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- PDB-5yl8: The crystal structure of inactive dimeric peptidyl-tRNA hydrolase... -

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Basic information

Entry
Database: PDB / ID: 5yl8
TitleThe crystal structure of inactive dimeric peptidyl-tRNA hydrolase from Acinetobacter baumannii at 1.79 A resolution
ComponentsPeptidyl-tRNA hydrolase
KeywordsHYDROLASE
Function / homology
Function and homology information


peptidyl-tRNA hydrolase / aminoacyl-tRNA hydrolase activity / translation / cytoplasm
Similarity search - Function
Peptidyl-tRNA hydrolase / Peptidyl-tRNA hydrolase signature 2. / Peptidyl-tRNA hydrolase signature 1. / Peptidyl-tRNA hydrolase / Peptidyl-tRNA hydrolase, conserved site / Peptidyl-tRNA hydrolase superfamily / Peptidyl-tRNA hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Peptidyl-tRNA hydrolase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsBairagya, H.R. / Sharma, P. / Iqbal, N. / Singh, P.K. / Kaur, P. / Sharma, S. / Singh, T.P.
CitationJournal: To Be Published
Title: The crystal structure of inactive dimeric peptidyl-tRNA hydrolase from Acinetobacter baumannii at 1.79 A resolution
Authors: Bairagya, H.R. / Sharma, P. / Iqbal, N. / Kaur, P. / Sharma, S. / Singh, T.P.
History
DepositionOct 17, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 1, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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.ptnr3_auth_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptidyl-tRNA hydrolase
B: Peptidyl-tRNA hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9824
Polymers41,9362
Non-polymers462
Water3,711206
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-15 kcal/mol
Surface area16650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.530, 98.490, 123.090
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Peptidyl-tRNA hydrolase / PTH


Mass: 20967.957 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81) (bacteria)
Strain: ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81
Gene: pth, F911_03144, HMPREF0010_01329 / Production host: Escherichia coli (E. coli) / References: UniProt: D0C9L6, peptidyl-tRNA hydrolase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 2.5 Å3/Da / Density % sol: 50.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 50mM Na HEPES, PEG 1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9724 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 17, 2017 / Details: MIRROR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9724 Å / Relative weight: 1
ReflectionResolution: 1.79→76.9 Å / Num. obs: 37544 / % possible obs: 92 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 13.1
Reflection shellResolution: 1.79→1.818 Å / Rmerge(I) obs: 0.622 / Num. unique obs: 1911 / % possible all: 94.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5Y98

5y98


Resolution: 1.79→76.9 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.983 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.122 / ESU R Free: 0.116 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2084 1805 4.8 %RANDOM
Rwork0.17506 ---
obs0.1767 35530 91.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 28.62 Å2
Baniso -1Baniso -2Baniso -3
1--1.31 Å2-0 Å2-0 Å2
2---0.53 Å20 Å2
3---1.84 Å2
Refinement stepCycle: 1 / Resolution: 1.79→76.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2950 0 2 206 3158
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0193020
X-RAY DIFFRACTIONr_bond_other_d0.0020.022800
X-RAY DIFFRACTIONr_angle_refined_deg2.0871.9524080
X-RAY DIFFRACTIONr_angle_other_deg1.15636514
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5295384
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.92523.971136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.29315504
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5171518
X-RAY DIFFRACTIONr_chiral_restr0.1270.2432
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0213406
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02588
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.9962.5471542
X-RAY DIFFRACTIONr_mcbond_other2.9962.5431541
X-RAY DIFFRACTIONr_mcangle_it4.4073.7941924
X-RAY DIFFRACTIONr_mcangle_other4.4063.7981925
X-RAY DIFFRACTIONr_scbond_it4.3033.0951478
X-RAY DIFFRACTIONr_scbond_other4.3023.0981479
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.6144.412157
X-RAY DIFFRACTIONr_long_range_B_refined8.32750.30912826
X-RAY DIFFRACTIONr_long_range_B_other8.29550.11812699
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.79→1.837 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 139 -
Rwork0.278 2677 -
obs--95.95 %

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