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- PDB-3ofv: Crystal structure of peptidyl-tRNA hydrolase from Escherichia Col... -

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Basic information

Entry
Database: PDB / ID: 3ofv
TitleCrystal structure of peptidyl-tRNA hydrolase from Escherichia Coli, I222 crystal form
ComponentsPeptidyl-tRNA hydrolase
KeywordsHYDROLASE / PEPTIDYL-TRNA
Function / homology
Function and homology information


peptidyl-tRNA hydrolase / peptidyl-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 speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.2 Å
AuthorsLam, R. / McGrath, T.E. / Romanov, V. / Gothe, S.A. / Peddi, S.R. / Razumova, E. / Lipman, R.S. / Branstrom, A.A. / Chirgadze, N.Y.
CitationJournal: To be Published
Title: Crystal structure of peptidyl-tRNA hydrolase from Escherichia Coli, I222 crystal form
Authors: Lam, R. / McGrath, T.E. / Romanov, V. / Gothe, S.A. / Peddi, S.R. / Razumova, E. / Lipman, R.S. / Branstrom, A.A. / Chirgadze, N.Y.
History
DepositionAug 16, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software
Revision 1.2Sep 6, 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 / struct_ref_seq_dif
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 / _struct_ref_seq_dif.details

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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
C: Peptidyl-tRNA hydrolase


Theoretical massNumber of molelcules
Total (without water)68,7733
Polymers68,7733
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4890 Å2
ΔGint-16 kcal/mol
Surface area24590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.380, 96.960, 207.678
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 3 / Auth seq-ID: 1 - 170 / Label seq-ID: 22 - 191

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC

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Components

#1: Protein Peptidyl-tRNA hydrolase / PTH


Mass: 22924.225 Da / Num. of mol.: 3 / Mutation: M1V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: B354 / Gene: ECEG_00530, ECs1709, pth / Plasmid: PET15B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) CODONPLUS RIPL / References: UniProt: D6J9H8, peptidyl-tRNA hydrolase

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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: 2.72 Å3/Da / Density % sol: 54.82 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20% PEG3350, 0.2M K/NA TARTRATE, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 26, 2007 / Details: VARIMAX HR
RadiationMonochromator: VARIMAX HR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 12759 / % possible obs: 99.9 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.211 / Net I/σ(I): 4.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
3.2-3.317.30.5591100
3.31-3.457.30.4411100
3.45-3.67.30.371100
3.6-3.797.30.3081100
3.79-4.037.20.2471100
4.03-4.347.30.1651100
4.34-4.787.30.1421100
4.78-5.477.30.1531100
5.47-6.897.20.1551100
6.89-506.60.059198.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 46.55 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.5 Å29.86 Å
Translation3.5 Å29.86 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMACrefmac_5.6.0081refinement
PDB_EXTRACT3.1data extraction
StructureStudiodata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2PTH

2pth


Resolution: 3.2→48.48 Å / Cor.coef. Fo:Fc: 0.877 / Cor.coef. Fo:Fc free: 0.779 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 59.476 / SU ML: 0.436 / Cross valid method: THROUGHOUT / ESU R Free: 0.551 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.28298 625 4.9 %RANDOM
Rwork0.22644 ---
obs0.22927 12131 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 32.495 Å2
Baniso -1Baniso -2Baniso -3
1-1.27 Å20 Å20 Å2
2--1.67 Å20 Å2
3----2.93 Å2
Refinement stepCycle: LAST / Resolution: 3.2→48.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4330 0 0 0 4330
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0194433
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4771.9335990
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0835578
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.05623.474190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.5461529
X-RAY DIFFRACTIONr_chiral_restr0.0820.2673
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023304
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A680TIGHT POSITIONAL0.060.05
2B680TIGHT POSITIONAL0.060.05
3C680TIGHT POSITIONAL0.050.05
1A549LOOSE POSITIONAL0.085
2B549LOOSE POSITIONAL0.075
3C549LOOSE POSITIONAL0.085
1A680TIGHT THERMAL8.260.5
2B680TIGHT THERMAL5.260.5
3C680TIGHT THERMAL11.660.5
1A549LOOSE THERMAL8.1710
2B549LOOSE THERMAL6.8510
3C549LOOSE THERMAL11.7410
LS refinement shellResolution: 3.201→3.284 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 42 -
Rwork0.276 866 -
obs--99.67 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.6684-0.2615-0.21232.2505-0.68242.8293-0.00570.16890.0838-0.02330.04150.0415-0.0152-0.0901-0.03580.01210.0137-0.02540.11580.01120.0711-4.559-27.52454.881
22.1826-0.07860.63170.5256-0.50163.5568-0.0547-0.09690.03390.17790.12880.12-0.1336-0.5075-0.07410.2568-0.00970.03660.164-0.00560.1161-12.318-32.67487.8
30.32650.242-0.5591.5852-2.69511.6710.1999-0.1047-0.01030.7891-0.3506-0.1566-2.0851.01830.15060.6401-0.2915-0.09040.20030.01810.174413.236-16.06579.575
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 190
2X-RAY DIFFRACTION2B-10 - 190
3X-RAY DIFFRACTION3C1 - 190

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