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- PDB-2r41: Crystal structure of the protein of unknown function from Enteroc... -

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Basic information

Entry
Database: PDB / ID: 2r41
TitleCrystal structure of the protein of unknown function from Enterococcus faecalis
ComponentsUncharacterized protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / alpha-beta structure / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologyenterococcus faecalis protein / Protein of unknown function DUF960 / Staphylococcal protein of unknown function (DUF960) / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta / GTP cyclohydrolase
Function and homology information
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å
AuthorsKim, Y. / Li, H. / Moy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of the protein of unknown function from Enterococcus faecalis.
Authors: Kim, Y. / Li, H. / Moy, S. / Joachimiak, A.
History
DepositionAug 30, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Nov 6, 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
C: Uncharacterized protein
D: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)49,8344
Polymers49,8344
Non-polymers00
Water1,838102
1
A: Uncharacterized protein
B: Uncharacterized protein
C: Uncharacterized protein
D: Uncharacterized protein

A: Uncharacterized protein
B: Uncharacterized protein
C: Uncharacterized protein
D: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)99,6688
Polymers99,6688
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area12500 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4450 Å2
MethodPISA
3
A: Uncharacterized protein
C: Uncharacterized protein

B: Uncharacterized protein
D: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)49,8344
Polymers49,8344
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_544-y+1/2,x-1/2,z-1/41
Buried area4900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.983, 81.983, 181.849
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11D-127-

HOH

Detailstetramer or octamer, but none are confirmed. for tetramer, as they are in the asymetric unit or A and C are as in the asymetric unit and B and D are by -y+1/2,x-1/2,z-1/4 with translation of 40.991 -40.992 -45.462. For octamer: ABCD in the asymmetric unit + another set from -y+1,-x+1,-z+1/2 with translation of 81.983 81.983 90.924.

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Components

#1: Protein
Uncharacterized protein


Mass: 12458.516 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Strain: V583 / Gene: EF_0819 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q837L7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 3.07 Å3/Da / Density % sol: 59.88 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M Ammonium Acetate, 0.1M Bis-Tris pH 6.5, 25% PEG 3350, 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 315 / Detector: CCD / Date: Apr 8, 2007 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.9→41 Å / Num. all: 14597 / Num. obs: 14597 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.9 % / Rsym value: 0.118 / Net I/σ(I): 10.1
Reflection shellResolution: 2.9→3 Å / Redundancy: 10 % / Mean I/σ(I) obs: 6.2 / Num. unique all: 1410 / Rsym value: 0.604 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.9→40.99 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.912 / SU B: 26.647 / SU ML: 0.255 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.359
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.241 722 5 %RANDOM
Rwork0.182 ---
all0.185 13628 --
obs0.185 13628 99.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.408 Å2
Baniso -1Baniso -2Baniso -3
1-3.51 Å20 Å20 Å2
2--3.51 Å20 Å2
3----7.02 Å2
Refinement stepCycle: LAST / Resolution: 2.9→40.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3306 0 0 102 3408
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0213463
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6451.964715
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4375427
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.27723.892167
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.08615567
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.571521
X-RAY DIFFRACTIONr_chiral_restr0.0990.2531
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022664
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2480.21499
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3350.22416
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2176
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2150.256
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2610.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6841.52123
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.3723449
X-RAY DIFFRACTIONr_scbond_it2.09831340
X-RAY DIFFRACTIONr_scangle_it3.4014.51266
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 56 -
Rwork0.301 958 -
obs-1014 99.31 %
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)
12.76090.36770.75091.1020.92945.17270.1401-0.1293-0.06770.0385-0.0754-0.01010.4146-0.1689-0.0646-0.0388-0.0102-0.0195-0.08440.0208-0.12635.32857.75949.4647
22.04980.1061.84043.5409-0.22923.5537-0.1468-0.21760.03590.13990.0425-0.00510.0527-0.31540.1043-0.08750.043-0.0215-0.0064-0.0208-0.108844.042218.891469.8602
34.06561.47381.21782.47610.76693.24990.01060.0386-0.048-0.1577-0.0197-0.042-0.0571-0.13820.0091-0.09650.0998-0.0463-0.0465-0.0139-0.06831.844229.723942.5726
42.61910.23030.03472.3492-1.31897.61020.08940.09730.10640.082-0.0391-0.0556-0.10390.2086-0.0503-0.09070.04720.0437-0.07270.0359-0.106264.291713.58160.0404
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 1056 - 108
2X-RAY DIFFRACTION2BB1 - 1044 - 107
3X-RAY DIFFRACTION3CC1 - 1064 - 109
4X-RAY DIFFRACTION4DD2 - 1055 - 108

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