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- PDB-1lmh: Crystal Structure of S. aureus peptide deformylase -

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Basic information

Entry
Database: PDB / ID: 1lmh
TitleCrystal Structure of S. aureus peptide deformylase
ComponentsPROTEIN (S.aureus peptide deformylase)
KeywordsHYDROLASE / zinc peptidase
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
Peptide deformylase / Peptide deformylase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsBaldwin, E.T. / Harris, M.S.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Crystal Structure of Type II peptide deformylase from Staphylococcus aureus
Authors: Baldwin, E.T. / Harris, M.S. / Yem, A.W. / Wolfe, C.L. / Vosters, A.F. / Curry, K.A. / Murray, R.W. / Bock, J.H. / Marshall, V.P. / Cialdella, J.I. / Merchant, M.H. / Choi, G. / Deibel Jr., M.R.
History
DepositionMay 1, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Remark 999 sequence Author has indicated that protein sequence is not yet publically available and that ... sequence Author has indicated that protein sequence is not yet publically available and that residue Arg 127 was mutated to Lys 127

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (S.aureus peptide deformylase)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0462
Polymers20,9811
Non-polymers651
Water7,692427
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.131, 121.873, 47.579
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein PROTEIN (S.aureus peptide deformylase)


Mass: 20981.064 Da / Num. of mol.: 1 / Mutation: R127K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: DEF / Plasmid: pQE60 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109
References: UniProt: Q9F4L4, UniProt: P68826*PLUS, EC: 3.5.1.27
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 427 / 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: 3.585 Å3/Da / Density % sol: 65.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 10% PEG4000; 200mM MgCl2; 100mM Tris HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop / Details: used seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
117-27 %PEG40001reservoir
2200 mM1reservoirMgCl2
3100 mMTris-HCl1reservoirpH8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1.03321, 0.97939, 0.97928
DetectorType: BRUKER / Detector: CCD / Date: Jul 12, 1998 / Details: unfocused
RadiationMonochromator: Si 111 reflection / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.033211
20.979391
30.979281
ReflectionResolution: 1.9→10 Å / % possible obs: 97.52 % / Redundancy: 4.5 % / Biso Wilson estimate: 7.2 Å2 / Rsym value: 0.042 / Net I/σ(I): 7.97
Reflection shellResolution: 1.899→1.968 Å / Rsym value: 0.107
Reflection
*PLUS
Lowest resolution: 10 Å / Num. obs: 21519 / % possible obs: 97.5 % / Rmerge(I) obs: 0.042
Reflection shell
*PLUS
Highest resolution: 1.89 Å / Lowest resolution: 1.96 Å / Rmerge(I) obs: 0.107

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Processing

Software
NameVersionClassification
SAINTdata scaling
SAINTdata reduction
MLPHAREphasing
CNX2000.1refinement
RefinementMethod to determine structure: MAD / Resolution: 1.9→9.99 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1085747.93 / Data cutoff high rms absF: 1085747.93 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.212 2067 9.9 %RANDOM
Rwork0.18 ---
obs-20886 95.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 75.0392 Å2 / ksol: 0.459536 e/Å3
Displacement parametersBiso mean: 18.8 Å2
Baniso -1Baniso -2Baniso -3
1-5.89 Å20 Å20 Å2
2---5.04 Å20 Å2
3----0.85 Å2
Refine analyzeLuzzati coordinate error free: 0.22 Å / Luzzati sigma a free: 0.1 Å
Refinement stepCycle: LAST / Resolution: 1.9→9.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1452 0 1 427 1880
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.71
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.531.5
X-RAY DIFFRACTIONc_mcangle_it0.922
X-RAY DIFFRACTIONc_scbond_it0.722
X-RAY DIFFRACTIONc_scangle_it1.162.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.231 310 10.1 %
Rwork0.192 2764 -
obs--85.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5GLYCEROL.PRMGLYCEROL.TOP
Refinement
*PLUS
Lowest resolution: 10 Å / % reflection Rfree: 9.4 % / Rfactor obs: 0.18 / Rfactor Rwork: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.71
LS refinement shell
*PLUS
Rfactor obs: 0.192

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