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- PDB-3mvk: The Crystal Structure of FucU from Bifidobacterium longum to 1.65A -

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Basic information

Entry
Database: PDB / ID: 3mvk
TitleThe Crystal Structure of FucU from Bifidobacterium longum to 1.65A
Componentsprotein FucU
KeywordsISOMERASE / PSI / MCSG / Structural Genomics / Midwest Center for Structural Genomics / Protein Structure Initiative
Function / homology
Function and homology information


monosaccharide metabolic process / D-ribose pyranase / D-ribose pyranase activity / monosaccharide binding
Similarity search - Function
RbsD-like fold / RbsD-like domain / D-ribose pyranase RbsD/L-fucose mutarotase FucU / RbsD-like superfamily / RbsD / FucU transport protein family / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / D-ribose pyranase
Similarity search - Component
Biological speciesBifidobacterium longum subsp. infantis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.65 Å
AuthorsStein, A.J. / Xu, X. / Cui, H. / Savchenko, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The Crystal Structure of FucU from Bifidobacterium longum to 1.65A
Authors: Stein, A.J. / Xu, X. / Cui, H. / Savchenko, A. / Joachimiak, A.
History
DepositionMay 4, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: protein FucU
B: protein FucU
C: protein FucU
D: protein FucU
E: protein FucU
F: protein FucU
G: protein FucU
H: protein FucU
I: protein FucU
J: protein FucU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,01942
Polymers161,47010
Non-polymers2,54932
Water23,7261317
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: protein FucU
E: protein FucU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,02111
Polymers32,2942
Non-polymers7279
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-57 kcal/mol
Surface area13070 Å2
MethodPISA
3
B: protein FucU
G: protein FucU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8479
Polymers32,2942
Non-polymers5547
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2270 Å2
ΔGint-39 kcal/mol
Surface area13650 Å2
MethodPISA
4
C: protein FucU
J: protein FucU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9418
Polymers32,2942
Non-polymers6476
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint-28 kcal/mol
Surface area13800 Å2
MethodPISA
5
D: protein FucU
I: protein FucU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3404
Polymers32,2942
Non-polymers462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-29 kcal/mol
Surface area13550 Å2
MethodPISA
6
F: protein FucU
H: protein FucU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,87010
Polymers32,2942
Non-polymers5768
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1780 Å2
ΔGint-58 kcal/mol
Surface area13140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.047, 83.859, 144.813
Angle α, β, γ (deg.)90.000, 95.110, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
protein FucU / protein RbsD


Mass: 16146.951 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bifidobacterium longum subsp. infantis (bacteria)
Strain: ATCC 15697 / Gene: Blon_2305 / Plasmid: pET derivative / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B7GNK7
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1317 / 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: 2.5 Å3/Da / Density % sol: 50.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5
Details: 25% PEG 3350, 0.1M Hepes pH 7.5, 0.2M Sodium chloride, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 1, 2010
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 189426 / % possible obs: 99.9 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.085 / Χ2: 2.17 / Net I/σ(I): 8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.65-1.713.30.579188440.999100
1.71-1.783.30.435188801.032100
1.78-1.863.30.295188651.021100
1.86-1.963.30.229188941.297100
1.96-2.083.40.152188991.449100
2.08-2.243.40.11188991.676100
2.24-2.463.40.099189592.091100
2.46-2.823.40.087189442.777100
2.82-3.553.40.073190443.90699.9
3.55-503.30.06191985.41799.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.004data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
SHELXphasing
MLPHAREphasing
DMphasing
ARP/wARPmodel building
Cootmodel building
RefinementResolution: 1.65→40.72 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.727 / SU ML: 0.059 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.205 9500 5 %RANDOM
Rwork0.182 ---
obs0.183 189234 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.613 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.65→40.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10544 0 161 1317 12022
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02210949
X-RAY DIFFRACTIONr_angle_refined_deg1.3381.98514857
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.22551425
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.08425.397428
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.678151737
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.6281530
X-RAY DIFFRACTIONr_chiral_restr0.0860.21700
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0218167
X-RAY DIFFRACTIONr_mcbond_it0.7751.57010
X-RAY DIFFRACTIONr_mcangle_it1.398211250
X-RAY DIFFRACTIONr_scbond_it2.62333939
X-RAY DIFFRACTIONr_scangle_it3.6574.53593
LS refinement shellResolution: 1.648→1.691 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 702 -
Rwork0.295 13131 -
all-13833 -
obs--99.41 %

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