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- PDB-2gbo: Protein of Unknown Function EF2458 from Enterococcus faecalis -

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Basic information

Entry
Database: PDB / ID: 2gbo
TitleProtein of Unknown Function EF2458 from Enterococcus faecalis
ComponentsUPF0358 protein EF2458
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / hypothetical protein / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologyUncharacterised protein family UPF0358 / Protein of unknown function (DUF1507) / SO2669-like / UPF0358 superfamily / Helix Hairpins / Orthogonal Bundle / Mainly Alpha / UPF0358 protein EF_2458
Function and homology information
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsOsipiuk, J. / Wu, R. / Bargassa, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: X-ray crystal structure of conserved hypothetical protein EF_2458 from Enterococcus faecalis.
Authors: Osipiuk, J. / Wu, R. / Bargassa, M. / Joachimiak, A.
History
DepositionMar 10, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Nov 13, 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 / pdbx_struct_special_symmetry / struct_conn / struct_ref_seq_dif
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
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). THE AUTHORS STATE THE BIOLOGICAL UNIT IS UNKNOWN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UPF0358 protein EF2458
B: UPF0358 protein EF2458


Theoretical massNumber of molelcules
Total (without water)24,3282
Polymers24,3282
Non-polymers00
Water1,00956
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint-38 kcal/mol
Surface area12000 Å2
MethodPISA
2
A: UPF0358 protein EF2458
B: UPF0358 protein EF2458

A: UPF0358 protein EF2458
B: UPF0358 protein EF2458


Theoretical massNumber of molelcules
Total (without water)48,6564
Polymers48,6564
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545-x,-y-1,z1
Buried area12830 Å2
ΔGint-128 kcal/mol
Surface area17780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.614, 54.614, 142.121
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62
Components on special symmetry positions
IDModelComponents
11A-109-

HOH

21A-110-

HOH

31A-119-

HOH

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Components

#1: Protein UPF0358 protein EF2458


Mass: 12164.123 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Strain: V583 / Gene: EF_2458 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q831P3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.51 Å3/Da / Density % sol: 51.09 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 35% (v/v) 2-methyl-2,4-pentanediol, 0.1 M HEPES, 0.2 M NaCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97933 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 27, 2006
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 2.2→39.4 Å / Num. all: 12040 / Num. obs: 12040 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 15.9 % / Biso Wilson estimate: 49.4 Å2 / Rmerge(I) obs: 0.104 / Net I/σ(I): 34.5
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 8.4 % / Rmerge(I) obs: 0.669 / Mean I/σ(I) obs: 1.83 / Num. unique all: 933 / % possible all: 91.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
SCALEPACKdata scaling
HKL-3000phasing
SHELXDphasing
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→39.5 Å / Cor.coef. Fo:Fc: 0.961 / SU B: 9.843 / SU ML: 0.123 / TLS residual ADP flag: LIKELY RESIDUAL / σ(F): 0 / σ(I): 0 / ESU R: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. R-FACTOR-ALL CORRESPONDS TO DEPOSITED FILE. R-WORK AND R-FREE FACTORS ARE TAKEN FROM SECOND TO LAST ROUND OF REFINEMENT WHICH USED TEST DATA SET.
RfactorNum. reflection% reflectionSelection details
Rfree0.2436 1176 -RANDOM
Rwork0.1992 ---
all0.1989 11997 --
obs0.1989 11997 98.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.532 Å2
Baniso -1Baniso -2Baniso -3
1-2.58 Å21.29 Å20 Å2
2--2.58 Å20 Å2
3----3.87 Å2
Refinement stepCycle: LAST / Resolution: 2.2→39.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1326 0 0 56 1382
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221338
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5351.9721790
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.215162
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.4292572
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.88515274
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0581512
X-RAY DIFFRACTIONr_chiral_restr0.1150.2202
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02986
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2220.2595
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.2946
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.257
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2620.286
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1180.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.271.5835
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.80421300
X-RAY DIFFRACTIONr_scbond_it2.6943549
X-RAY DIFFRACTIONr_scangle_it4.2414.5490
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.202→2.259 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 82 -
Rwork0.232 807 -
obs-807 90.57 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.86781.9236-1.63124.4821-2.268211.38010.0407-0.0417-0.23650.1866-0.1441-0.58920.8413-0.0650.10340.1141-0.1388-0.0086-0.16840.0037-0.079517.4221-27.902828.4759
20.9680.4766-3.20521.58770.113212.72640.13320.22690.31220.3268-0.25670.15210.1525-0.03040.1234-0.19380.00260.02510.1768-0.0476-0.107821.5067-22.3442-14.7413
36.16111.79931.04860.5902-0.35036.84160.28680.55981.19740.0623-0.3857-0.1979-0.6436-0.05630.0989-0.1493-0.01020.0035-0.00420.07790.00220.5779-11.8899-29.272
45.4009-0.65932.93140.54372.178715.48280.04350.19660.6026-0.016-0.0397-0.1528-0.1338-0.6598-0.0038-0.23170.0405-0.00550.1540.0132-0.077811.849-18.226-28.3251
50.84720.18870.49160.95553.388712.0568-0.01160.3016-0.18540.1374-0.1065-0.1455-0.0878-0.28370.1180.096-0.16570.0251-0.0904-0.0314-0.124618.7474-17.479514.8207
62.52193.49130.09094.90581.193415.76270.02610.177-0.5180.5914-0.133-1.16770.20141.32770.107-0.0757-0.0583-0.0857-0.08290.03870.022927.2884-23.560829.4065
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 304 - 33
2X-RAY DIFFRACTION2AA31 - 5634 - 59
3X-RAY DIFFRACTION3AA57 - 8260 - 85
4X-RAY DIFFRACTION4BB1 - 304 - 33
5X-RAY DIFFRACTION5BB31 - 5634 - 59
6X-RAY DIFFRACTION6BB57 - 8260 - 85

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