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- PDB-1yn3: Crystal Structures of EAP Domains from Staphylococcus aureus Reve... -

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Basic information

Entry
Database: PDB / ID: 1yn3
TitleCrystal Structures of EAP Domains from Staphylococcus aureus Reveal an Unexpected Homology to Bacterial Superantigens
Componentstruncated cell surface protein map-w
KeywordsTOXIN / PROTEIN BINDING / Virulence-factor / Extracellular-adherence protein / Staphylococcus
Function / homologyMAP domain / MAP domain / MAP repeat profile. / Ubiquitin-like (UB roll) - #120 / Ubiquitin-like (UB roll) / Roll / Alpha Beta / Protein map
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 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 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: truncated cell surface protein map-w
B: truncated cell surface protein map-w


Theoretical massNumber of molelcules
Total (without water)21,6202
Polymers21,6202
Non-polymers00
Water5,477304
1
A: truncated cell surface protein map-w


Theoretical massNumber of molelcules
Total (without water)10,8101
Polymers10,8101
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: truncated cell surface protein map-w


Theoretical massNumber of molelcules
Total (without water)10,8101
Polymers10,8101
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.116, 64.116, 141.706
Angle α, β, γ (deg.)90, 90, 120
Int Tables number146
Space group name H-MH3

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Components

#1: Protein truncated cell surface protein map-w / EAP2


Mass: 10810.184 Da / Num. of mol.: 2 / Fragment: residues 160-254 / Mutation: V253I
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: Q99QS1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 304 / 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: 2.59 Å3/Da / Density % sol: 52.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: PEG 8000, ammonium sulfate, MES, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.35→30 Å / Num. obs: 40720 / % possible obs: 88.8 % / Biso Wilson estimate: 13.9 Å2
Reflection shellResolution: 1.35→1.45 Å / % possible all: 70.3

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: EapH1, pdb entry 1YN5

1yn5


Resolution: 1.35→29.87 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 546804.14 / 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
Rfree0.23 2031 5 %RANDOM
Rwork0.218 ---
obs0.218 40720 85.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.4792 Å2 / ksol: 0.363177 e/Å3
Displacement parametersBiso mean: 16.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20.55 Å20 Å2
2--0.18 Å20 Å2
3----0.36 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.18 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.1 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.35→29.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1520 0 0 304 1824
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.02
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_deg2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.3
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.291.5
X-RAY DIFFRACTIONc_mcangle_it2.092
X-RAY DIFFRACTIONc_scbond_it2.012
X-RAY DIFFRACTIONc_scangle_it2.922.5
LS refinement shellResolution: 1.35→1.43 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.283 262 5.1 %
Rwork0.277 4897 -
obs--64.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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