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- PDB-3nrh: Crystal Structure of protein BF1032 from Bacteroides fragilis, No... -

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Basic information

Entry
Database: PDB / ID: 3nrh
TitleCrystal Structure of protein BF1032 from Bacteroides fragilis, Northeast Structural Genomics Consortium Target BfR309
Componentsuncharacterized protein BF1032
Keywordsstructural genomics / unknown function / Predominantly alpha-helical protein / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologyProtein of unknown function DUF5063 / Protein of unknown function DUF5063 / DUF5063 superfamily / Domain of unknown function (DUF5063) / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha / Uncharacterized protein
Function and homology information
Biological speciesBacteroides fragilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsSeetharaman, J. / Lew, S. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Wang, D. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. ...Seetharaman, J. / Lew, S. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Wang, D. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published / Year: 2010
Title: Northeast Structural Genomics Consortium Target BfR309
Authors: Seetharaman, J. / Lew, S. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Wang, D. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionJun 30, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: uncharacterized protein BF1032
B: uncharacterized protein BF1032


Theoretical massNumber of molelcules
Total (without water)42,9532
Polymers42,9532
Non-polymers00
Water4,216234
1
A: uncharacterized protein BF1032

B: uncharacterized protein BF1032


Theoretical massNumber of molelcules
Total (without water)42,9532
Polymers42,9532
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y+1/2,-x+1/2,z+1/41
Buried area1860 Å2
ΔGint-16 kcal/mol
Surface area15180 Å2
MethodPISA
2
A: uncharacterized protein BF1032

A: uncharacterized protein BF1032

B: uncharacterized protein BF1032

B: uncharacterized protein BF1032


Theoretical massNumber of molelcules
Total (without water)85,9064
Polymers85,9064
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
crystal symmetry operation4_555y+1/2,-x+1/2,z+1/41
crystal symmetry operation6_555x+1/2,-y+1/2,-z+1/41
Buried area5750 Å2
ΔGint-35 kcal/mol
Surface area28320 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1790 Å2
ΔGint-6 kcal/mol
Surface area15240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.442, 67.442, 157.063
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein uncharacterized protein BF1032


Mass: 21476.564 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis (bacteria) / Strain: YCH46 / Gene: BF1032 / Plasmid: pET 21-23C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: Q64XJ4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 234 / Source method: isolated from a natural source / Formula: H2O

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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: 2.08 Å3/Da / Density % sol: 40.84 %
Crystal growTemperature: 291 K / Method: microbatch under oil / pH: 7.5
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution: 0.1M HEPES (pH 7.5), 12% PEG 20K, and 0.1M NH4H2PO4. , Microbatch under oil, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97907 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 4, 2010 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97907 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 64045 / Num. obs: 63917 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 17.2 Å2 / Rmerge(I) obs: 0.089 / Rsym value: 0.071 / Net I/σ(I): 34.5
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.464 / Mean I/σ(I) obs: 3.7 / Num. unique all: 3216 / Rsym value: 0.421 / % possible all: 99.4

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXthen SOLVE/RESOLVEphasing
CNS1.2refinement
RefinementMethod to determine structure: SAD / Resolution: 1.8→33.93 Å / Rfactor Rfree error: 0.004 / Occupancy max: 1 / Occupancy min: 1 / Data cutoff high absF: 152203 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.224 3012 4.9 %RANDOM
Rwork0.196 ---
all0.2 64052 --
obs0.198 61042 95.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 57.842 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 64.06 Å2 / Biso mean: 22.677 Å2 / Biso min: 5.46 Å2
Baniso -1Baniso -2Baniso -3
1-2.82 Å20 Å20 Å2
2--2.82 Å20 Å2
3----5.64 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.8→33.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2484 0 0 234 2718
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.26 497 5.5 %
Rwork0.273 8605 -
all-9102 -
obs-8605 85.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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