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- PDB-5fce: The crystal structure of the ligand binding region of Serine-glut... -

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Basic information

Entry
Database: PDB / ID: 5fce
TitleThe crystal structure of the ligand binding region of Serine-glutamate repeat protein A (SgrA) of Enterococcus faecium
ComponentsLPXTG family cell surface protein Fms2
KeywordsCELL ADHESION / Flattened barrel
Function / homology: / SgrA, immunoglobulin-like / membrane / LPXTG family cell surface protein Fms2
Function and homology information
Biological speciesEnterococcus faecium DO (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.798 Å
AuthorsPonnuraj, K. / Nagarajan, R.
CitationJournal: FEBS J. / Year: 2016
Title: The crystal structure of the ligand-binding region of serine-glutamate repeat containing protein A (SgrA) of Enterococcus faecium reveals a new protein fold: functional characterization and ...Title: The crystal structure of the ligand-binding region of serine-glutamate repeat containing protein A (SgrA) of Enterococcus faecium reveals a new protein fold: functional characterization and insights into its adhesion function.
Authors: Nagarajan, R. / Hendrickx, A.P. / Ponnuraj, K.
History
DepositionDec 15, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 6, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2017Group: Data collection / Derived calculations / Category: pdbx_struct_oper_list / reflns_shell
Item: _pdbx_struct_oper_list.symmetry_operation / _reflns_shell.percent_possible_all
Revision 1.2Dec 6, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LPXTG family cell surface protein Fms2
B: LPXTG family cell surface protein Fms2


Theoretical massNumber of molelcules
Total (without water)26,1632
Polymers26,1632
Non-polymers00
Water4,990277
1
A: LPXTG family cell surface protein Fms2


Theoretical massNumber of molelcules
Total (without water)13,0811
Polymers13,0811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: LPXTG family cell surface protein Fms2


Theoretical massNumber of molelcules
Total (without water)13,0811
Polymers13,0811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.901, 56.722, 59.746
Angle α, β, γ (deg.)90.000, 107.220, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein LPXTG family cell surface protein Fms2 / Cell wall anchored protein SgrA


Mass: 13081.272 Da / Num. of mol.: 2 / Fragment: ligand binding domain (UNP RESIDUES 32-147)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecium DO (bacteria) / Gene: fms2, HMPREF0351_11523 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q3Y373
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 277 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 44.62 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS. Thin needle like.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 40% PEG 2K MME, 100mM imidazole, 25mm Magnesium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.79→40.231 Å / Num. obs: 21433 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 10.43 % / Biso Wilson estimate: 16.64 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.101 / Rrim(I) all: 0.106 / Χ2: 1.196 / Net I/σ(I): 18.92 / Num. measured all: 436641
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.8-1.849.60.8990.7643.8729351304530450.807100
1.84-1.90.9570.5265.4530524308630830.55499.9
1.9-1.950.9740.436.9531170290028970.45199.9
1.95-2.010.9820.3528.3131126289528900.3799.8
2.01-2.080.9860.2929.8829372273727400.307100
2.08-2.150.9910.23611.6128537268626800.24899.8
2.15-2.230.9920.20613.227908263726330.21699.8
2.23-2.320.9920.18214.5925073242724270.191100
2.32-2.420.9940.15315.9323716241124020.16199.6
2.42-2.540.9950.13318.222807227022730.14100
2.54-2.680.9960.11220.7521660215121500.118100
2.68-2.840.9970.09424.9522173207220630.09999.6
2.84-3.040.9980.07728.9321259192319230.081100
3.04-3.280.9990.06434.1519755179717930.06799.8
3.28-3.60.9990.05638.4517669164216340.05899.5
3.6-4.020.9980.0544115194149114830.05799.5
4.02-4.640.9990.04444.0612635130513060.047100
4.64-5.690.9990.04346.5211380110611060.045100
5.69-8.040.9990.04846.28100378628580.05199.5
8.040.9990.03954.952954714680.0499.4

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
XSCALENovember 3, 2014data scaling
PHENIX1.8-1069refinement
PDB_EXTRACT3.15data extraction
XDSNovember 3, 2014data reduction
PHENIX1.8-1069phasing
RefinementMethod to determine structure: SAD / Resolution: 1.798→40.231 Å / FOM work R set: 0.8398 / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 0.87 / Phase error: 23.35 / Stereochemistry target values: MLHL
Details: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.2308 3913 9.35 %
Rwork0.188 37958 -
obs0.192 21433 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 55.85 Å2 / Biso mean: 22.28 Å2 / Biso min: 14.56 Å2
Refinement stepCycle: final / Resolution: 1.798→40.231 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1810 0 0 277 2087
Biso mean---26.88 -
Num. residues----231
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071844
X-RAY DIFFRACTIONf_angle_d1.1192511
X-RAY DIFFRACTIONf_chiral_restr0.076299
X-RAY DIFFRACTIONf_plane_restr0.004312
X-RAY DIFFRACTIONf_dihedral_angle_d13.488667
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7976-1.81950.33331310.26741361X-RAY DIFFRACTION100
1.8195-1.84260.30021460.23821299X-RAY DIFFRACTION100
1.8426-1.86680.29651410.22491427X-RAY DIFFRACTION100
1.8668-1.89240.23271450.2081338X-RAY DIFFRACTION100
1.8924-1.91940.25431340.2091375X-RAY DIFFRACTION100
1.9194-1.94810.2231340.19461319X-RAY DIFFRACTION100
1.9481-1.97850.27291380.17971378X-RAY DIFFRACTION100
1.9785-2.01090.21011340.19561368X-RAY DIFFRACTION100
2.0109-2.04560.2351360.19521328X-RAY DIFFRACTION100
2.0456-2.08280.23271400.19431358X-RAY DIFFRACTION100
2.0828-2.12290.21511460.18581393X-RAY DIFFRACTION100
2.1229-2.16620.22311360.18411335X-RAY DIFFRACTION100
2.1662-2.21330.24371400.2051355X-RAY DIFFRACTION100
2.2133-2.26480.28771400.19621355X-RAY DIFFRACTION100
2.2648-2.32140.30271360.21131350X-RAY DIFFRACTION100
2.3214-2.38420.27971500.20081372X-RAY DIFFRACTION100
2.3842-2.45430.20641280.19471321X-RAY DIFFRACTION100
2.4543-2.53350.23491490.20151361X-RAY DIFFRACTION100
2.5335-2.6240.28781390.19831349X-RAY DIFFRACTION100
2.624-2.72910.24211460.20751382X-RAY DIFFRACTION100
2.7291-2.85330.25391440.20081348X-RAY DIFFRACTION100
2.8533-3.00360.22761410.20671364X-RAY DIFFRACTION100
3.0036-3.19180.26721350.19991337X-RAY DIFFRACTION100
3.1918-3.43810.18911400.16931367X-RAY DIFFRACTION100
3.4381-3.78380.18451410.15741349X-RAY DIFFRACTION99
3.7838-4.33080.21031460.16781358X-RAY DIFFRACTION100
4.3308-5.45420.1851390.14511342X-RAY DIFFRACTION100

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