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- PDB-2dgj: Crystal structure of EbhA (756-1003 domain) from Staphylococcus aureus -

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Basic information

Entry
Database: PDB / ID: 2dgj
TitleCrystal structure of EbhA (756-1003 domain) from Staphylococcus aureus
Componentshypothetical protein ebhA
KeywordsCELL ADHESION / helix-bundle / rod-like structure / adhesin
Function / homology
Function and homology information


: / membrane => GO:0016020 / plasma membrane
Similarity search - Function
Ebh helix bundles repeating unit (S and A modules) / Domain of unknown function DUF1542 / Domain of Unknown Function (DUF1542) / Protein G-related albumin-binding (GA) module / Extracellular matrix-binding protein ebh, GA module / GA module / GA module / FIVAR domain / Immunoglobulin/albumin-binding domain superfamily / Four Helix Bundle (Hemerythrin (Met), subunit A) ...Ebh helix bundles repeating unit (S and A modules) / Domain of unknown function DUF1542 / Domain of Unknown Function (DUF1542) / Protein G-related albumin-binding (GA) module / Extracellular matrix-binding protein ebh, GA module / GA module / GA module / FIVAR domain / Immunoglobulin/albumin-binding domain superfamily / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETIC ACID / Extracellular matrix-binding protein EbhA
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.35 Å
AuthorsTanaka, Y. / Yao, M. / Kuroda, M. / Watanabe, N. / Ohta, T. / Tanaka, I.
CitationJournal: Structure / Year: 2008
Title: A helical string of alternately connected three-helix bundles for the cell wall-associated adhesion protein Ebh from Staphylococcus aureus
Authors: Tanaka, Y. / Sakamoto, S. / Kuroda, M. / Goda, S. / Gao, Y.-G. / Tsumoto, K. / Hiragi, Y. / Yao, M. / Watanabe, N. / Ohta, T. / Tanaka, I.
History
DepositionMar 14, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 20, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: hypothetical protein ebhA
B: hypothetical protein ebhA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4546
Polymers55,1092
Non-polymers3444
Water5,044280
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: hypothetical protein ebhA
hetero molecules

A: hypothetical protein ebhA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4546
Polymers55,1092
Non-polymers3444
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_554-x+1/2,y+1/2,-z-1/21
Buried area1410 Å2
ΔGint-34 kcal/mol
Surface area26980 Å2
MethodPISA
3
B: hypothetical protein ebhA
hetero molecules

B: hypothetical protein ebhA
hetero molecules

A: hypothetical protein ebhA
hetero molecules

A: hypothetical protein ebhA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,90712
Polymers110,2194
Non-polymers6898
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
crystal symmetry operation5_455x-1/2,y+1/2,z1
crystal symmetry operation7_554-x+1/2,y+1/2,-z-1/21
Buried area6530 Å2
ΔGint-86 kcal/mol
Surface area50260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.265, 161.848, 133.366
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 hypothetical protein ebhA


Mass: 27554.725 Da / Num. of mol.: 2 / Fragment: Residues 2-249
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: Mu50 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q931R6
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / 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: 2.22 Å3/Da / Density % sol: 44.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.1M acetate, 2.3M ammonium sulfate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 0.97904 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Sep 30, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97904 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 20244 / % possible obs: 96.4 % / Observed criterion σ(I): 0.6 / Redundancy: 6.1 % / Biso Wilson estimate: 17.2 Å2 / Rsym value: 0.08
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 4.7 % / Num. unique all: 1839 / Rsym value: 0.131 / % possible all: 89.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
OASISV. 2004phasing
DMphasing
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.35→19.8 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2600153.16 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.287 1975 9.8 %RANDOM
Rwork0.241 ---
obs0.241 20173 96.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 32.572 Å2 / ksol: 0.389521 e/Å3
Displacement parametersBiso mean: 23.1 Å2
Baniso -1Baniso -2Baniso -3
1--3.89 Å20 Å20 Å2
2---11.11 Å20 Å2
3---15 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2.35→19.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3629 0 20 280 3929
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
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d18.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.59
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.291.5
X-RAY DIFFRACTIONc_mcangle_it0.542
X-RAY DIFFRACTIONc_scbond_it0.262
X-RAY DIFFRACTIONc_scangle_it0.442.5
LS refinement shellResolution: 2.35→2.5 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.327 311 10 %
Rwork0.267 2785 -
obs--90.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein_rep.top
X-RAY DIFFRACTION2water_rep.paramwater_rep.top
X-RAY DIFFRACTION3ligand.paramligand.top
X-RAY DIFFRACTION4ion.paramion.top

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