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- PDB-5yn4: Crystal structure of dimeric peptidyl tRNA hydrolase from Acineto... -

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Basic information

Entry
Database: PDB / ID: 5yn4
TitleCrystal structure of dimeric peptidyl tRNA hydrolase from Acinetobacter baumannii with occluded substrate binding site at 1.47 A resolution
ComponentsPeptidyl-tRNA hydrolase
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: 1.47 Å
AuthorsSingh, P.K. / Sharma, P. / Kaur, P. / Sharma, S. / Singh, T.P.
CitationJournal: To Be Published
Title: Crystal structure of dimeric peptidyl tRNA hydrolase from Acinetobacter baumannii with occluded substrate binding site at 1.47 A resolution
Authors: Singh, P.K. / Sharma, P. / Kaur, P. / Sharma, S. / Singh, T.P.
History
DepositionOct 24, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
Water9,098505
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint1 kcal/mol
Surface area16430 Å2
Unit cell
Length a, b, c (Å)34.556, 98.080, 123.812
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 1 - 193 / Label seq-ID: 1 - 193

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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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, F911_03144, 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.: 505 / 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: 2.42 Å3/Da / Density % sol: 49.12 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 50mm HEPES, pH 7.5, PEG 1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 5, 2017 / Details: mirror
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 1.47→45.59 Å / Num. obs: 55852 / % possible obs: 98.4 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.136 / Net I/σ(I): 9.1
Reflection shellResolution: 1.47→1.49 Å / Rmerge(I) obs: 0.605 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1978 / % possible all: 92.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5Y98

5y98


Resolution: 1.47→45.59 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.852 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.08 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20069 2101 3.6 %RANDOM
Rwork0.17019 ---
obs0.17128 55852 79.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 19.701 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å2-0 Å2-0 Å2
2--0.03 Å2-0 Å2
3---0.32 Å2
Refinement stepCycle: 1 / Resolution: 1.47→45.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2952 0 0 505 3457
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0193031
X-RAY DIFFRACTIONr_bond_other_d0.0020.022804
X-RAY DIFFRACTIONr_angle_refined_deg1.8921.9534096
X-RAY DIFFRACTIONr_angle_other_deg1.20936528
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.775384
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.12624.058138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.09915508
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1171518
X-RAY DIFFRACTIONr_chiral_restr0.1230.2432
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213426
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02588
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_it2.0341.5951543
X-RAY DIFFRACTIONr_mcbond_other2.0321.5921542
X-RAY DIFFRACTIONr_mcangle_it2.9512.3731926
X-RAY DIFFRACTIONr_mcangle_other2.9532.3751927
X-RAY DIFFRACTIONr_scbond_it3.5192.0251488
X-RAY DIFFRACTIONr_scbond_other3.5182.0251488
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.3232.8472170
X-RAY DIFFRACTIONr_long_range_B_refined10.99522.2693552
X-RAY DIFFRACTIONr_long_range_B_other9.00820.7293384
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 12278 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.469→1.508 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.425 56 -
Rwork0.43 1477 -
obs--28.64 %

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