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- PDB-6jkx: Crystal structure of peptidyl-tRNA hydrolase with multiple sodium... -

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Basic information

Entry
Database: PDB / ID: 6jkx
TitleCrystal structure of peptidyl-tRNA hydrolase with multiple sodium and chloride ions at 1.08 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 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
METHANOL / Peptidyl-tRNA hydrolase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.08 Å
AuthorsViswanathan, V. / Sharma, P. / Bhushan, A. / Sharma, S. / Singh, T.P.
CitationJournal: To Be Published
Title: Crystal structure of peptidyl-tRNA hydrolase with multiple sodium and chloride ions at 1.08 A resolution.
Authors: Viswanathan, V. / Sharma, P. / Bhushan, A. / Sharma, S. / Singh, T.P.
History
DepositionMar 3, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 13, 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 / 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_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_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)21,97627
Polymers21,2501
Non-polymers72626
Water4,071226
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint-25 kcal/mol
Surface area8920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.151, 66.264, 76.299
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 BL21 (bacteria) / References: UniProt: D0C9L6, peptidyl-tRNA hydrolase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-MOH / METHANOL


Mass: 32.042 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: CH4O
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / 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: 2.03 Å3/Da / Density % sol: 39.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 12% PEG 1500, 0.1M HEPES PH 7.5

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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: 1.08→50.03 Å / Num. obs: 71837 / % possible obs: 98.59 % / Redundancy: 7.9 % / CC1/2: 0.99 / Rmerge(I) obs: 0.169 / Rpim(I) all: 0.057 / Rrim(I) all: 0.178 / Net I/σ(I): 6.9
Reflection shellResolution: 1.08→1.16 Å / Rmerge(I) obs: 1.497 / Num. unique obs: 2990 / CC1/2: 0.565 / Rpim(I) all: 0.517 / Rrim(I) all: 1.588 / % possible all: 67.3

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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: 1.08→50.03 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.974 / SU B: 1.298 / SU ML: 0.026 / Cross valid method: THROUGHOUT / ESU R: 0.028 / ESU R Free: 0.031 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.17762 2198 3 %RANDOM
Rwork0.14192 ---
obs0.143 71837 98.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 16.944 Å2
Baniso -1Baniso -2Baniso -3
1--0.52 Å2-0 Å2-0 Å2
2--0.07 Å2-0 Å2
3---0.44 Å2
Refinement stepCycle: 1 / Resolution: 1.08→50.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1496 0 36 226 1758
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0121567
X-RAY DIFFRACTIONr_bond_other_d0.0020.0171517
X-RAY DIFFRACTIONr_angle_refined_deg1.8961.6262110
X-RAY DIFFRACTIONr_angle_other_deg0.6481.5743443
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1025203
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.14722.580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.115262
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.246159
X-RAY DIFFRACTIONr_chiral_restr0.1220.2194
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021821
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02362
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_it3.111.323801
X-RAY DIFFRACTIONr_mcbond_other3.0383.626790
X-RAY DIFFRACTIONr_mcangle_it3.5941.972989
X-RAY DIFFRACTIONr_mcangle_other3.60924.068990
X-RAY DIFFRACTIONr_scbond_it4.1371.676766
X-RAY DIFFRACTIONr_scbond_other4.135767
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3232.3551116
X-RAY DIFFRACTIONr_long_range_B_refined4.83518.7071896
X-RAY DIFFRACTIONr_long_range_B_other4.83418.6941896
X-RAY DIFFRACTIONr_rigid_bond_restr7.15131567
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.08→1.108 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 128 -
Rwork0.313 4684 -
obs--87.57 %
Refinement TLS params.Method: refined / Origin x: 7.3229 Å / Origin y: 8.9041 Å / Origin z: 15.5818 Å
111213212223313233
T0.0185 Å2-0.0043 Å2-0.0007 Å2-0.0073 Å20.0002 Å2--0.0051 Å2
L0.1893 °2-0.0876 °20.0664 °2-0.3385 °2-0.0889 °2--0.3508 °2
S0.0096 Å °-0.0215 Å °-0.0055 Å °0.0053 Å °0.0185 Å °0.0349 Å °-0.0018 Å °0.0221 Å °-0.0281 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 193
2X-RAY DIFFRACTION1A201 - 226
3X-RAY DIFFRACTION1A301 - 524

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