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- PDB-2i4o: Rhodopseudomonas palustris prolyl-tRNA synthetase in complex with ATP -

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Basic information

Entry
Database: PDB / ID: 2i4o
TitleRhodopseudomonas palustris prolyl-tRNA synthetase in complex with ATP
ComponentsProline-tRNA ligase
KeywordsLIGASE / alpha beta
Function / homology
Function and homology information


proline-tRNA ligase / proline-tRNA ligase activity / prolyl-tRNA aminoacylation / ATP binding / cytoplasm
Similarity search - Function
Proline-tRNA ligase, class IIa, type 2 / Prolyl-tRNA synthetase, class IIa, bacterial-type / Prokaryote proline-tRNA ligase core domain / Proline--tRNA ligase, anticodon binding domain / Proline-tRNA ligase, class IIa / 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 ...Proline-tRNA ligase, class IIa, type 2 / Prolyl-tRNA synthetase, class IIa, bacterial-type / Prokaryote proline-tRNA ligase core domain / Proline--tRNA ligase, anticodon binding domain / Proline-tRNA ligase, class IIa / 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
ADENOSINE-5'-TRIPHOSPHATE / Proline--tRNA ligase
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsCrepin, T. / Yaremchuk, A. / Tukalo, M. / Cusack, S.
CitationJournal: Structure / Year: 2006
Title: Structures of Two Bacterial Prolyl-tRNA Synthetases with and without a cis-Editing Domain.
Authors: Crepin, T. / Yaremchuk, A. / Tukalo, M. / Cusack, S.
History
DepositionAug 22, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.3Feb 21, 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_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.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_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
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Proline-tRNA ligase
B: Proline-tRNA ligase
C: Proline-tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,35214
Polymers154,6363
Non-polymers1,71611
Water5,026279
1
A: Proline-tRNA ligase
B: Proline-tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,25110
Polymers103,0912
Non-polymers1,1608
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7120 Å2
ΔGint-77 kcal/mol
Surface area34700 Å2
MethodPISA
2
C: Proline-tRNA ligase
hetero molecules

C: Proline-tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,2038
Polymers103,0912
Non-polymers1,1126
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x-1,y,-z-1/21
Unit cell
Length a, b, c (Å)114.200, 211.210, 148.210
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsThe biological unit is a dimer. The asymmetric unit contains one biological dimer (Chain A,B) and one monomer (Chain C). The corresponding dimer can be obtain with the symmetric operations.

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Components

#1: Protein Proline-tRNA ligase


Mass: 51545.465 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic)
Strain: CGA009-ATCC BAA-98 / Gene: proS,RPA2928 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus-RIL / References: UniProt: Q6N5P6, proline-tRNA ligase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 279 / 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: 2.89 Å3/Da / Density % sol: 57.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M hepes (pH 7.0), 8-10 % PEG 8K, 5-10 % ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 11, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. all: 70163 / Num. obs: 65656 / % possible obs: 93.6 % / Observed criterion σ(F): 2.4 / Observed criterion σ(I): 2.4 / Redundancy: 4 % / Rsym value: 0.0086
Reflection shellResolution: 2.4→2.55 Å / Redundancy: 3.7 % / Rsym value: 0.474 / % possible all: 93.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MxCuBEdata collection
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: native R. palustris Prolyl-tRNA synthetase

Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.905 / Highest resolution: 2.4 Å / SU B: 11.328 / SU ML: 0.197 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.356 / ESU R Free: 0.266 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26104 3397 5 %RANDOM
Rwork0.19735 ---
obs0.20051 63935 95.97 %-
all-70163 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.851 Å2
Baniso -1Baniso -2Baniso -3
1-1.48 Å20 Å20 Å2
2---2.3 Å20 Å2
3---0.83 Å2
Refinement stepCycle: LAST / Highest resolution: 2.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10485 0 101 279 10865
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02210809
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5661.97714646
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.52451320
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.20923.046522
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.307151836
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.09915108
X-RAY DIFFRACTIONr_chiral_restr0.0980.21566
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028295
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2120.24773
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.27196
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2510
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0390.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2140.276
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2050.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7111.56768
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.227210524
X-RAY DIFFRACTIONr_scbond_it1.76134635
X-RAY DIFFRACTIONr_scangle_it2.724.54122
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 236 -
Rwork0.263 4825 -
obs--98.92 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.2814-0.0351-0.06720.3079-0.0060.1598-0.0389-0.006-0.01230.01870.0127-0.00570.05730.06580.0262-0.00050.0518-0.0021-0.03890.0097-0.0071-7.0441-42.6565-16.3281
20.3428-0.02880.02670.1460.05730.2109-0.0282-0.0366-0.01560.03810.02970.03660.01280.0049-0.00150.00540.03150.012-0.040.0064-0.0142-30.9713-29.6843-9.7596
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 438
2X-RAY DIFFRACTION2B-2 - 438

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