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- PDB-1lrz: x-ray crystal structure of staphylococcus aureus femA -

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Basic information

Entry
Database: PDB / ID: 1lrz
Titlex-ray crystal structure of staphylococcus aureus femA
Componentsfactor essential for expression of methicillin resistance
KeywordsANTIBIOTIC INHIBITOR / Peptidoglycan / Staphylococcus aureus / multiple anomalous dispersion
Function / homology
Function and homology information


N-acetylmuramoyl-L-alanyl-D-glutamyl-L-lysyl-(N6-glycyl)-D-alanyl-D-alanine-diphosphoundecaprenyl-N-acetylglucosamine:glycine glycyltransferase / aminoacyltransferase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / nucleotide binding / cytoplasm
Similarity search - Function
FemABX peptidyl transferase / FemAB family / FemABX peptidyl transferase family profile. / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #90 / Class I and II aminoacyl-tRNA synthetase, tRNA-binding arm / Gcn5-related N-acetyltransferase (GNAT) / Acyl-CoA N-acyltransferase / Aminopeptidase / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle ...FemABX peptidyl transferase / FemAB family / FemABX peptidyl transferase family profile. / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #90 / Class I and II aminoacyl-tRNA synthetase, tRNA-binding arm / Gcn5-related N-acetyltransferase (GNAT) / Acyl-CoA N-acyltransferase / Aminopeptidase / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Aminoacyltransferase FemA
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsBenson, T. / Prince, D. / Mutchler, V. / Curry, K. / Ho, A. / Sarver, R. / Hagadorn, J. / Choi, G. / Garlick, R.
CitationJournal: Structure / Year: 2002
Title: X-ray crystal structure of Staphylococcus aureus FemA.
Authors: Benson, T.E. / Prince, D.B. / Mutchler, V.T. / Curry, K.A. / Ho, A.M. / Sarver, R.W. / Hagadorn, J.C. / Choi, G.H. / Garlick, R.L.
History
DepositionMay 16, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: factor essential for expression of methicillin resistance


Theoretical massNumber of molelcules
Total (without water)50,0261
Polymers50,0261
Non-polymers00
Water5,729318
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.930, 90.360, 109.350
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein factor essential for expression of methicillin resistance / fema


Mass: 50026.441 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: FemA / Production host: Escherichia coli (E. coli) / References: UniProt: P0A0A5
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 318 / 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: 2.66 Å3/Da / Density % sol: 53.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 8000, calcium acetate, imidazole, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 10 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
150 mMethanolamine12
21 mMdithiothreitol12pH10.0
312 mg/mlprotein11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.96863, 0.97949, 0.97923
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 29, 2000
RadiationMonochromator: Si(111) double-crystal system / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.968631
20.979491
30.979231
ReflectionResolution: 2.1→50 Å / Num. all: 31869 / Num. obs: 31500 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 15.1 Å2 / Rsym value: 0.06 / Net I/σ(I): 22.3
Reflection shellResolution: 2.1→2.17 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 3 / Rsym value: 0.246 / % possible all: 97.9
Reflection
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 50 Å / Num. obs: 32411 / % possible obs: 99.7 % / Num. measured all: 236796 / Rmerge(I) obs: 0.06
Reflection shell
*PLUS
% possible obs: 97.9 % / Rmerge(I) obs: 0.246

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Processing

Software
NameVersionClassification
MLPHAREphasing
CNX2000.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.1→20 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.212 3160 10 %RANDOM
Rwork0.18 ---
all0.183 31869 --
obs0.183 31500 98.8 %-
Displacement parametersBiso mean: 26.7 Å2
Baniso -1Baniso -2Baniso -3
1--1.944 Å20 Å20 Å2
2--2.938 Å20 Å2
3----0.994 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3313 0 0 318 3631
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d22.1
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_mcbond_it1.891.5
X-RAY DIFFRACTIONc_mcangle_it2.652
X-RAY DIFFRACTIONc_scbond_it3.212
X-RAY DIFFRACTIONc_scangle_it4.452.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.246 523 10.4 %
Rwork0.216 4519 -
obs--96.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor all: 0.183 / Rfactor Rfree: 0.212 / Rfactor Rwork: 0.183
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.35
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.81
LS refinement shell
*PLUS
Rfactor Rfree: 0.246 / Rfactor Rwork: 0.216

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