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- PDB-5yzx: Crystal structure of E.coli LysU T146D mutant -

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Basic information

Entry
Database: PDB / ID: 5yzx
TitleCrystal structure of E.coli LysU T146D mutant
ComponentsLysine--tRNA ligase, heat inducible
KeywordsLIGASE / Class II aminoacyl-tRNA synthetase / LysRS
Function / homology
Function and homology information


RNA capping / lysine-tRNA ligase / lysine-tRNA ligase activity / lysyl-tRNA aminoacylation / tRNA aminoacylation for protein translation / ligase activity / cellular response to heat / tRNA binding / magnesium ion binding / protein homodimerization activity ...RNA capping / lysine-tRNA ligase / lysine-tRNA ligase activity / lysyl-tRNA aminoacylation / tRNA aminoacylation for protein translation / ligase activity / cellular response to heat / tRNA binding / magnesium ion binding / protein homodimerization activity / ATP binding / membrane / cytosol
Similarity search - Function
Bacterial/eukaryotic lysine-tRNA ligase, class II / Lysine-tRNA ligase, class II, N-terminal / Lysine-tRNA ligase, class II / 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 / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 ...Bacterial/eukaryotic lysine-tRNA ligase, class II / Lysine-tRNA ligase, class II, N-terminal / Lysine-tRNA ligase, class II / 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 / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / 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 proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
BIS(ADENOSINE)-5'-TETRAPHOSPHATE / Lysine--tRNA ligase, heat inducible
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsFang, P. / Guo, M.
Funding support United States, China, 5items
OrganizationGrant numberCountry
National Institutes of HealthGM100136 United States
National Institutes of HealthGM106134 United States
Shanghai Pujiang Program17PJ1410800 China
National Natural Science Foundation of China21778067 China
National Natural Science Foundation of China21778064 China
CitationJournal: To Be Published
Title: A proposed role for MSC to reserve the canonical function in high eukaryotes prior to stimuli
Authors: Zheng, L. / Ali, H. / Wang, J. / Guo, M. / Fang, P.
History
DepositionDec 16, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 19, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lysine--tRNA ligase, heat inducible
B: Lysine--tRNA ligase, heat inducible
C: Lysine--tRNA ligase, heat inducible
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,12115
Polymers180,2513
Non-polymers2,87012
Water0
1
A: Lysine--tRNA ligase, heat inducible
C: Lysine--tRNA ligase, heat inducible
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,08110
Polymers120,1672
Non-polymers1,9138
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11730 Å2
ΔGint-122 kcal/mol
Surface area36400 Å2
MethodPISA
2
B: Lysine--tRNA ligase, heat inducible
hetero molecules

B: Lysine--tRNA ligase, heat inducible
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,08110
Polymers120,1672
Non-polymers1,9138
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area11770 Å2
ΔGint-119 kcal/mol
Surface area36510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.544, 249.855, 179.652
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 60083.730 Da / Num. of mol.: 3 / Mutation: T146D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: lysU, b4129, JW4090 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A8N5, lysine-tRNA ligase
#2: Chemical ChemComp-B4P / BIS(ADENOSINE)-5'-TETRAPHOSPHATE / Ap4A


Mass: 836.387 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C20H28N10O19P4
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Ca

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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: 72.66 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M NH4SO4, 0.3M Na Formate, 0.1 M Na Cacodylate pH 6.5, 3% PGA, and 30% PEG400,

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 3.2→40 Å / Num. obs: 56309 / % possible obs: 99.5 % / Redundancy: 4.9 % / Biso Wilson estimate: 54.18 Å2 / Rmerge(I) obs: 0.22 / Rpim(I) all: 0.108 / Rrim(I) all: 0.246 / Χ2: 2.669 / Net I/σ(I): 5.4 / Num. measured all: 278081
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.2-3.313.90.58655400.7110.330.6761.12198.9
3.31-3.454.10.53555810.7520.2950.6141.36299.4
3.45-3.64.20.44955700.8280.2430.5131.74499.6
3.6-3.7940.34355630.8860.190.3942.26499.1
3.79-4.035.10.3256020.930.1560.3572.57599.7
4.03-4.345.30.2756250.9610.1270.2993.14899.8
4.34-4.785.50.2156190.9720.0990.2333.53299.5
4.78-5.475.30.18956430.9740.0890.213.29299.6
5.47-6.886.20.18256910.9770.0790.1992.82999.7
6.88-405.70.09458750.9940.0430.1033.37199.5

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
HKL-3000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 1.0E+22 / Resolution: 3.2→38.147 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2685 2674 5 %
Rwork0.2359 50769 -
obs0.2376 53443 99.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 143.34 Å2 / Biso mean: 50.3493 Å2 / Biso min: 27.53 Å2
Refinement stepCycle: final / Resolution: 3.2→38.147 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11406 0 168 0 11574
Biso mean--70.86 --
Num. residues----1453
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00311808
X-RAY DIFFRACTIONf_angle_d0.62616025
X-RAY DIFFRACTIONf_chiral_restr0.0441771
X-RAY DIFFRACTIONf_plane_restr0.0042092
X-RAY DIFFRACTIONf_dihedral_angle_d11.0267006
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2001-3.25820.33151520.28592592274499
3.2582-3.32080.38261590.29982635279499
3.3208-3.38860.35711220.29422678280099
3.3886-3.46220.33511160.29672662277899
3.4622-3.54270.3008960.29132692278899
3.5427-3.63120.33671340.27642632276699
3.6312-3.72930.31451410.27542653279499
3.7293-3.8390.27361480.25226702818100
3.839-3.96280.32531160.247726762792100
3.9628-4.10420.27231460.238626802826100
4.1042-4.26840.23911280.227526842812100
4.2684-4.46230.23721550.21712636279199
4.4623-4.69720.25991650.21942640280599
4.6972-4.99090.24321560.210526912847100
4.9909-5.37530.26131560.2162649280599
5.3753-5.91440.26121310.21272704283599
5.9144-6.76610.2631630.219726972860100
6.7661-8.5090.21451400.193127742914100
8.509-38.14970.19861500.19392724287496
Refinement TLS params.Method: refined / Origin x: 96.3344 Å / Origin y: 77.5421 Å / Origin z: 53.7536 Å
111213212223313233
T0.3073 Å2-0.0129 Å20.0805 Å2-0.4891 Å20.0096 Å2--0.3014 Å2
L-0.0192 °2-0.1536 °2-0.0405 °2-0.2785 °20.1301 °2--0.1503 °2
S0.0285 Å °0.0077 Å °0.0348 Å °0.0104 Å °0.0842 Å °-0.0645 Å °-0.0294 Å °0.062 Å °-0.0846 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA12 - 502
2X-RAY DIFFRACTION1allB12 - 502
3X-RAY DIFFRACTION1allC12 - 502
4X-RAY DIFFRACTION1allD1 - 3
5X-RAY DIFFRACTION1allE1 - 9

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