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- PDB-2i4m: Rhodopseudomonas palustris prolyl-tRNA synthetase in complex with... -

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Basic information

Entry
Database: PDB / ID: 2i4m
TitleRhodopseudomonas palustris prolyl-tRNA synthetase in complex with ProAMS
ComponentsProline-tRNA ligaseProline—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 / Anticodon binding domain ...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
'5'-O-(N-(L-PROLYL)-SULFAMOYL)ADENOSINE / Proline--tRNA ligase
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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 5, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 2.0Aug 16, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_distant_solvent_atoms / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_validate_close_contact / struct_ref_seq_dif / struct_site
Item: _atom_site.auth_atom_id / _atom_site.auth_comp_id ..._atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_validate_close_contact.auth_comp_id_2 / _struct_ref_seq_dif.details / _struct_site.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

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)155,5235
Polymers154,6363
Non-polymers8872
Water1,11762
1
A: Proline-tRNA ligase
B: Proline-tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,5343
Polymers103,0912
Non-polymers4431
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5620 Å2
ΔGint-23 kcal/mol
Surface area34800 Å2
MethodPISA
2
C: Proline-tRNA ligase
hetero molecules

C: Proline-tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,9784
Polymers103,0912
Non-polymers8872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Unit cell
Length a, b, c (Å)110.360, 211.900, 150.200
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 ome 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 / 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-P5A / '5'-O-(N-(L-PROLYL)-SULFAMOYL)ADENOSINE


Mass: 443.435 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H21N7O7S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 2.84 Å3/Da / Density % sol: 56.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M Citric acid pH 5.5, 10-11 % PEG 3000, 15-20 % ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 31, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. all: 43712 / Num. obs: 43346 / % possible obs: 96.2 % / Observed criterion σ(F): 2.8 / Observed criterion σ(I): 2.8 / Redundancy: 4.1 % / Rsym value: 0.0077
Reflection shellResolution: 2.8→3.04 Å / Rsym value: 0.345 / % possible all: 91.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQUANTUMdata collection
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.882 / Highest resolution: 2.8 Å / SU B: 32.274 / SU ML: 0.295 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.392 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26938 2208 5.1 %RANDOM
Rwork0.20612 ---
obs0.20932 41139 99.16 %-
all-43155 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.785 Å2
Baniso -1Baniso -2Baniso -3
1-3.05 Å20 Å20 Å2
2---2.38 Å20 Å2
3----0.67 Å2
Refinement stepCycle: LAST / Highest resolution: 2.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10469 0 60 62 10591
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02210857
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4191.97314701
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.32851333
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.49123.061526
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.81151844
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.83815108
X-RAY DIFFRACTIONr_chiral_restr0.0910.21573
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028371
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2310.25154
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3150.27270
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2397
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.190.272
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1910.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.641.56803
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.107210632
X-RAY DIFFRACTIONr_scbond_it1.43634610
X-RAY DIFFRACTIONr_scangle_it2.4284.54069
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.474 168 -
Rwork0.355 3014 -
obs--99.66 %
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)
10.32940.03790.02710.4140.05880.1553-0.01640.0178-0.02480-0.030.03190.0071-0.10260.04650.0134-0.0320.00290.0137-0.0176-0.00366.158663.198916.6292
20.46860.11060.02370.18450.0650.1283-0.02210.0245-0.0418-0.11130.0365-0.0412-0.0572-0.0121-0.01450.1051-0.044-0.0005-0.0367-0.005-0.025229.766776.56549.6305
30.14470.0404-0.01980.34020.0210.1101-0.0666-0.02020.0108-0.07270.03410.0596-0.0236-0.00630.03250.0574-0.0071-0.0102-0.0295-0.00520.007443.0496110.509330.2934
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA-2 - 43618 - 456
2X-RAY DIFFRACTION2BB-2 - 43818 - 458
3X-RAY DIFFRACTION3CC-2 - 43818 - 458

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