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- PDB-6ori: Enterococcal surface protein, partial N-terminal region -

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Basic information

Entry
Database: PDB / ID: 6ori
TitleEnterococcal surface protein, partial N-terminal region
ComponentsEF0056
KeywordsUNKNOWN FUNCTION / Immunoglobin / biofilm / Enterococcus
Function / homology
Function and homology information


Bacterial Ig domain / Bacterial Ig domain / Long Rib domain / Long Rib domain / Rib/alpha/Esp surface antigen / Rib domain / YSIRK type signal peptide / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. ...Bacterial Ig domain / Bacterial Ig domain / Long Rib domain / Long Rib domain / Rib/alpha/Esp surface antigen / Rib domain / YSIRK type signal peptide / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Immunoglobulin-like fold
Similarity search - Domain/homology
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsSpiegelman, L. / Zhang, L. / Tezcan, A. / Ghosh, P.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)DMR-1602537 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)5T32GM007240 United States
CitationJournal: To Be Published
Title: Enterococcal surface protein, partial N-terminal region (CASP target)
Authors: Spiegelman, L. / Zhang, L. / Tezcan, A. / Ghosh, P.
History
DepositionApr 30, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: EF0056
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4192
Polymers46,3791
Non-polymers401
Water7,800433
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.85, 49.96, 51.2399
Angle α, β, γ (deg.)107.36, 111.42, 90.43
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein EF0056 / Surface protein


Mass: 46379.219 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Gene: ef0056, esp
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9Z4N7
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 433 / 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: 2.08 Å3/Da / Density % sol: 37.26 % / Description: large, triangular crystals
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Crystallization condition: protein: 7.5 mg/mL in 10 mM Tris and 10 mM NaCl Mother liquid: 0.2 M ammonium acetate, pH 7.0, 16% PEG3350, 1 uL mother liquid + 1 uL protein The crystal was ...Details: Crystallization condition: protein: 7.5 mg/mL in 10 mM Tris and 10 mM NaCl Mother liquid: 0.2 M ammonium acetate, pH 7.0, 16% PEG3350, 1 uL mother liquid + 1 uL protein The crystal was soaked in 8.625%(w/v) sodium acrylate, 2.5%(w/v) acrylamide and 0.2%(w/v) bis-acrylamide in mother liquid (0.2 M ammonium acetate, pH 7.0, 16% PEG 3350). after soaking for over 48 hours, the crystal was transferred to 1% APS and 1% TEMED in mother liquid (0.2 M ammonium acetate, pH 7.0, 16% PEG 3350). after 10 min, calcium chloride was added to the crystal with a final concentration of 100 mM.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9801 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 1.4→47.27 Å / Num. obs: 58580 / % possible obs: 85.4095 % / Redundancy: 3.17 % / Biso Wilson estimate: 8.90025571117 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 15.1
Reflection shellResolution: 1.4→1.42 Å / Num. unique obs: 410 / % possible all: 78.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
ELVES1.9_1692data processing
MOSFLM1.9_1692data reduction
Aimlessdata scaling
PHENIXmodel building
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Crystals with selenomethionine previously determined by our lab but unpublished

Resolution: 1.4→47.27 Å / SU ML: 0.122 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 16.37
RfactorNum. reflection% reflection
Rfree0.1738 2932 5 %
Rwork0.152 55645 -
obs0.1531 58577 85.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 13.1 Å2
Refinement stepCycle: LAST / Resolution: 1.4→47.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3025 0 1 433 3459
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00928611633313256
X-RAY DIFFRACTIONf_angle_d1.240427779974434
X-RAY DIFFRACTIONf_chiral_restr0.0763462994011473
X-RAY DIFFRACTIONf_plane_restr0.0056447185071597
X-RAY DIFFRACTIONf_dihedral_angle_d13.84614482091210
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.4230.218567863551510.1633129907212845X-RAY DIFFRACTION89.8620275945
1.423-1.44750.1956966476711330.1632539011282632X-RAY DIFFRACTION93.2231962239
1.4475-1.47380.1927771343851210.153782847412120X-RAY DIFFRACTION92.2601893783
1.4738-1.50220.1754549374711100.1573198427821932X-RAY DIFFRACTION63.258983891
1.5022-1.53280.1626218332071110.15177199022159X-RAY DIFFRACTION92.8045789043
1.5328-1.56620.1990979130181560.1496334070062801X-RAY DIFFRACTION94.624
1.5662-1.60260.1917748587021530.1510175964562928X-RAY DIFFRACTION93.3353529234
1.6026-1.64270.1938925333041530.1519245258942887X-RAY DIFFRACTION93.972179289
1.6427-1.68710.1962371950731310.1468922132532962X-RAY DIFFRACTION94.3275388838
1.6871-1.73670.1839650425171500.1463752317652917X-RAY DIFFRACTION93.8781756964
1.7367-1.79280.1791249911951630.1502365033432905X-RAY DIFFRACTION94.6621413144
1.7928-1.85690.171234560121730.1515170401432926X-RAY DIFFRACTION94.8867115738
1.8569-1.93120.1934097017721030.1641766355141761X-RAY DIFFRACTION70.847586469
1.9312-2.01910.1962257662931110.1532465607052298X-RAY DIFFRACTION77.3354735152
2.0191-2.12560.1564730938681400.1510212704832492X-RAY DIFFRACTION80.170575693
2.1256-2.25870.1580337920391350.1566918451992752X-RAY DIFFRACTION95.7863304579
2.2587-2.43310.201569957731270.1557054714962776X-RAY DIFFRACTION96.7666666667
2.4331-2.6780.2059717446081700.1608498971682909X-RAY DIFFRACTION97.0375039395
2.678-3.06540.1655164506411600.1615042630292905X-RAY DIFFRACTION97.3324865037
3.0654-3.86180.1506401362071440.1401796181052748X-RAY DIFFRACTION89.5356037152
3.8618-47.29980.1418483753431370.1444556937582990X-RAY DIFFRACTION95.2772699573

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