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- PDB-3h9c: Structure of methionyl-tRNA synthetase: crystal form 2 -

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Basic information

Entry
Database: PDB / ID: 3h9c
TitleStructure of methionyl-tRNA synthetase: crystal form 2
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 / Methionine--tRNA ligase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 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 1.2Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name
Revision 1.3Sep 6, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Methionyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,7293
Polymers62,4721
Non-polymers2582
Water18,8801048
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.890, 45.400, 86.210
Angle α, β, γ (deg.)90.000, 107.300, 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: 62471.551 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: pBSM547 / 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-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1048 / 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: 2.36 Å3/Da / Density % sol: 47.87 %
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: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 19, 2009
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. all: 109028 / Num. obs: 109028 / % possible obs: 94.7 % / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Biso Wilson estimate: 19.108 Å2 / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Net I/σ(I): 11.4
Reflection shellResolution: 1.4→1.5 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 2.9 / Num. unique all: 19290 / Num. unique obs: 19290 / Rsym value: 0.3 / % possible all: 90.1

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Phasing

PhasingMethod: molecular replacement

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Processing

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

3h97


Resolution: 1.4→29.54 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.899 / SU ML: 0.18 / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflection
Rfree0.191 6565 6.02 %
Rwork0.165 --
obs0.167 109028 94.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.75 Å2 / ksol: 0.381 e/Å3
Displacement parametersBiso max: 49.85 Å2 / Biso mean: 15.238 Å2 / Biso min: 4.69 Å2
Baniso -1Baniso -2Baniso -3
1-1.689 Å20 Å2-0.207 Å2
2--0.275 Å2-0 Å2
3----1.963 Å2
Refinement stepCycle: LAST / Resolution: 1.4→29.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4375 0 14 1048 5437
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064499
X-RAY DIFFRACTIONf_angle_d1.0556091
X-RAY DIFFRACTIONf_chiral_restr0.072638
X-RAY DIFFRACTIONf_plane_restr0.005795
X-RAY DIFFRACTIONf_dihedral_angle_d17.6811627
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4-1.4160.2731810.2372943312481
1.416-1.4330.2592100.2263032324286
1.433-1.450.2381870.2183213340089
1.45-1.4680.2272330.2093331356493
1.468-1.4880.1812200.1933437365796
1.488-1.5080.2252200.1853526374699
1.508-1.530.2112390.1783485372498
1.53-1.5530.2092190.1783525374498
1.553-1.5770.1922320.1743509374198
1.577-1.6030.1982490.1713504375398
1.603-1.630.1772250.1633524374998
1.63-1.660.1932080.1623490369898
1.66-1.6920.1812190.1613551377097
1.692-1.7260.1822050.1533455366097
1.726-1.7640.1832110.1573547375898
1.764-1.8050.2032320.1553470370297
1.805-1.850.1782210.1533475369697
1.85-1.90.1792350.1543480371597
1.9-1.9560.1862050.1553473367896
1.956-2.0190.1672100.1483444365496
2.019-2.0910.1652250.1493440366596
2.091-2.1750.1772020.1483484368695
2.175-2.2740.1872380.1633438367695
2.274-2.3940.1922160.1593447366395
2.394-2.5430.1942100.1653429363995
2.543-2.740.212350.1753372360794
2.74-3.0150.1962370.1693398363594
3.015-3.4510.1812210.1553375359693
3.451-4.3460.1592080.1393351355991
4.346-29.5470.1822120.1573315352788

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