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- PDB-3h9b: Structure of a mutant methionyl-tRNA synthetase with modified spe... -

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Basic information

Entry
Database: PDB / ID: 3h9b
TitleStructure of a mutant methionyl-tRNA synthetase with modified specificity complexed with azidonorleucine
ComponentsMethionyl-tRNA synthetase
KeywordsLIGASE / Rossmann fold / Aminoacyl-tRNA synthetase / ATP-binding / Metal-binding / Nucleotide-binding / Protein biosynthesis / RNA-binding / tRNA-binding
Function / homology
Function and homology information


methionine-tRNA ligase / methionine-tRNA ligase activity / methionyl-tRNA aminoacylation / tRNA binding / protein homodimerization activity / zinc ion binding / ATP binding / membrane / cytosol
Similarity search - Function
Methionyl-tRNA synthetase, Zn-domain / Methionine-tRNA ligase, type 1 / Methionyl-tRNA synthetase, Zn-domain / Methionyl-tRNA synthetase, beta subunit, C-terminal / Anticodon binding domain of methionyl tRNA ligase / Methionyl-tRNA synthetase / Methioninyl-tRNA synthetase core domain / Methionyl-tRNA synthetase, anticodon-binding domain / Isoleucyl-tRNA Synthetase; Domain 1 / Isoleucyl-tRNA Synthetase; Domain 1 ...Methionyl-tRNA synthetase, Zn-domain / Methionine-tRNA ligase, type 1 / Methionyl-tRNA synthetase, Zn-domain / Methionyl-tRNA synthetase, beta subunit, C-terminal / Anticodon binding domain of methionyl tRNA ligase / Methionyl-tRNA synthetase / Methioninyl-tRNA synthetase core domain / Methionyl-tRNA synthetase, anticodon-binding domain / Isoleucyl-tRNA Synthetase; Domain 1 / Isoleucyl-tRNA Synthetase; Domain 1 / tRNA-binding domain / Putative tRNA binding domain / tRNA-binding domain profile. / Methionyl/Leucyl tRNA synthetase / tRNA synthetases class I (M) / Aminoacyl-tRNA synthetase, class Ia, anticodon-binding / Rubrerythrin, domain 2 / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / HUPs / Single Sheet / Rossmann-like alpha/beta/alpha sandwich fold / Nucleic acid-binding, OB-fold / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / 6-azido-L-norleucine / Methionine--tRNA ligase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsSchmitt, E. / Tanrikulu, I.C. / Yoo, T.H. / Panvert, M. / Tirrell, D.A. / Mechulam, Y.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Switching from an induced-fit to a lock-and-key mechanism in an aminoacyl-tRNA synthetase with modified specificity.
Authors: Schmitt, E. / Tanrikulu, I.C. / Yoo, T.H. / Panvert, M. / Tirrell, D.A. / Mechulam, Y.
History
DepositionApr 30, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Methionyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5295
Polymers63,9071
Non-polymers6224
Water20,9151161
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.259, 45.377, 85.890
Angle α, β, γ (deg.)90.000, 107.240, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Methionyl-tRNA synthetase / Methionine-tRNA ligase / MetRS


Mass: 63907.199 Da / Num. of mol.: 1 / Fragment: M547 domain: UNP residues 2-548
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: b2114, JW2101, metG / Plasmid: pMTY21 / Production host: Escherichia coli (E. coli) / Strain (production host): JM101Tr / References: UniProt: P00959, methionine-tRNA ligase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-NOT / 6-azido-L-norleucine / AZIDONORLEUCINE


Type: L-peptide linking / Mass: 172.185 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12N4O2
#4: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1161 / 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: 2.34 Å3/Da / Density % sol: 47.33 %
Crystal growTemperature: 279 K / Method: vapor diffusion, sitting drop / pH: 7.1
Details: Ammonium citrate, pH 7.1, VAPOR DIFFUSION, SITTING DROP, temperature 279K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 13, 2007
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. all: 86282 / Num. obs: 86282 / % possible obs: 93.1 % / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Biso Wilson estimate: 15.822 Å2 / Rmerge(I) obs: 0.026 / Rsym value: 0.026 / Net I/σ(I): 27.6
Reflection shellResolution: 1.5→1.6 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.094 / Mean I/σ(I) obs: 10.1 / Num. unique all: 15200 / Num. unique obs: 15200 / Rsym value: 0.094 / % possible all: 93.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
CNSrefinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
XDSdata reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3H97

3h97


Resolution: 1.5→50 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.902 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.188 5245 5.7 %
Rwork0.165 --
obs0.165 86281 93.1 %
Solvent computationBsol: 37.948 Å2
Displacement parametersBiso max: 41.7 Å2 / Biso mean: 12.076 Å2 / Biso min: 1.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.211 Å20 Å20.105 Å2
2---0.914 Å20 Å2
3---0.703 Å2
Refinement stepCycle: LAST / Resolution: 1.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4368 0 39 1161 5568
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg1.216
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:ion.param
X-RAY DIFFRACTION3anl.par
X-RAY DIFFRACTION4CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION5cit.par

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