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- PDB-6jjq: Crystal structure of peptidyl-tRNA hydrolase from Acinetobacter b... -

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Basic information

Entry
Database: PDB / ID: 6jjq
TitleCrystal structure of peptidyl-tRNA hydrolase from Acinetobacter baumannii at 0.99 A resolution.
ComponentsPeptidyl-tRNA hydrolase
KeywordsHYDROLASE
Function / homology
Function and homology information


peptidyl-tRNA hydrolase / peptidyl-tRNA hydrolase activity / protein quality control for misfolded or incompletely synthesized proteins / rescue of stalled cytosolic ribosome / tRNA binding / 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
DI(HYDROXYETHYL)ETHER / Peptidyl-tRNA hydrolase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.99 Å
AuthorsViswanathan, V. / Bairagya, H.R. / Sharma, P. / Sharma, S. / Singh, T.P.
CitationJournal: To Be Published
Title: Crystal structure of peptidyl-tRNA hydrolase from Acinetobacter baumannii at 0.99 A resolution.
Authors: Viswanathan, V. / Bairagya, H.R. / Sharma, P. / Sharma, S. / Singh, T.P.
History
DepositionFeb 26, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 6, 2019Provider: 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peptidyl-tRNA hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5097
Polymers21,2501
Non-polymers2586
Water3,801211
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-12 kcal/mol
Surface area9090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.139, 65.976, 76.011
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: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 211 / 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: 38.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: HEPES, PEG 1500, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298 K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97201 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: 0.97201 Å / Relative weight: 1
ReflectionResolution: 0.99→49.83 Å / Num. obs: 86816 / % possible obs: 92 % / Redundancy: 5.64 % / CC1/2: 0.99 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.025 / Rrim(I) all: 0.063 / Net I/σ(I): 9.8
Reflection shellResolution: 0.99→1.01 Å / Rmerge(I) obs: 2.3 / Mean I/σ(I) obs: 0.4 / Num. unique obs: 5381 / CC1/2: 0.11 / Rpim(I) all: 1.71 / Rrim(I) all: 2.89 / % possible all: 29.3

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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: 0.99→49.83 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.983 / SU B: 0.707 / SU ML: 0.015 / Cross valid method: THROUGHOUT / ESU R: 0.021 / ESU R Free: 0.02 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.13932 1794 2 %RANDOM
Rwork0.12972 ---
obs0.12993 86816 92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 16.252 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å2-0 Å20 Å2
2--0.17 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 0.99→49.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1496 0 12 211 1719
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0121569
X-RAY DIFFRACTIONr_bond_other_d0.0030.0171540
X-RAY DIFFRACTIONr_angle_refined_deg2.0961.6252125
X-RAY DIFFRACTIONr_angle_other_deg0.7161.5733516
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1945205
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.41922.59381
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.37915263
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.581159
X-RAY DIFFRACTIONr_chiral_restr0.1230.2195
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021842
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02379
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_it4.5481.187793
X-RAY DIFFRACTIONr_mcbond_other4.55792
X-RAY DIFFRACTIONr_mcangle_it4.1471.785992
X-RAY DIFFRACTIONr_mcangle_other4.14524.218993
X-RAY DIFFRACTIONr_scbond_it6.2181.706776
X-RAY DIFFRACTIONr_scbond_other6.228777
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.5382.3461129
X-RAY DIFFRACTIONr_long_range_B_refined6.19716.3271774
X-RAY DIFFRACTIONr_long_range_B_other6.19516.3561775
X-RAY DIFFRACTIONr_rigid_bond_restr16.68431569
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 0.99→1.016 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 63 -
Rwork0.316 3525 -
obs--51.08 %
Refinement TLS params.Method: refined / Origin x: 7.2714 Å / Origin y: 8.8122 Å / Origin z: 15.5436 Å
111213212223313233
T0.0015 Å2-0.0006 Å20.0001 Å2-0.0052 Å20.0005 Å2--0.003 Å2
L0.1344 °2-0.0552 °20.1049 °2-0.2726 °2-0.0924 °2--0.3118 °2
S-0.001 Å °-0.0173 Å °-0.0031 Å °0.0012 Å °0.0202 Å °0.0248 Å °-0.004 Å °0.0059 Å °-0.0191 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 193
2X-RAY DIFFRACTION1A201 - 206

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