.0616.405
103.21293640032-0.2039403275014.627065873795.854896434322.828100073219.043279636560.0791907734419-0.0816813941452-0.04042633316470.397119750666-0.1611708855370.1844897155110.316633185293-0.5153043161380.05980414157910.207639991736-0.04016161918750.006554595459070.2148818388950.005128241309830.145062203957-14.731-6.2055.978
119.026350590822.86069350414-5.178365802837.25709080681-2.986037793313.475136761850.07316344630530.3587903772260.393419369861-0.0642854568321-0.212793646427-0.222288206085-0.5626997367310.1353600697030.1758589155830.316636378942-0.0295651763722-0.04177098908890.3168944352690.01372514809630.186214211028-13.942-2.113-4.35
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 191:196 )A191 - 196
2X-RAY DIFFRACTION2( CHAIN A AND RESID 197:206 )A197 - 206
3X-RAY DIFFRACTION3( CHAIN A AND RESID 207:217 )A207 - 217
4X-RAY DIFFRACTION4( CHAIN A AND RESID 218:227 )A218 - 227
5X-RAY DIFFRACTION5( CHAIN A AND RESID 228:239 )A228 - 239
6X-RAY DIFFRACTION6( CHAIN A AND RESID 240:251 )A240 - 251
7X-RAY DIFFRACTION7( CHAIN A AND RESID 252:253 )A252 - 253
8X-RAY DIFFRACTION8( CHAIN B AND RESID 192:205 )B192 - 205
9X-RAY DIFFRACTION9( CHAIN B AND RESID 206:217 )B206 - 217
10X-RAY DIFFRACTION10( CHAIN B AND RESID 218:239 )B218 - 239
11X-RAY DIFFRACTION11( CHAIN B AND RESID 240:253 )B240 - 253

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