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- PDB-4ann: Crystal Structure Staphylococcus aureus ESSB cytoplasmic fragment -

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Basic information

Entry
Database: PDB / ID: 4ann
TitleCrystal Structure Staphylococcus aureus ESSB cytoplasmic fragment
ComponentsESSB
KeywordsMEMBRANE PROTEIN / MEMBRANE SECRETION / ESS TYPE VII SECRETION SYSTEM / VIRULENCE
Function / homologyType VII secretion system EssB / Type VII secretion system EssB, C-terminal / WXG100 protein secretion system (Wss), protein YukC / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Orthogonal Bundle / Mainly Alpha / plasma membrane / Type VII secretion system protein EssB
Function and homology information
Biological speciesSTAPHYLOCOCCUS AUREUS SUBSP. AUREUS NCTC 8325 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.05 Å
AuthorsZoltner, M. / Fyfe, P.K. / Palmer, T. / Hunter, W.N.
CitationJournal: Biochem.J. / Year: 2013
Title: Characterization of Staphylococcus Aureus Essb, an Integral Membrane Component of the Type Vii Secretion System: Atomic Resolution Crystal Structure of the Cytoplasmic Segment.
Authors: Zoltner, M. / Fyfe, P.K. / Palmer, T. / Hunter, W.N.
History
DepositionMar 21, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 23, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 7, 2012Group: Database references
Revision 1.2Dec 26, 2012Group: Database references / Structure summary
Revision 1.3May 22, 2019Group: Data collection / Other / Refinement description
Category: pdbx_database_proc / pdbx_database_status / refine
Item: _pdbx_database_status.recvd_author_approval / _refine.pdbx_ls_cross_valid_method
Revision 1.4May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ESSB


Theoretical massNumber of molelcules
Total (without water)25,1231
Polymers25,1231
Non-polymers00
Water3,585199
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.704, 58.646, 95.273
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 ESSB


Mass: 25123.406 Da / Num. of mol.: 1 / Fragment: CYTOPLASMIC FRAGMENT, RESIDUES 12-226
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STAPHYLOCOCCUS AUREUS SUBSP. AUREUS NCTC 8325 (bacteria)
Plasmid: MODIFIED PET27 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2G185
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / 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: 2.28 Å3/Da / Density % sol: 46.1 % / Description: NONE
Crystal growpH: 5
Details: 0.18 M AMMONIUM CITRATE PH5.0, 20 % (W/V) PEG3350, 0.25 MM TRIS(2-CARBOXYETHYL)PHOSPHINEHYDROCHLORIDE, 5% GLYCEROL

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9814
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 14, 2009 / Details: MIRRORS
RadiationMonochromator: SILICON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9814 Å / Relative weight: 1
ReflectionResolution: 1.05→58.74 Å / Num. obs: 100245 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 18
Reflection shellResolution: 1.05→1.15 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 3.6 / % possible all: 92.8

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Processing

Software
NameClassification
SHELXL-97refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.05→50 Å / Num. parameters: 17570 / Num. restraintsaints: 25556 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 3.0 PERCENT (FINAL RFREE 0.158)
RfactorNum. reflection% reflectionSelection details
Rfree0.1808 4965 5.2 %RANDOM
all0.1384 95173 --
obs--93.7 %-
Solvent computationSolvent model: MOEWS & KRETSINGER
Refine analyzeNum. disordered residues: 201 / Occupancy sum hydrogen: 1420.97 / Occupancy sum non hydrogen: 1636.02
Refinement stepCycle: LAST / Resolution: 1.05→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1453 0 0 199 1652
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.016
X-RAY DIFFRACTIONs_angle_d0.033
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0275
X-RAY DIFFRACTIONs_zero_chiral_vol0.078
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.085
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.062
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.038
X-RAY DIFFRACTIONs_approx_iso_adps0.098

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