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- PDB-4klk: Phage-related protein DUF2815 from Enterococcus faecalis -

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Basic information

Entry
Database: PDB / ID: 4klk
TitlePhage-related protein DUF2815 from Enterococcus faecalis
ComponentsPhage-related protein DUF2815
KeywordsUNKNOWN FUNCTION / structural genomics / phage-related protein / DUF2815 / pfam10991 / PSI-Biology / Midwest Center for Structural Genomics / MCSG
Function / homologyEnterobacter phage Enc34, ssDNA-binding protein / Enterobacter phage Enc34, ssDNA-binding protein / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta / ETHANOL / DUF2815 family protein
Function and homology information
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.93 Å
AuthorsOsipiuk, J. / Wu, R. / Endres, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Phage-related protein DUF2815 from Enterococcus faecalis
Authors: Osipiuk, J. / Wu, R. / Endres, M. / Joachimiak, A.
History
DepositionMay 7, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2016Group: Other
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phage-related protein DUF2815
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2373
Polymers20,0991
Non-polymers1382
Water1,40578
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.527, 68.133, 86.807
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Phage-related protein DUF2815


Mass: 20098.926 Da / Num. of mol.: 1 / Fragment: UNP residues 4-180
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Strain: V583 / Gene: EF_0322 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q838W1
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 2.73 Å3/Da / Density % sol: 54.97 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M Tris buffer, 15% ethanol, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 11, 2012
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.93→36.6 Å / Num. all: 18291 / Num. obs: 18291 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Biso Wilson estimate: 46.8 Å2 / Rmerge(I) obs: 0.096 / Χ2: 4.645 / Net I/σ(I): 12.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.93-1.965.30.6812.027910.8788.5
1.96-25.60.5448340.92690.6
2-2.045.90.58480.95392
2.04-2.085.90.4468571.09495.5
2.08-2.126.10.4149181.26799.5
2.12-2.176.60.3549071.27399.6
2.17-2.236.70.3269051.39199.7
2.23-2.296.80.2759191.6499.5
2.29-2.366.80.2429261.80799.8
2.36-2.436.80.2119122.06799.9
2.43-2.526.80.1789352.46799.9
2.52-2.626.80.1719192.92999.9
2.62-2.746.80.1559443.506100
2.74-2.886.90.1299273.974100
2.88-3.066.80.129265.74199.9
3.06-3.36.50.1049357.193100
3.3-3.636.30.0899488.26899.8
3.63-4.166.30.0799579.6699.6
4.16-5.246.50.07496710.77799.6
5.24-506.30.08101620.93696.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.7.0029refinement
PDB_EXTRACT3.11data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
SHELXDphasing
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.93→36.6 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.939 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 11.226 / SU ML: 0.147 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.141 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2501 936 5.1 %RANDOM
Rwork0.206 ---
all0.208 18248 --
obs0.208 18248 97.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 146.75 Å2 / Biso mean: 59.7512 Å2 / Biso min: 31.45 Å2
Baniso -1Baniso -2Baniso -3
1--2.33 Å20 Å20 Å2
2---4.84 Å20 Å2
3---7.17 Å2
Refinement stepCycle: LAST / Resolution: 1.93→36.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1295 0 9 78 1382
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0191348
X-RAY DIFFRACTIONr_bond_other_d0.0030.021304
X-RAY DIFFRACTIONr_angle_refined_deg1.7621.9941812
X-RAY DIFFRACTIONr_angle_other_deg0.80133028
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7375171
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.60125.71463
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.6615243
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.638156
X-RAY DIFFRACTIONr_chiral_restr0.1040.2203
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021507
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02275
LS refinement shellResolution: 1.928→1.978 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 55 -
Rwork0.346 1012 -
all-1067 -
obs-1067 80.35 %
Refinement TLS params.Method: refined / Origin x: 19.0239 Å / Origin y: 58.5566 Å / Origin z: 15.959 Å
111213212223313233
T0.3003 Å20.0225 Å20.0273 Å2-0.267 Å20.0318 Å2--0.0462 Å2
L0.8658 °2-0.0442 °2-0.1183 °2-5.8892 °21.2936 °2--0.3673 °2
S0.0017 Å °0.0698 Å °0.1206 Å °-0.8809 Å °0.0814 Å °-0.3599 Å °-0.1527 Å °0.1404 Å °-0.0832 Å °

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