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- PDB-8hyr: Crystal structure of human KARS apo -

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Basic information

Entry
Database: PDB / ID: 8hyr
TitleCrystal structure of human KARS apo
ComponentsLysine--tRNA ligase
KeywordsBIOSYNTHETIC PROTEIN / Lysyl-tRNA synthetase / KARS
Function / homology
Function and homology information


ATP:ADP adenylyltransferase activity / basophil activation involved in immune response / positive regulation of inflammatory response to antigenic stimulus / Mitochondrial tRNA aminoacylation / Selenoamino acid metabolism / lysine-tRNA ligase / lysine-tRNA ligase activity / lysyl-tRNA aminoacylation / diadenosine tetraphosphate biosynthetic process / Cytosolic tRNA aminoacylation ...ATP:ADP adenylyltransferase activity / basophil activation involved in immune response / positive regulation of inflammatory response to antigenic stimulus / Mitochondrial tRNA aminoacylation / Selenoamino acid metabolism / lysine-tRNA ligase / lysine-tRNA ligase activity / lysyl-tRNA aminoacylation / diadenosine tetraphosphate biosynthetic process / Cytosolic tRNA aminoacylation / aminoacyl-tRNA synthetase multienzyme complex / positive regulation of macrophage activation / tRNA processing / amino acid binding / response to X-ray / ERK1 and ERK2 cascade / Transcriptional and post-translational regulation of MITF-M expression and activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / tRNA binding / mitochondrial matrix / positive regulation of DNA-templated transcription / protein homodimerization activity / mitochondrion / extracellular space / nucleoplasm / ATP binding / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Bacterial/eukaryotic lysine-tRNA ligase, class II / Lysine-tRNA ligase, class II / Lysine-tRNA ligase, class II, N-terminal / Lysyl-tRNA synthetase, class II, C-terminal / Aminoacyl-tRNA synthetase, class II (D/K/N) / tRNA synthetases class II (D, K and N) / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. ...Bacterial/eukaryotic lysine-tRNA ligase, class II / Lysine-tRNA ligase, class II / Lysine-tRNA ligase, class II, N-terminal / Lysyl-tRNA synthetase, class II, C-terminal / Aminoacyl-tRNA synthetase, class II (D/K/N) / tRNA synthetases class II (D, K and N) / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsZhang, X. / Wang, Y.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31870751 China
Ministry of Science and Technology (MoST, China)2018YFE0204500 China
CitationJournal: To Be Published
Title: Crystal structure of human KARS apo
Authors: Zhang, X. / Wang, Y. / Ouyang, Z.
History
DepositionJan 7, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lysine--tRNA ligase
B: Lysine--tRNA ligase


Theoretical massNumber of molelcules
Total (without water)120,3942
Polymers120,3942
Non-polymers00
Water3,297183
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8270 Å2
ΔGint-42 kcal/mol
Surface area43950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.331, 107.664, 130.516
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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and ((resid 70 and (name N or name...
d_2ens_1(chain "B" and ((resid 70 and (name N or name...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11SERSERGLUGLUAA70 - 5662 - 498
d_21SERSERLYSLYSBB70 - 5172 - 449
d_22PHEPHEGLUGLUBB528 - 566460 - 498

NCS oper: (Code: givenMatrix: (-0.999978102251, -0.00653717132516, 0.00102976222449), (-0.00654785426751, 0.999920918381, -0.0107369729668), (-0.000959491357428, -0.0107434805843, -0.999941826809) ...NCS oper: (Code: given
Matrix: (-0.999978102251, -0.00653717132516, 0.00102976222449), (-0.00654785426751, 0.999920918381, -0.0107369729668), (-0.000959491357428, -0.0107434805843, -0.999941826809)
Vector: -0.0160336185251, 0.0791000865951, 28.230642563)

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Components

#1: Protein Lysine--tRNA ligase / Lysyl-tRNA synthetase / LysRS


Mass: 60197.199 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KARS1, KARS, KIAA0070 / Production host: Escherichia phage EcSzw-2 (virus)
References: UniProt: Q15046, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases, lysine-tRNA ligase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / Source method: isolated from a natural source / Formula: H2O

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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: 2.64 Å3/Da / Density % sol: 53.33 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.06M Morpheus Divalents, 0.1M Morpheus Buffer system 1, pH 6.5, 30% Morpheus Precipitant Mix 2

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Data collection

DiffractionMean temperature: 77 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 2, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. obs: 42172 / % possible obs: 99.7 % / Redundancy: 6.5 % / Biso Wilson estimate: 39.66 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.152 / Rpim(I) all: 0.064 / Rrim(I) all: 0.165 / Net I/σ(I): 13.5
Reflection shellResolution: 2.55→2.59 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.93 / Num. unique obs: 4151 / CC1/2: 0.865 / Rpim(I) all: 0.383 / Rrim(I) all: 0.961 / % possible all: 99.71

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.55→46.24 Å / SU ML: 0.2824 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.9554
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2453 1995 4.74 %
Rwork0.2147 40133 -
obs0.2162 42128 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.37 Å2
Refinement stepCycle: LAST / Resolution: 2.55→46.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8111 0 0 183 8294
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00478303
X-RAY DIFFRACTIONf_angle_d0.666311213
X-RAY DIFFRACTIONf_chiral_restr0.04511215
X-RAY DIFFRACTIONf_plane_restr0.00651451
X-RAY DIFFRACTIONf_dihedral_angle_d13.7743177
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.515430016446 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.610.33481390.28092804X-RAY DIFFRACTION98.69
2.61-2.680.31191420.26352822X-RAY DIFFRACTION99.9
2.68-2.760.3141400.25942848X-RAY DIFFRACTION99.8
2.76-2.850.32721410.25992825X-RAY DIFFRACTION99.9
2.85-2.950.31511410.25412831X-RAY DIFFRACTION99.93
2.95-3.070.28521410.23882853X-RAY DIFFRACTION99.9
3.07-3.210.27551420.22622835X-RAY DIFFRACTION99.87
3.21-3.380.24711410.22942863X-RAY DIFFRACTION99.87
3.38-3.590.29571430.22222870X-RAY DIFFRACTION99.9
3.59-3.870.2561420.20372857X-RAY DIFFRACTION99.87
3.87-4.260.19391440.18192882X-RAY DIFFRACTION99.9
4.26-4.870.17011430.16062897X-RAY DIFFRACTION99.8
4.87-6.140.19951470.20572934X-RAY DIFFRACTION99.94
6.14-46.240.23651490.21913012X-RAY DIFFRACTION98.11
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)
12.746811911311.118229956370.6607424648555.784825395370.4598579829052.05449500919-0.0787055626765-0.02259618974-0.09658214029740.2633138811250.14085327835-0.1921954345490.1971773894080.192692438464-0.06873808866970.3461620081150.053415107323-0.03730650401520.3503058243540.06368546094190.25571427081929.9380253638-9.6592688682836.5546182028
22.516090629130.07265778234520.693070632440.7022822249020.1285239014341.56375401634-0.125847751055-0.1604700139210.2127404512860.0279428950298-0.04094138958830.0181180638337-0.12453491384-0.1185102565840.1165043725860.2335420506390.004160045708330.02847740463390.246800260796-0.007825577622310.214498690267-2.358092505724.5044939301320.4142296718
34.50514886157-2.1872521893-0.3946219499863.429432221890.9182600827492.03997036127-0.25312571436-0.0284267736066-0.1470166457530.1187701077450.0962310386220.376069375911-0.118382221388-0.2265064415520.1507670931340.2738374680350.007735770328570.06720348801660.3544608543770.07446283695670.29623699998-26.40675137980.28262142584329.8826832217
42.0043446241-0.777788556171.403463784150.6077016216780.3834585710943.9578232182-0.2853189503060.1135387740970.3412335588760.07311494013650.006624661788820.124580614605-0.507943174167-0.2915200902730.291404217210.3142585452820.003110343089540.004038690155370.3399573481030.03501348898460.409355705728-15.58762260476.0820287533918.1805472126
51.73085282725-0.1653079813210.9446652459180.329260056211-0.0841638008781.433190172170.02736201245920.173320670267-0.163599478312-0.141915919553-0.03807831750960.01313140377270.126330837174-0.00494223876110.003983677378140.313521697784-0.003548286194340.03873528299250.289205438303-0.01126522278040.275257879643-10.3675611061-3.49458440897-0.261331063637
62.214558042860.1291609891450.5743710366030.1317116861690.5344202197681.45813377938-0.2271909218180.7010901713430.427474084042-0.1283934273530.0545111690558-0.203761556968-0.333878364350.5487233393320.1292629613010.440787441024-0.07178769265150.007874168330370.6380738853960.1712877978710.48714932702623.98184572114.842352745063.79235981841
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 70 through 207 )AA70 - 2071 - 138
22chain 'A' and (resid 208 through 346 )AA208 - 346139 - 277
33chain 'A' and (resid 347 through 484 )AA347 - 484278 - 415
44chain 'A' and (resid 485 through 576 )AA485 - 576416 - 499
55chain 'B' and (resid 70 through 382 )BB70 - 3821 - 313
66chain 'B' and (resid 383 through 576 )BB383 - 576314 - 500

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