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- PDB-3f2z: Crystal structure of the C-terminal domain of a chitobiase (BF357... -

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Basic information

Entry
Database: PDB / ID: 3f2z
TitleCrystal structure of the C-terminal domain of a chitobiase (BF3579) from Bacteroides fragilis, Northeast Structural Genomics Consortium Target BfR260B
Componentsuncharacterized protein BF3579
Keywordsstructural genomics / unknown function / The present C-terminal domain is predominantly composed of beta strands. / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


Domain of unknown function DUF1735 / BT_3987-like, N-terminal domain / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
F5/8 type C domain-containing protein
Similarity search - Component
Biological speciesBacteroides fragilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.3 Å
AuthorsForouhar, F. / Lew, S. / Seetharaman, J. / Janjua, H. / Xiao, R. / Foote, E.L. / Ciccosanti, C. / Lee, D. / Nair, R. / Everett, J.K. ...Forouhar, F. / Lew, S. / Seetharaman, J. / Janjua, H. / Xiao, R. / Foote, E.L. / Ciccosanti, C. / Lee, D. / Nair, R. / Everett, J.K. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of the C-terminal domain of a chitobiase (BF3579) from Bacteroides fragilis, Northeast Structural Genomics Consortium Target BfR260B
Authors: Forouhar, F. / Lew, S. / Seetharaman, J. / Janjua, H. / Xiao, R. / Foote, E.L. / Ciccosanti, C. / Lee, D. / Nair, R. / Everett, J.K. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionOct 30, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Dec 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 BF3579


Theoretical massNumber of molelcules
Total (without water)17,9051
Polymers17,9051
Non-polymers00
Water6,954386
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.893, 51.684, 63.960
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe C-terminal domain is monomer in solution and crystal.

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Components

#1: Protein uncharacterized protein BF3579


Mass: 17904.631 Da / Num. of mol.: 1 / Fragment: C-terminal domain, residues 291-440
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis (bacteria) / Strain: NCTC 9343 / Gene: BF3579 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q5L9G5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 386 / 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: 2.21 Å3/Da / Density % sol: 44.36 %
Crystal growTemperature: 277 K / Method: microbatch under oil / pH: 5
Details: Protein solution: 10 mM Tris (pH 7.5), 100 mM sodium chloride, and 5 mM DTT. Reservoir solution: 100 mM NaAcetate (pH 5), 40% PEG 8K, and 100 mM NH4Cl , microbatch under oil, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97914
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 16, 2008 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97914 Å / Relative weight: 1
ReflectionResolution: 1.3→30 Å / Num. all: 75798 / Num. obs: 67612 / % possible obs: 89.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5 % / Biso Wilson estimate: 9.1 Å2 / Rmerge(I) obs: 0.039 / Rsym value: 0.044 / Net I/σ(I): 43.3
Reflection shellResolution: 1.3→1.35 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.081 / Mean I/σ(I) obs: 11.54 / Num. unique all: 7565 / Rsym value: 0.089 / % possible all: 72.1

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
RESOLVEmodel building
CNS& XtalView & REFMAC 5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.3→10 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.283 / SU ML: 0.026 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.055 / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17455 1854 5 %RANDOM
Rwork0.1552 ---
all0.15628 35268 --
obs0.15618 35268 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.287 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å20 Å20 Å2
2--0.38 Å20 Å2
3----0.16 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.14 Å0.13 Å
Luzzati d res low-5 Å
Luzzati sigma a0.07 Å0.05 Å
Refinement stepCycle: LAST / Resolution: 1.3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1168 0 0 386 1554
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0221193
X-RAY DIFFRACTIONr_angle_refined_deg1.0681.9281616
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.085148
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.75224.3158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.43815200
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.307158
X-RAY DIFFRACTIONr_chiral_restr0.0740.2175
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02915
X-RAY DIFFRACTIONr_nbd_refined0.1790.2554
X-RAY DIFFRACTIONr_nbtor_refined0.3030.2821
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0960.2318
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1210.224
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0590.231
X-RAY DIFFRACTIONr_mcbond_it0.6551.5758
X-RAY DIFFRACTIONr_mcangle_it0.98721183
X-RAY DIFFRACTIONr_scbond_it1.4243504
X-RAY DIFFRACTIONr_scangle_it2.014.5433
X-RAY DIFFRACTIONr_rigid_bond_restr0.83331262
X-RAY DIFFRACTIONr_sphericity_free1.8643386
X-RAY DIFFRACTIONr_sphericity_bonded1.48431168
LS refinement shellResolution: 1.3→1.333 Å / Rfactor Rfree error: 0.003 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.192 105 -
Rwork0.137 2100 -
obs-2100 100 %

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