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- PDB-6jgu: Crystal structure at atomic resolution reveals the catalytic mech... -

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Basic information

Entry
Database: PDB / ID: 6jgu
TitleCrystal structure at atomic resolution reveals the catalytic mechanism in peptidyl-tRNA hydrolase from Acinetobacter baumannii.
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: 1.02 Å
AuthorsViswanathan, V. / Sharma, P. / Sharma, S. / Singh, T.P.
CitationJournal: To Be Published
Title: Crystal structure at atomic resolution reveals the catalytic mechanism in peptidyl-tRNA hydrolase from Acinetobacter baumannii.
Authors: Viswanathan, V. / Sharma, P. / Sharma, S. / Singh, T.P.
History
DepositionFeb 14, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 6, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peptidyl-tRNA hydrolase


Theoretical massNumber of molelcules
Total (without water)21,2501
Polymers21,2501
Non-polymers00
Water4,197233
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.964, 66.194, 75.983
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: 21250.232 Da / Num. of mol.: 1
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, HMPREF0010_01329 / Production host: Escherichia coli (E. coli) / References: UniProt: D0C9L6, peptidyl-tRNA hydrolase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / 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: 2.01 Å3/Da / Density % sol: 38.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 12% PEG 1500, 0.1M HEPES (4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid), pH 7.5, 20% Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97199 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97199 Å / Relative weight: 1
ReflectionResolution: 1.02→49.92 Å / Num. obs: 73420 / % possible obs: 88.37 % / Redundancy: 8.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.039 / Net I/σ(I): 8.45
Reflection shellResolution: 1.022→1.049 Å / Rmerge(I) obs: 2.236 / Mean I/σ(I) obs: 0.756 / Num. unique obs: 6369 / CC1/2: 0.243 / Rpim(I) all: 0.983

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5Y9A

5y9a


Resolution: 1.02→49.91 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.978 / SU B: 0.953 / SU ML: 0.02 / Cross valid method: THROUGHOUT / ESU R: 0.026 / ESU R Free: 0.026 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.15726 3778 4.9 %RANDOM
Rwork0.13671 ---
obs0.13772 73420 88.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 13.758 Å2
Baniso -1Baniso -2Baniso -3
1--0.79 Å2-0 Å20 Å2
2--0.58 Å2-0 Å2
3---0.21 Å2
Refinement stepCycle: 1 / Resolution: 1.02→49.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1496 0 0 233 1729
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0121563
X-RAY DIFFRACTIONr_bond_other_d0.0070.0171538
X-RAY DIFFRACTIONr_angle_refined_deg1.8971.6262120
X-RAY DIFFRACTIONr_angle_other_deg0.7451.5753511
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0995205
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.55722.59381
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.79115263
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.316159
X-RAY DIFFRACTIONr_chiral_restr0.1150.2195
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021842
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02385
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_it1.8660.958793
X-RAY DIFFRACTIONr_mcbond_other1.868792
X-RAY DIFFRACTIONr_mcangle_it2.1581.446992
X-RAY DIFFRACTIONr_mcangle_other2.15916.955993
X-RAY DIFFRACTIONr_scbond_it8.1991.357770
X-RAY DIFFRACTIONr_scbond_other8.2770
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.4751.8581123
X-RAY DIFFRACTIONr_long_range_B_refined6.30814.2151792
X-RAY DIFFRACTIONr_long_range_B_other6.20713.3361735
X-RAY DIFFRACTIONr_rigid_bond_restr11.25831563
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.022→1.049 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 31 -
Rwork0.33 619 -
obs--10.21 %
Refinement TLS params.Method: refined / Origin x: 7.276 Å / Origin y: 8.874 Å / Origin z: 15.474 Å
111213212223313233
T0.0058 Å2-0.001 Å20.0001 Å2-0.0047 Å20.0001 Å2--0.004 Å2
L0.2967 °2-0.0827 °20.1184 °2-0.5146 °2-0.1039 °2--0.4509 °2
S0.006 Å °-0.0256 Å °-0.0038 Å °0.0127 Å °0.0226 Å °0.0364 Å °0.0003 Å °0.0147 Å °-0.0287 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 193
2X-RAY DIFFRACTION1A202 - 433

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