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- PDB-1nj2: Crystal structure of Prolyl-tRNA Synthetase from Methanothermobac... -

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Basic information

Entry
Database: PDB / ID: 1nj2
TitleCrystal structure of Prolyl-tRNA Synthetase from Methanothermobacter thermautotrophicus
ComponentsProline-tRNA Synthetase
KeywordsLIGASE / Class-II tRNA synthetase
Function / homology
Function and homology information


proline-tRNA ligase / proline-tRNA ligase activity / prolyl-tRNA aminoacylation / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
C-terminal domain of ProRS / Proline-tRNA ligase, class IIa / Prolyl-tRNA synthetase, catalytic domain / Proline-tRNA ligase, class II, C-terminal / Prolyl-tRNA synthetase, C-terminal / Prolyl-tRNA synthetase, C-terminal / Proline-tRNA ligase, class IIa, archaeal-type / Prolyl-tRNA synthetase, class II / Translation Initiation Factor IF3 / Anticodon-binding domain ...C-terminal domain of ProRS / Proline-tRNA ligase, class IIa / Prolyl-tRNA synthetase, catalytic domain / Proline-tRNA ligase, class II, C-terminal / Prolyl-tRNA synthetase, C-terminal / Prolyl-tRNA synthetase, C-terminal / Proline-tRNA ligase, class IIa, archaeal-type / Prolyl-tRNA synthetase, class II / Translation Initiation Factor IF3 / Anticodon-binding domain / Aminoacyl-tRNA synthetase, class II (G/ P/ S/T) / tRNA synthetase class II core domain (G, H, P, S and T) / Anticodon-binding / Anticodon binding domain / Anticodon-binding domain superfamily / 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) / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Proline--tRNA ligase
Similarity search - Component
Biological speciesMethanothermobacter thermautotrophicus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.11 Å
AuthorsKamtekar, S. / Kennedy, W.D. / Wang, J. / Stathopoulos, C. / Soll, D. / Steitz, T.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: The structural basis of cysteine aminoacylation of tRNAPro by prolyl-tRNA synthetases
Authors: Kamtekar, S. / Kennedy, W.D. / Wang, J. / Stathopoulos, C. / Soll, D. / Steitz, T.A.
History
DepositionDec 30, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _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: Proline-tRNA Synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,2603
Polymers58,1701
Non-polymers902
Water23413
1
A: Proline-tRNA Synthetase
hetero molecules

A: Proline-tRNA Synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,5206
Polymers116,3412
Non-polymers1794
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+2/31
Buried area4510 Å2
ΔGint-50 kcal/mol
Surface area41670 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)145.077, 145.077, 170.359
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Cell settinghexagonal
Space group name H-MP6522
DetailsThe biological assembly is a dimer constructed by a twofold rotation.

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Components

#1: Protein Proline-tRNA Synthetase / E.C.6.1.1.15 / Prolyl-tRNA synthetase / Proline--tRNA ligase / ProRS


Mass: 58170.258 Da / Num. of mol.: 1 / Fragment: N terminally His Tagged Enzyme
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea)
Strain: Delta H
Description: Strain supplemented with additional plasmid encoding rare tRNAs
Gene: MTH611 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 RecA- / References: UniProt: O26708, proline-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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 4.98 Å3/Da / Density % sol: 75.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Tris, Beta-Mercaptoethanol, MgCl2,NaCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 12-25 ℃ / pH: 8.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
15 mg/mlprotein1drop
220 mMTris1droppH8.5
3200 mM1dropNaCl
45 mM2-mercaptoethanol1drop
50.2 Mammonium sulfate1reservoir
620-30 %PEG40001reservoir
75 mM2-mercaptoethanol1reservoir
80.1 M1reservoirpH4.5NaOAc

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.945 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 20, 2000
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.945 Å / Relative weight: 1
ReflectionResolution: 3.1→30 Å / Num. all: 36062 / Num. obs: 35918 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 22.8
Reflection shellResolution: 3.1→3.21 Å / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 2 / % possible all: 99.7
Reflection
*PLUS
Highest resolution: 3.1 Å
Reflection shell
*PLUS
% possible obs: 99.7 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Methanocaldococcus janaschii Proline tRNA Synthetase

Resolution: 3.11→29.95 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.273 3457 10 %RANDOM
Rwork0.239 ---
all0.239 36056 --
obs0.239 34613 96 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 24.3074 Å2 / ksol: 0.264032 e/Å3
Displacement parametersBiso mean: 89.4 Å2
Baniso -1Baniso -2Baniso -3
1-7.03 Å214.95 Å20 Å2
2--7.03 Å20 Å2
3----14.06 Å2
Refine analyzeLuzzati coordinate error free: 0.52 Å / Luzzati sigma a free: 0.75 Å
Refinement stepCycle: LAST / Resolution: 3.11→29.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3693 0 2 13 3708
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.92
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.611.5
X-RAY DIFFRACTIONc_mcangle_it2.922
X-RAY DIFFRACTIONc_scbond_it2.232
X-RAY DIFFRACTIONc_scangle_it3.772.5
LS refinement shellResolution: 3.11→3.29 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.387 479 9.5 %
Rwork0.366 4549 -
obs--82.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAM
X-RAY DIFFRACTION3WATER_REP.PARAM
Refinement
*PLUS
Highest resolution: 3.1 Å / Lowest resolution: 30 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.92

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