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- PDB-6a31: Crystal structure of Na+ bound Peptidyl-tRNA Hydrolase from Acine... -

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Basic information

Entry
Database: PDB / ID: 6a31
TitleCrystal structure of Na+ bound Peptidyl-tRNA Hydrolase from Acinetobacter baumannii at 2.19 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
Peptidyl-tRNA hydrolase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsBairagya, H.R. / Sharma, P. / Singh, P.K. / Sharma, S. / Singh, T.P.
CitationJournal: To Be Published
Title: Crystal structure of Na+ bound Peptidyl-tRNA Hydrolase from Acinetobacter baumannii at 2.19 A resolution
Authors: Bairagya, H.R. / Sharma, P. / Singh, P.K. / Sharma, S. / Singh, T.P.
History
DepositionJun 14, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 27, 2018Provider: 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_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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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)21,0143
Polymers20,9681
Non-polymers462
Water3,549197
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area260 Å2
ΔGint-18 kcal/mol
Surface area8810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.290, 58.750, 109.210
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221

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Components

#1: Protein Peptidyl-tRNA hydrolase / PTH


Mass: 20967.957 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, BIT33_16330, HMPREF0010_01329 / Plasmid: pET28a / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: D0C9L6, peptidyl-tRNA hydrolase
#2: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 197 / 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: 2.62 Å3/Da / Density % sol: 53.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 100 mM NaHEPES pH 7.5 25% PEG 1500

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9537 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.19→54.6 Å / Num. obs: 11810 / % possible obs: 98.7 % / Redundancy: 9.1 % / Biso Wilson estimate: 37.5 Å2 / Rmerge(I) obs: 0.165 / Rpim(I) all: 0.058 / Rrim(I) all: 0.176 / Net I/σ(I): 8.7
Reflection shellResolution: 2.19→2.23 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 11810 / Rpim(I) all: 0.301 / Rrim(I) all: 0.935 / % possible all: 97

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JY7

4jy7


Resolution: 2.19→54.6 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.925 / SU B: 6.242 / SU ML: 0.156 / Cross valid method: THROUGHOUT / ESU R: 0.242 / ESU R Free: 0.204 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23406 567 4.9 %RANDOM
Rwork0.17408 ---
obs0.17708 11810 98.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 37.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å2-0 Å2-0 Å2
2--0.03 Å2-0 Å2
3---0.09 Å2
Refinement stepCycle: 1 / Resolution: 2.19→54.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1476 0 2 197 1675
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0191511
X-RAY DIFFRACTIONr_bond_other_d0.0020.021400
X-RAY DIFFRACTIONr_angle_refined_deg1.7321.9532042
X-RAY DIFFRACTIONr_angle_other_deg1.05633257
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5645192
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.6423.97168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.51315252
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.508159
X-RAY DIFFRACTIONr_chiral_restr0.1030.2216
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211707
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02294
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_it2.9593.587771
X-RAY DIFFRACTIONr_mcbond_other2.9483.58770
X-RAY DIFFRACTIONr_mcangle_it4.2925.359962
X-RAY DIFFRACTIONr_mcangle_other4.2955.367963
X-RAY DIFFRACTIONr_scbond_it3.8314.046740
X-RAY DIFFRACTIONr_scbond_other3.8314.045740
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.9025.8641080
X-RAY DIFFRACTIONr_long_range_B_refined9.26645.7921754
X-RAY DIFFRACTIONr_long_range_B_other8.87244.7441697
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.199→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 43 -
Rwork0.267 796 -
obs--97.67 %

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