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- PDB-6now: Human Mitochondrial Alanyl-tRNA Synthetase C-Ala domain -

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Basic information

Entry
Database: PDB / ID: 6now
TitleHuman Mitochondrial Alanyl-tRNA Synthetase C-Ala domain
ComponentsAlanine--tRNA ligase, mitochondrial
KeywordsLIGASE / Alanyl-tRNA synthetase / mitochondria / C-terminal domain / alpha-beta domain
Function / homology
Function and homology information


mitochondrial alanyl-tRNA aminoacylation / alanine-tRNA ligase / alanine-tRNA ligase activity / alanyl-tRNA aminoacylation / Mitochondrial tRNA aminoacylation / aminoacyl-tRNA editing activity / tRNA binding / mitochondrion / zinc ion binding / ATP binding
Similarity search - Function
Alanine-tRNA ligase, eukaryota/bacteria / Alanine-tRNA ligase, class IIc / Alanine-tRNA ligase, class IIc, anti-codon-binding domain superfamily / Alanyl-tRNA synthetase, class IIc, N-terminal / Alanyl-tRNA synthetase, class IIc, core domain / tRNA synthetases class II (A) / Alanyl-transfer RNA synthetases family profile. / Threonyl/alanyl tRNA synthetase, SAD / Threonyl and Alanyl tRNA synthetase second additional domain / Threonyl and Alanyl tRNA synthetase second additional domain ...Alanine-tRNA ligase, eukaryota/bacteria / Alanine-tRNA ligase, class IIc / Alanine-tRNA ligase, class IIc, anti-codon-binding domain superfamily / Alanyl-tRNA synthetase, class IIc, N-terminal / Alanyl-tRNA synthetase, class IIc, core domain / tRNA synthetases class II (A) / Alanyl-transfer RNA synthetases family profile. / Threonyl/alanyl tRNA synthetase, SAD / Threonyl and Alanyl tRNA synthetase second additional domain / Threonyl and Alanyl tRNA synthetase second additional domain / Threonyl/alanyl tRNA synthetase, class II-like, putative editing domain superfamily / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Translation protein, beta-barrel domain superfamily
Similarity search - Domain/homology
Alanine--tRNA ligase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 4.099 Å
AuthorsKuhle, B. / Schimmel, P.
CitationJournal: Nat Commun / Year: 2020
Title: Relaxed sequence constraints favor mutational freedom in idiosyncratic metazoan mitochondrial tRNAs.
Authors: Kuhle, B. / Chihade, J. / Schimmel, P.
History
DepositionJan 16, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Database references / Structure summary / Category: citation / citation_author / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _struct.title
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alanine--tRNA ligase, mitochondrial
B: Alanine--tRNA ligase, mitochondrial


Theoretical massNumber of molelcules
Total (without water)44,0332
Polymers44,0332
Non-polymers00
Water0
1
A: Alanine--tRNA ligase, mitochondrial


Theoretical massNumber of molelcules
Total (without water)22,0161
Polymers22,0161
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Alanine--tRNA ligase, mitochondrial


Theoretical massNumber of molelcules
Total (without water)22,0161
Polymers22,0161
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.420, 104.420, 164.270
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 793 or (resid 794 and (name...
21(chain B and (resseq 793:797 or resseq 799:810 or resseq...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYGLYGLY(chain A and (resseq 793 or (resid 794 and (name...AA79311
12GLNGLNGLNGLN(chain A and (resseq 793 or (resid 794 and (name...AA79412
13ALAALALEULEU(chain A and (resseq 793 or (resid 794 and (name...AA786 - 9864 - 204
14ALAALALEULEU(chain A and (resseq 793 or (resid 794 and (name...AA786 - 9864 - 204
15ALAALALEULEU(chain A and (resseq 793 or (resid 794 and (name...AA786 - 9864 - 204
16ALAALALEULEU(chain A and (resseq 793 or (resid 794 and (name...AA786 - 9864 - 204
17ALAALALEULEU(chain A and (resseq 793 or (resid 794 and (name...AA786 - 9864 - 204
21GLYGLYALAALA(chain B and (resseq 793:797 or resseq 799:810 or resseq...BB793 - 79711 - 15
22GLUGLUGLYGLY(chain B and (resseq 793:797 or resseq 799:810 or resseq...BB799 - 81017 - 28
23ARGARGALAALA(chain B and (resseq 793:797 or resseq 799:810 or resseq...BB812 - 81530 - 33
24ARGARGGLYGLY(chain B and (resseq 793:797 or resseq 799:810 or resseq...BB817 - 82535 - 43
25ARGARGARGARG(chain B and (resseq 793:797 or resseq 799:810 or resseq...BB82644
26GLUGLULEULEU(chain B and (resseq 793:797 or resseq 799:810 or resseq...BB791 - 9869 - 204
27GLUGLULEULEU(chain B and (resseq 793:797 or resseq 799:810 or resseq...BB791 - 9869 - 204
28GLUGLULEULEU(chain B and (resseq 793:797 or resseq 799:810 or resseq...BB791 - 9869 - 204
29GLUGLULEULEU(chain B and (resseq 793:797 or resseq 799:810 or resseq...BB791 - 9869 - 204

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Components

#1: Protein Alanine--tRNA ligase, mitochondrial / Alanyl-tRNA synthetase / AlaRS


Mass: 22016.475 Da / Num. of mol.: 2 / Fragment: C-terminal domain (UNP residues 783-985)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AARS2, AARSL, KIAA1270 / Plasmid: pET21 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5JTZ9, alanine-tRNA ligase

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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: 5.08 Å3/Da / Density % sol: 75.81 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 7 / Details: 0.1 M imidazole, 2 M sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97938 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 24, 2017
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97938 Å / Relative weight: 1
ReflectionResolution: 4.1→35.89 Å / Num. obs: 6904 / % possible obs: 99.7 % / Redundancy: 7.568 % / Biso Wilson estimate: 205.59 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.055 / Rrim(I) all: 0.059 / Χ2: 1.012 / Net I/σ(I): 17.45 / Num. measured all: 52247
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
4.1-4.217.0280.6842.7435425065040.8730.73899.6
4.21-4.328.0020.4094.6238734844840.9830.438100
4.32-4.457.9440.3056.1938614864860.9790.326100
4.45-4.587.8780.2397.4237424764750.9890.25699.8
4.58-4.737.8640.2188.3935944574570.990.233100
4.73-4.97.60.2228.431924224200.9830.23899.5
4.9-5.087.2410.18310.231284324320.9860.197100
5.08-5.297.5150.18110.4431944254250.990.194100
5.29-5.538.0080.15612.2830993873870.9940.167100
5.53-5.87.9640.15712.7230583843840.9890.168100
5.8-6.117.7490.11216.9427203513510.9950.12100
6.11-6.487.5880.0822.7326183463450.9960.08699.7
6.48-6.936.8980.05727.8721733163150.9980.06299.7
6.93-7.487.9050.04933.3223322952950.9990.052100
7.48-8.27.6870.03941.2420602682680.9990.041100
8.2-9.177.2330.03544.618592572570.9990.038100
9.17-10.586.7040.02847.0114482182160.9990.0399.1
10.58-12.967.3910.03149.5513601841840.9990.033100
12.96-18.336.8950.0348.85104815215210.033100
18.33-35.895.1640.0442.7934678670.9980.04485.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.1 Å35.89 Å
Translation4.1 Å35.89 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASER2.7.17phasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6NLY

6nly


Resolution: 4.099→35.89 Å / SU ML: 0.51 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 40.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.282 345 5.01 %
Rwork0.2332 6539 -
obs0.2358 6884 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 527.07 Å2 / Biso mean: 259.1622 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 4.099→35.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2909 0 0 0 2909
Num. residues----397
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032949
X-RAY DIFFRACTIONf_angle_d0.6533993
X-RAY DIFFRACTIONf_chiral_restr0.038498
X-RAY DIFFRACTIONf_plane_restr0.003502
X-RAY DIFFRACTIONf_dihedral_angle_d19.2721835
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1742X-RAY DIFFRACTION3.415TORSIONAL
12B1742X-RAY DIFFRACTION3.415TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 2

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
4.0995-5.16250.34761710.26963246341799
5.1625-35.8910.26341740.222432933467100
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)
10.4245-0.25-0.13244.07322.73871.13482.27123.3852.5523-2.1003-0.08090.23822.06141.2055-0.05534.0553-0.21161.06483.60370.04612.40251.6285-47.1482-55.5778
28.2434-4.1274-3.95091.1788-0.02325.54231.3971-1.88641.3632-1.2633-1.8441-0.42621.0822-0.8202-0.49821.8787-0.3797-0.26742.22770.32881.9326-8.66-44.6529-43.7987
39.37780.15011.51350.5239-2.90089.2649-0.72330.67420.25250.28180.07911.8072-0.55830.14330.79651.6781-0.23680.36251.8888-0.07472.3683-22.7827-48.4274-17.2004
40.061-0.13280.0050.17970.10241.1657-1.44540.61171.39421.00880.93035.33150.1735-1.3278-1.42752.5946-0.1557-0.44564.95040.35183.84-9.711-54.39099.9096
52.24173.53489.79368.58643.18327.7452-0.25352.4134-1.52634.72441.40941.79581.67195.31921.74242.8198-0.1510.49962.68820.04041.4939-11.9576-55.55730.5226
60.663-3.2912-2.31646.5501-2.31599.15710.1161-0.71090.67360.8889-0.681-0.6433-1.76221.80610.93861.4088-0.626-0.46392.30870.41191.8438-7.6536-37.7243-19.6512
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 786 through 809 )A786 - 809
2X-RAY DIFFRACTION2chain 'A' and (resid 810 through 875 )A810 - 875
3X-RAY DIFFRACTION3chain 'A' and (resid 876 through 986 )A876 - 986
4X-RAY DIFFRACTION4chain 'B' and (resid 791 through 809 )B791 - 809
5X-RAY DIFFRACTION5chain 'B' and (resid 810 through 837 )B810 - 837
6X-RAY DIFFRACTION6chain 'B' and (resid 838 through 986 )B838 - 986

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