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- PDB-1lme: Crystal Structure of Peptide Deformylase from Thermotoga maritima -

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Basic information

Entry
Database: PDB / ID: 1lme
TitleCrystal Structure of Peptide Deformylase from Thermotoga maritima
Componentspeptide deformylase
KeywordsHYDROLASE / thermophile / PDF / peptide deformylase / metalloenzyme / deformylation / Structural Genomics / PSI / Protein Structure Initiative / Joint Center for Structural Genomics / JCSG
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 speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKreusch, A. / Spraggon, G. / Lee, C.C. / Klock, H. / McMullan, D. / Ng, K. / Shin, T. / Vincent, J. / Warner, I. / Ericson, C. ...Kreusch, A. / Spraggon, G. / Lee, C.C. / Klock, H. / McMullan, D. / Ng, K. / Shin, T. / Vincent, J. / Warner, I. / Ericson, C. / Lesley, S.A. / Joint Center for Structural Genomics (JCSG)
CitationJournal: J.MOL.BIOL. / Year: 2003
Title: Structure analysis of peptide deformylases from streptococcus pneumoniae,staphylococcus aureus, thermotoga maritima, and pseudomonas aeruginosa: snapshots of the oxygen sensitivity of peptide deformylase
Authors: Kreusch, A. / Spraggon, G. / Lee, C.C. / Klock, H. / McMullan, D. / Ng, K. / Shin, T. / Vincent, J. / Warner, I. / Ericson, C. / Lesley, S.A.
History
DepositionMay 1, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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 / 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
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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)41,1282
Polymers41,1282
Non-polymers00
Water1,856103
1
A: peptide deformylase


Theoretical massNumber of molelcules
Total (without water)20,5641
Polymers20,5641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: peptide deformylase


Theoretical massNumber of molelcules
Total (without water)20,5641
Polymers20,5641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.048, 65.048, 151.371
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein peptide deformylase / PDF


Mass: 20563.771 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Plasmid: pMH1 / Production host: Escherichia coli (E. coli) / References: UniProt: P96113, peptide deformylase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.25 Å3/Da / Density % sol: 45.26 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.9
Details: PEG 3350, potassium nitrate, pH 6.9, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 %(w/v)PEG33501reservoir
20.2 Mpotassium nitrate1reservoirpH6.9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 8, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→45.2 Å / Num. obs: 19503 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Biso Wilson estimate: 27.7 Å2 / Rsym value: 0.075 / Net I/σ(I): 10.8
Reflection shellResolution: 2.2→2.34 Å / Num. unique all: 3137 / Rsym value: 0.327 / % possible all: 98.9
Reflection
*PLUS
Lowest resolution: 50 Å / % possible obs: 99.6 % / Rmerge(I) obs: 0.075
Reflection shell
*PLUS
% possible obs: 98.8 % / Rmerge(I) obs: 0.327

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BS4

1bs4


Resolution: 2.2→45.19 Å / Rfactor Rfree error: 0.008 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.249 985 5.1 %RANDOM
Rwork0.198 ---
obs0.198 19503 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 29.2696 Å2 / ksol: 0.379437 e/Å3
Displacement parametersBiso mean: 27.6 Å2
Baniso -1Baniso -2Baniso -3
1-1.74 Å23.99 Å20 Å2
2--1.74 Å20 Å2
3----3.49 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 2.2→45.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2467 0 0 103 2570
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d24.4
X-RAY DIFFRACTIONc_improper_angle_d1.37
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.276 161 5.1 %
Rwork0.21 2986 -
obs--98.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP_NEW.PARAMPROTEIN_NEW.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 50 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.37

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