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- PDB-6lso: Crystal structure of a dimeric inhibited of peptidyl tRNA hydrola... -

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Basic information

Entry
Database: PDB / ID: 6lso
TitleCrystal structure of a dimeric inhibited of peptidyl tRNA hydrolase at 1.76A 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
Peptidyl-tRNA hydrolase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsBairagya, H.R. / Ahmad, M.I. / Sharma, P. / Singh, T.P.
CitationJournal: To Be Published
Title: Crystal structure of a dimeric inhibited of peptidyl tRNA hydrolase at 1.76A resolution
Authors: Bairagya, H.R. / Ahmad, M.I. / Sharma, P. / Sharma, S. / Singh, T.P.
History
DepositionJan 17, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 5, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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


Theoretical massNumber of molelcules
Total (without water)41,9362
Polymers41,9362
Non-polymers00
Water8,827490
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint1 kcal/mol
Surface area16500 Å2
Unit cell
Length a, b, c (Å)34.560, 98.330, 123.930
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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, BIT33_16330, 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.: 490 / 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: 2.51 Å3/Da / Density % sol: 51.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 100mM HEPES, 20% PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.97 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.76→45.74 Å / Num. obs: 42085 / % possible obs: 98 % / Redundancy: 6.2 % / CC1/2: 0.991 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.058 / Rrim(I) all: 0.14 / Net I/σ(I): 8.4
Reflection shellResolution: 1.76→1.8 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 3123 / CC1/2: 0.84 / Rpim(I) all: 0.2 / Rrim(I) all: 0.51 / % possible all: 95

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YN4

5yn4


Resolution: 1.76→45.74 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.913 / SU B: 2.567 / SU ML: 0.081 / Cross valid method: FREE R-VALUE / ESU R: 0.119 / ESU R Free: 0.115
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2184 2063 4.902 %
Rwork0.1826 --
all0.184 --
obs-42085 98.002 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 14.094 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å2-0 Å2
2---0.577 Å2-0 Å2
3---0.507 Å2
Refinement stepCycle: LAST / Resolution: 1.76→45.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2952 0 0 490 3442
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0133023
X-RAY DIFFRACTIONr_bond_other_d0.0020.0172800
X-RAY DIFFRACTIONr_angle_refined_deg1.6171.6334086
X-RAY DIFFRACTIONr_angle_other_deg1.4821.5756514
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3595384
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.38222.338154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.92315504
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7461518
X-RAY DIFFRACTIONr_chiral_restr0.0860.2374
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023444
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02606
X-RAY DIFFRACTIONr_nbd_refined0.2170.2636
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1930.22669
X-RAY DIFFRACTIONr_nbtor_refined0.1620.21466
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.21282
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2380.2353
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.2850.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3140.212
X-RAY DIFFRACTIONr_nbd_other0.2630.251
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1870.241
X-RAY DIFFRACTIONr_mcbond_it1.4851.2461543
X-RAY DIFFRACTIONr_mcbond_other1.4861.2451542
X-RAY DIFFRACTIONr_mcangle_it2.431.8561926
X-RAY DIFFRACTIONr_mcangle_other2.431.8581927
X-RAY DIFFRACTIONr_scbond_it2.1791.511480
X-RAY DIFFRACTIONr_scbond_other2.1781.511480
X-RAY DIFFRACTIONr_scangle_it3.4212.1432160
X-RAY DIFFRACTIONr_scangle_other3.4212.1432160
X-RAY DIFFRACTIONr_lrange_it6.26516.9963547
X-RAY DIFFRACTIONr_lrange_other5.94516.5823487
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.76-1.8060.2371380.1992833X-RAY DIFFRACTION95.1329
1.806-1.8550.2391450.1952703X-RAY DIFFRACTION93.5304
1.855-1.9090.251330.2372725X-RAY DIFFRACTION96.229
1.909-1.9680.3091650.2992579X-RAY DIFFRACTION95.6431
1.968-2.0320.2271290.1712608X-RAY DIFFRACTION97.1601
2.032-2.1030.21330.1692519X-RAY DIFFRACTION98.5141
2.103-2.1830.2311140.1832466X-RAY DIFFRACTION98.2857
2.183-2.2720.331110.3182375X-RAY DIFFRACTION99.0438
2.272-2.3730.2321030.1742282X-RAY DIFFRACTION98.8396
2.373-2.4880.2221150.1552213X-RAY DIFFRACTION99.2751
2.488-2.6230.1721130.142083X-RAY DIFFRACTION99.5016
2.623-2.7820.1641030.1341976X-RAY DIFFRACTION99.6167
2.782-2.9740.208990.161893X-RAY DIFFRACTION99.7496
2.974-3.2110.232980.161739X-RAY DIFFRACTION99.8912
3.211-3.5170.182860.1691643X-RAY DIFFRACTION99.9422
3.517-3.9310.197820.1891470X-RAY DIFFRACTION99.8071
3.931-4.5380.164700.1451321X-RAY DIFFRACTION99.9282
4.538-5.5530.174500.141149X-RAY DIFFRACTION100
5.553-7.8320.234510.172895X-RAY DIFFRACTION100
7.832-45.740.205250.169550X-RAY DIFFRACTION98.9673

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