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- PDB-1v3y: The crystal structure of peptide deformylase from Thermus thermop... -

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Basic information

Entry
Database: PDB / ID: 1v3y
TitleThe crystal structure of peptide deformylase from Thermus thermophilus HB8
ComponentsPeptide deformylase
KeywordsHYDROLASE / peptide deformylase / protein synthesis / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
Function / homology
Function and homology information


peptide deformylase / peptide deformylase activity / : / translation / metal ion binding
Similarity search - Function
Peptide Deformylase / Peptide deformylase / Peptide deformylase / Peptide deformylase superfamily / Polypeptide deformylase / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsKamo, M. / Kudo, N. / Lee, W.C. / Ito, K. / Motoshim, H. / Tanokura, M. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: to be published
Title: The crystal structure of peptide deformylase from Thermus thermophilus HB8
Authors: Kamo, M. / Kudo, N. / Lee, W.C. / Ito, K. / Motoshim, H. / Tanokura, M.
History
DepositionNov 7, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 28, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptide deformylase
B: Peptide deformylase


Theoretical massNumber of molelcules
Total (without water)44,3432
Polymers44,3432
Non-polymers00
Water5,296294
1
A: Peptide deformylase


Theoretical massNumber of molelcules
Total (without water)22,1711
Polymers22,1711
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Peptide deformylase


Theoretical massNumber of molelcules
Total (without water)22,1711
Polymers22,1711
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.582, 62.582, 105.271
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Peptide deformylase / PDF / Polypeptide deformylase


Mass: 22171.316 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Plasmid: PET11A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLys S / References: UniProt: P43522, peptide deformylase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 294 / 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: 2.43 Å3/Da / Density % sol: 48.88 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20% PEG 4000, 0.1M Tris-HCl, 200MM Sodium Acetate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 23, 2002
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.81→19.96 Å / Num. obs: 36563 / % possible obs: 99.4 % / Biso Wilson estimate: 34.4 Å2

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.81→19.8 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.059 / SU ML: 0.066 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.116 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20849 1830 5 %RANDOM
Rwork0.17086 ---
obs0.17271 34733 99.42 %-
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: 25.589 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.81→19.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2745 0 0 294 3039
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222794
X-RAY DIFFRACTIONr_bond_other_d0.0020.022669
X-RAY DIFFRACTIONr_angle_refined_deg1.6171.9873764
X-RAY DIFFRACTIONr_angle_other_deg0.92336146
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1565333
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1050.2403
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023089
X-RAY DIFFRACTIONr_gen_planes_other0.0150.02623
X-RAY DIFFRACTIONr_nbd_refined0.230.2508
X-RAY DIFFRACTIONr_nbd_other0.2640.23025
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0830.21769
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2171
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1370.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3420.264
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2170.222
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.0671.51673
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.91622688
X-RAY DIFFRACTIONr_scbond_it3.22431121
X-RAY DIFFRACTIONr_scangle_it5.5214.51076
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.811→1.858 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.242 129
Rwork0.179 2487

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