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- PDB-2j3m: PROLYL-TRNA SYNTHETASE FROM ENTEROCOCCUS FAECALIS COMPLEXED WITH ... -

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Basic information

Entry
Database: PDB / ID: 2j3m
TitlePROLYL-TRNA SYNTHETASE FROM ENTEROCOCCUS FAECALIS COMPLEXED WITH ATP, manganese and prolinol
ComponentsPROLYL-TRNA SYNTHETASE
KeywordsLIGASE / BACTERIAL-TYPE PROLYL-TRNA SYNTHETASE / CLASS II AMINOACYL-TRNA SYNTHETASE / EDITING / TRANSLATION / ATP + L-PROLINE + TRNA (PRO) GIVES AMP + PPI + L-PROLYL-TRNA(PRO)
Function / homology
Function and homology information


proline-tRNA ligase / proline-tRNA ligase activity / prolyl-tRNA aminoacylation / aminoacyl-tRNA editing activity / transferase activity / ATP binding / cytoplasm
Similarity search - Function
Prolyl-tRNA synthetase, class IIa, type 1 / Prolyl-tRNA synthetase, class IIa, bacterial-type / Prokaryote proline-tRNA ligase core domain / Proline--tRNA ligase, anticodon binding domain / YbaK protein / YbaK/aminoacyl-tRNA synthetase-associated domain / YbaK/aminoacyl-tRNA synthetase-associated domain / Aminoacyl-tRNA editing domain / YbaK/aminoacyl-tRNA synthetase-associated domain superfamily / Proline-tRNA ligase, class IIa ...Prolyl-tRNA synthetase, class IIa, type 1 / Prolyl-tRNA synthetase, class IIa, bacterial-type / Prokaryote proline-tRNA ligase core domain / Proline--tRNA ligase, anticodon binding domain / YbaK protein / YbaK/aminoacyl-tRNA synthetase-associated domain / YbaK/aminoacyl-tRNA synthetase-associated domain / Aminoacyl-tRNA editing domain / YbaK/aminoacyl-tRNA synthetase-associated domain superfamily / 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) / Alpha-Beta Complex / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / : / PYRROLIDINE-2-CARBALDEHYDE / Proline--tRNA ligase
Similarity search - Component
Biological speciesENTEROCOCCUS FAECALIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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: PDBE / Processing site: PDBE
Revision 1.0Oct 11, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_asym_id / _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_asym_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" AND "BB" IN EACH CHAIN ON SHEET ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" AND "BB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROLYL-TRNA SYNTHETASE
B: PROLYL-TRNA SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,22512
Polymers128,6832
Non-polymers1,54210
Water6,539363
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)68.583, 92.679, 101.223
Angle α, β, γ (deg.)90.00, 106.11, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.998551, 0.002973, 0.053737), (-0.053388, -0.180733, -0.982082), (0.006792, -0.983528, 0.18063)
Vector: 33.0958, 20.3459, 15.6767)

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Components

#1: Protein PROLYL-TRNA SYNTHETASE


Mass: 64341.555 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ENTEROCOCCUS FAECALIS (bacteria) / Plasmid: PQE-60 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): M15 / References: UniProt: Q831W7, proline-tRNA ligase
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-PRI / PYRROLIDINE-2-CARBALDEHYDE / PROLINOL


Mass: 99.131 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO
#4: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 363 / 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: 2.4 Å3/Da / Density % sol: 49 %
Crystal growDetails: 20% PEG 6000, 1M LICL, 100MM MES, PH 6.5, 5MM PROLINOL, 2MM ATP, 6MM MGCL2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.0723
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 30, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0723 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 54112 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 6.44
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 1.95 / % possible all: 98.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2J3L

2j3l


Resolution: 2.3→29.49 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.879 / SU B: 7.24 / SU ML: 0.181 / Cross valid method: THROUGHOUT / ESU R: 0.355 / ESU R Free: 0.255 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.26 1894 3.5 %RANDOM
Rwork0.196 ---
obs0.198 52213 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.84 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20.47 Å2
2---0.26 Å20 Å2
3---0.55 Å2
Refinement stepCycle: LAST / Resolution: 2.3→29.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8791 0 82 363 9236
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0229028
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6941.98612193
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.07351109
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.85324.465439
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.968151626
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8491568
X-RAY DIFFRACTIONr_chiral_restr0.1050.21347
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026803
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2320.25602
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3160.26238
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.2820
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2410.2101
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3410.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8281.55639
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.35928895
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.3333757
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.6794.53298
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.31 138
Rwork0.258 3822

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