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- PDB-1nj1: Crystal structure of Prolyl-tRNA Synthetase from Methanothermobac... -

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Basic information

Entry
Database: PDB / ID: 1nj1
TitleCrystal structure of Prolyl-tRNA Synthetase from Methanothermobacter thermautotrophicus bound to cysteine sulfamoyl adenylate
ComponentsProline-tRNA Synthetase
KeywordsLIGASE / Protein-Aminoacyladenylate Complex Class-II tRNA synthetase
Function / homology
Function and homology information


proline-tRNA ligase / proline-tRNA ligase activity / prolyl-tRNA aminoacylation / aminoacyl-tRNA synthetase multienzyme complex / 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
5'-O-(N-(L-CYSTEINYL)-SULFAMOYL)ADENOSINE / Proline--tRNA ligase
Similarity search - Component
Biological speciesMethanothermobacter thermautotrophicus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 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 / 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)58,7094
Polymers58,1701
Non-polymers5393
Water54030
1
A: Proline-tRNA Synthetase
hetero molecules

A: Proline-tRNA Synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,4198
Polymers116,3412
Non-polymers1,0786
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_554y,x,-z-1/31
Buried area6400 Å2
ΔGint-55 kcal/mol
Surface area38160 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)143.750, 143.750, 163.890
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)
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: Chemical ChemComp-5CA / 5'-O-(N-(L-CYSTEINYL)-SULFAMOYL)ADENOSINE


Mass: 449.463 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H19N7O7S2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 4.54 Å3/Da / Density % sol: 72.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Tris, Beta-Mercaptoethanol, MgCl2, NaCl, Cysteine sulfamoyl adenylate, 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: APS / Beamline: 19-ID / Wavelength: 0.97903 Å
DetectorType: SBC-2 / Detector: CCD / Date: Apr 3, 2002
RadiationMonochromator: 2 double crystal monochromators / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97903 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. all: 33228 / Num. obs: 33200 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 14.8 % / Biso Wilson estimate: 57.1 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 48.9
Reflection shellResolution: 2.55→2.64 Å / Mean I/σ(I) obs: 2.6 / % possible all: 100
Reflection
*PLUS
% possible obs: 100 %
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Methanocaldococcus janaschii Proline tRNA Synthetase

Resolution: 2.55→50 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
Rfree0.257 2957 9.9 %RANDOM
Rwork0.225 ---
all0.225 33186 --
obs0.225 29801 89.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 30.1078 Å2 / ksol: 0.311281 e/Å3
Displacement parametersBiso mean: 72.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.84 Å25.99 Å20 Å2
2--0.84 Å20 Å2
3----1.68 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å-
Luzzati d res low-5 Å
Luzzati sigma a0.49 Å-
Refinement stepCycle: LAST / Resolution: 2.55→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3782 0 31 30 3843
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.94
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.521.5
X-RAY DIFFRACTIONc_mcangle_it2.662
X-RAY DIFFRACTIONc_scbond_it2.342
X-RAY DIFFRACTIONc_scangle_it3.792.5
LS refinement shellResolution: 2.55→2.71 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.43 393 9.6 %
Rwork0.377 3705 -
obs--75.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4FIFI
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.94

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