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- PDB-3fym: The 1A structure of YmfM, a putative DNA-binding membrane protein... -

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Basic information

Entry
Database: PDB / ID: 3fym
TitleThe 1A structure of YmfM, a putative DNA-binding membrane protein from Staphylococcus aureus
ComponentsPutative uncharacterized protein
KeywordsDNA BINDING PROTEIN / HTH DNA binding
Function / homology
Function and homology information


membrane => GO:0016020 / DNA binding / metal ion binding
Similarity search - Function
Helix-turn-helix domain / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / lambda repressor-like DNA-binding domains / Cro/C1-type helix-turn-helix domain / 434 Repressor (Amino-terminal Domain) / Lambda repressor-like, DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
HTH cro/C1-type domain-containing protein / HTH cro/C1-type domain-containing protein
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus Mu50 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1 Å
AuthorsXu, L. / Sedelnikova, S.E. / Baker, P.J. / Rice, D.W.
CitationJournal: To be Published
Title: The 1A structure of YmfM, a putative DNA-binding membrane protein from Staphylococcus aureus
Authors: Xu, L. / Sedelnikova, S.E. / Baker, P.J. / Rice, D.W.
History
DepositionJan 22, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1962
Polymers15,1311
Non-polymers651
Water2,612145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.456, 45.456, 72.903
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-3041-

HOH

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Components

#1: Protein Putative uncharacterized protein / hypothetical protein YmfM


Mass: 15130.502 Da / Num. of mol.: 1 / Fragment: N-terminal soluble domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus Mu50 (bacteria)
Plasmid: pETBLUE1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q99UJ0, UniProt: A0A0H3JZ73*PLUS
#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 / Water


Mass: 18.015 Da / Num. of mol.: 145 / 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

Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M MES pH6.5, 0.01M Zinc Sulphate, 25% PEG 550MME, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 2.07 Å
DetectorDate: Feb 2, 2006
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.07 Å / Relative weight: 1
ReflectionResolution: 1→20 Å / Num. all: 38933 / Num. obs: 38933 / % possible obs: 92.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 1→20 Å / % possible all: 92.5

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Processing

Software
NameVersionClassificationNB
SHELXrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
MOSFLMdata reduction
SCALAdata scaling
SHELXSphasing
SHELXLrefinement
RefinementResolution: 1→20 Å / Occupancy max: 1 / Occupancy min: 0.24 / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.14 14 5 %RANDOM
Rwork0.11 ---
obs0.11 38933 --
all-38933 --
Displacement parametersBiso max: 55.31 Å2 / Biso mean: 16.077 Å2 / Biso min: 6.99 Å2
Refinement stepCycle: LAST / Resolution: 1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms700 0 1 145 846
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.018
X-RAY DIFFRACTIONs_angle_d0.038

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