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- PDB-3ewl: Crystal Structure of Conserved protein BF1870 of Unknown Function... -

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Basic information

Entry
Database: PDB / ID: 3ewl
TitleCrystal Structure of Conserved protein BF1870 of Unknown Function from Bacteroides fragilis
Componentsuncharacterized conserved protein BF1870
Keywordsstructural genomics / unknown function / alpha-beta fold / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


Domain of unknown function DUF5106 / Domain of unknown function (DUF5106) / Thioredoxin-like domain / Thioredoxin-like fold / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Uncharacterized protein
Similarity search - Component
Biological speciesBacteroides fragilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsKim, Y. / Tesar, C. / Cobb, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of Conserved protein BF1870 of Unknown Function from Bacteroides fragilis
Authors: Kim, Y. / Tesar, C. / Cobb, G. / Joachimiak, A.
History
DepositionOct 15, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: uncharacterized conserved protein BF1870
B: uncharacterized conserved protein BF1870


Theoretical massNumber of molelcules
Total (without water)33,3542
Polymers33,3542
Non-polymers00
Water2,900161
1
A: uncharacterized conserved protein BF1870


Theoretical massNumber of molelcules
Total (without water)16,6771
Polymers16,6771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: uncharacterized conserved protein BF1870


Theoretical massNumber of molelcules
Total (without water)16,6771
Polymers16,6771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.905, 41.606, 65.600
Angle α, β, γ (deg.)90.00, 105.51, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein uncharacterized conserved protein BF1870


Mass: 16677.141 Da / Num. of mol.: 2 / Fragment: residues 189-327
Source method: isolated from a genetically manipulated source
Details: N-terminal maltose binding protein fusion and a 6-Histidine tag with a TEV protease cut-site, which was cleaved during the purification.
Source: (gene. exp.) Bacteroides fragilis (bacteria) / Strain: NCTC 9343 / Gene: BF1870 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: Q5LE83
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / 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

Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M Trimethylamine N-oxide dihydrate, 0.1M Tris pH 8.5, 20% w/v Polyethylene glycol monomethyl ether 2000, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9793, 0.9795
DetectorType: SBC-3 / Detector: CCD / Date: Oct 13, 2008 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
20.97951
ReflectionResolution: 2→29.66 Å / Num. all: 15373 / Num. obs: 15373 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 26.42 Å2 / Rmerge(I) obs: 0.101 / Net I/σ(I): 7.5
Reflection shellResolution: 2→2.03 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.329 / Mean I/σ(I) obs: 3 / Num. unique all: 674 / % possible all: 88.9

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
MLPHAREphasing
DMmodel building
SHELXDphasing
RESOLVEmodel building
Cootmodel building
REFMAC5.4.0078refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2→29.66 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.927 / SU B: 12.429 / SU ML: 0.155 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.274 / ESU R Free: 0.203
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.241 769 5 %RANDOM
Rwork0.184 ---
all0.187 14586 --
obs0.187 14586 98.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.322 Å2
Baniso -1Baniso -2Baniso -3
1--1.58 Å20 Å2-1.73 Å2
2---0.16 Å20 Å2
3---0.82 Å2
Refinement stepCycle: LAST / Resolution: 2→29.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2239 0 0 161 2400
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222374
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5961.9533224
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3265290
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.52523.559118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.53215418
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9591520
X-RAY DIFFRACTIONr_chiral_restr0.1070.2346
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211832
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8751.51422
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.65122305
X-RAY DIFFRACTIONr_scbond_it2.8443952
X-RAY DIFFRACTIONr_scangle_it4.6444.5919
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.001→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 34 -
Rwork0.21 911 -
obs-945 83.7 %
Refinement TLS params.Method: refined / Origin x: 17.7105 Å / Origin y: 4.0397 Å / Origin z: 16.4321 Å
111213212223313233
T0.0089 Å20.0051 Å20.014 Å2-0.0211 Å20.0047 Å2--0.0417 Å2
L0.3651 °2-0.0571 °20.4419 °2-0.262 °20.1146 °2--1.0652 °2
S0.0072 Å °-0.0087 Å °-0.0082 Å °-0.0036 Å °0.0074 Å °-0.0259 Å °0.0135 Å °0.0037 Å °-0.0146 Å °

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