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- PDB-1yn5: Crystal Structures of EAP Domains from Staphylococcus aureus Reve... -

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Basic information

Entry
Database: PDB / ID: 1yn5
TitleCrystal Structures of EAP Domains from Staphylococcus aureus Reveal an Unexpected Homology to Bacterial Superantigens
ComponentsEapH2
KeywordsUNKNOWN FUNCTION / Virulence factor / Toxin / Extracellular Adherence Protein / Staphylococcus aureus
Function / homologyMAP domain / MAP domain / MAP repeat profile. / Ubiquitin-like (UB roll) - #120 / Ubiquitin-like (UB roll) / Roll / Alpha Beta / MAP domain-containing protein / MAP domain-containing protein
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsGeisbrecht, B.V. / Hamaoka, B.Y. / Perman, B. / Zemla, A. / Leahy, D.J.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: The Crystal Structures of EAP Domains from Staphylococcus aureus Reveal an Unexpected Homology to Bacterial Superantigens.
Authors: Geisbrecht, B.V. / Hamaoka, B.Y. / Perman, B. / Zemla, A. / Leahy, D.J.
History
DepositionJan 23, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: EapH2
B: EapH2


Theoretical massNumber of molelcules
Total (without water)23,3312
Polymers23,3312
Non-polymers00
Water1,36976
1
A: EapH2


Theoretical massNumber of molelcules
Total (without water)11,6651
Polymers11,6651
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: EapH2


Theoretical massNumber of molelcules
Total (without water)11,6651
Polymers11,6651
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.01, 31.97, 67.98
Angle α, β, γ (deg.)90, 105.21, 90
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein EapH2


Mass: 11665.274 Da / Num. of mol.: 2 / Fragment: residues 42-144
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: Mu50 / Plasmid: pET28 Derivative / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q99VA9, UniProt: A0A0H3JUK5*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 45.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: PEG 8000, ammonium sulfate, 2,6-hexanediol, cacodylate, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 9383 / % possible obs: 91.6 % / Biso Wilson estimate: 19.8 Å2
Reflection shellResolution: 2.2→2.34 Å / % possible all: 51.3

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: EapH1, pdb entry 1YN4

1yn4


Resolution: 2.2→28.74 Å / Rfactor Rfree error: 0.014 / Data cutoff high absF: 414928.59 / 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
Rfree0.317 500 5.3 %RANDOM
Rwork0.258 ---
obs0.258 9383 86.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.5064 Å2 / ksol: 0.348524 e/Å3
Displacement parametersBiso mean: 31.6 Å2
Baniso -1Baniso -2Baniso -3
1--3.92 Å20 Å2-9.55 Å2
2---8.65 Å20 Å2
3---12.57 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.51 Å0.5 Å
Refinement stepCycle: LAST / Resolution: 2.2→28.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1591 0 0 76 1667
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
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_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.92
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.231.5
X-RAY DIFFRACTIONc_mcangle_it2.022
X-RAY DIFFRACTIONc_scbond_it1.882
X-RAY DIFFRACTIONc_scangle_it2.82.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.059 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.431 53 5.8 %
Rwork0.413 854 -
obs--51 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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