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- PDB-6kl8: Crystal structure of Piptidyl t-RNA hydrolase from Acinetobacter ... -

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Basic information

Entry
Database: PDB / ID: 6kl8
TitleCrystal structure of Piptidyl t-RNA hydrolase from Acinetobacter baumannii with bound NaCl at the substrate binding site
ComponentsPeptidyl-tRNA hydrolaseAlternative ribosome-rescue factor B
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: 1.94 Å
AuthorsViswanathan, V. / Sharma, P. / Singh, P.K. / Sharma, S. / Singh, T.P.
CitationJournal: To Be Published
Title: Crystal structure of Piptidyl t-RNA hydrolase from Acinetobacter baumannii with bound NaCl at the substrate binding site
Authors: Viswanathan, V. / Sharma, P. / Singh, P.K. / Sharma, S. / Singh, T.P.
History
DepositionJul 29, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 7, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3714
Polymers21,2501
Non-polymers1213
Water3,369187
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area310 Å2
ΔGint-25 kcal/mol
Surface area8930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.961, 66.099, 75.825
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 / Alternative ribosome-rescue factor B / 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-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 187 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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 Å3/Da / Density % sol: 38.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 12% PEG 1500, 0.1M HEPES, pH 7.5, 15% Glycerol

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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: 0.9795 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.94→31.01 Å / Num. obs: 12479 / % possible obs: 94.03 % / Redundancy: 2.89 % / CC1/2: 0.996 / Rrim(I) all: 0.043 / Net I/σ(I): 26.18
Reflection shellResolution: 1.94→2.05 Å / Redundancy: 2.72 % / Mean I/σ(I) obs: 21.11 / Num. unique obs: 3616 / CC1/2: 0.996 / Rrim(I) all: 0.049 / % possible all: 91.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6J93

6j93


Resolution: 1.94→31.01 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.269 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.16 / ESU R Free: 0.13
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1638 1261 10.105 %
Rwork0.1268 --
all0.131 --
obs-11218 94.025 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 13.263 Å2
Baniso -1Baniso -2Baniso -3
1--0.037 Å2-0 Å20 Å2
2--0.024 Å2-0 Å2
3---0.013 Å2
Refinement stepCycle: LAST / Resolution: 1.94→31.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1496 0 6 187 1689
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0131537
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171423
X-RAY DIFFRACTIONr_angle_refined_deg1.6611.6332075
X-RAY DIFFRACTIONr_angle_other_deg1.4571.5753311
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6235195
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.0522.30878
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.00915255
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.24159
X-RAY DIFFRACTIONr_chiral_restr0.0850.2190
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021747
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02308
X-RAY DIFFRACTIONr_nbd_refined0.210.2330
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2010.21388
X-RAY DIFFRACTIONr_nbtor_refined0.1610.2750
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.2632
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1930.2116
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.2140.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2130.232
X-RAY DIFFRACTIONr_nbd_other0.2830.273
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1870.228
X-RAY DIFFRACTIONr_mcbond_it1.5131.158783
X-RAY DIFFRACTIONr_mcbond_other1.5021.156782
X-RAY DIFFRACTIONr_mcangle_it2.4371.726977
X-RAY DIFFRACTIONr_mcangle_other2.4381.727978
X-RAY DIFFRACTIONr_scbond_it2.3191.471754
X-RAY DIFFRACTIONr_scbond_other2.3181.473755
X-RAY DIFFRACTIONr_scangle_it3.6782.0681098
X-RAY DIFFRACTIONr_scangle_other3.6762.071099
X-RAY DIFFRACTIONr_lrange_it6.13615.2751750
X-RAY DIFFRACTIONr_lrange_other6.13415.2881751
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.94-1.9870.172990.107828X-RAY DIFFRACTION96.2617
1.987-2.0420.164900.11801X-RAY DIFFRACTION96.533
2.042-2.1010.176790.108803X-RAY DIFFRACTION96.4989
2.101-2.1650.164870.106773X-RAY DIFFRACTION96.0894
2.165-2.2360.171820.112739X-RAY DIFFRACTION95.7993
2.236-2.3140.152850.11709X-RAY DIFFRACTION95.0898
2.314-2.4020.158870.114671X-RAY DIFFRACTION95.1067
2.402-2.4990.159800.114647X-RAY DIFFRACTION94.4156
2.499-2.610.184590.115661X-RAY DIFFRACTION94.9868
2.61-2.7370.139650.122592X-RAY DIFFRACTION92.7966
2.737-2.8850.164630.128589X-RAY DIFFRACTION93.813
2.885-3.0590.193730.129529X-RAY DIFFRACTION93.1889
3.059-3.270.187660.14492X-RAY DIFFRACTION92.2314
3.27-3.530.154500.128493X-RAY DIFFRACTION92.9795
3.53-3.8650.171430.125440X-RAY DIFFRACTION91.1321
3.865-4.3180.1510.121399X-RAY DIFFRACTION91.6497
4.318-4.980.178360.137351X-RAY DIFFRACTION89.7912
4.98-6.0840.229240.168314X-RAY DIFFRACTION90.3743
6.084-8.5410.207280.205245X-RAY DIFFRACTION88.6364
8.54-31.010.11140.261142X-RAY DIFFRACTION83.4225

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