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- PDB-3vnz: Crystal structure of beta-glucuronidase from Acidobacterium capsu... -

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Entry
Database: PDB / ID: 3vnz
TitleCrystal structure of beta-glucuronidase from Acidobacterium capsulatum in complex with D-glucuronic acid
Componentsbeta-GLUCURONIDASE
KeywordsHYDROLASE / TIM Barrel / Greek-key / Glycoside hydrolase family 79
Function / homologyGlycoside hydrolase, family 79 / Glycosyl hydrolase, all-beta / Glycoside hydrolase superfamily / Glycosyl hydrolase family 79, N-terminal domain / hydrolase activity, acting on glycosyl bonds / membrane / Uncharacterized protein
Function and homology information
Specimen sourceAcidobacterium capsulatum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 1.8 Å resolution
AuthorsMomma, M. / Fujimoto, Z. / Michikawa, M. / Ichinose, H. / Yoshida, M. / Kotake, Y. / Biely, P. / Tsumuraya, Y. / Kaneko, S.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structural and biochemical characterization of glycoside hydrolase family 79 beta-glucuronidase from Acidobacterium capsulatum
Authors: Michikawa, M. / Ichinose, H. / Momma, M. / Biely, P. / Jongkees, S. / Yoshida, M. / Kotake, T. / Tsumuraya, Y. / Withers, S.G. / Fujimoto, Z. / Kaneko, S.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jan 18, 2012 / Release: Feb 22, 2012
RevisionDateData content typeGroupProviderType
1.0Feb 22, 2012Structure modelrepositoryInitial release
1.1Aug 19, 2015Structure modelDatabase references

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Structure visualization

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Assembly

Deposited unit
A: beta-GLUCURONIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7214
Polyers52,3401
Non-polymers3813
Water6,287349
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: beta-GLUCURONIDASE
hetero molecules

A: beta-GLUCURONIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,4438
Polyers104,6812
Non-polymers7626
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_545y+1/2,x-1/2,-z+1/21
Buried area (Å2)3630
ΔGint (kcal/M)-16
Surface area (Å2)34250
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)101.271, 101.271, 217.768
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI 41 2 2

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Components

#1: Protein/peptide beta-GLUCURONIDASE /


Mass: 52340.289 Da / Num. of mol.: 1 / Source: (gene. exp.) Acidobacterium capsulatum (bacteria) / Strain: ATCC 51196 / Gene: ACP_2665 / Plasmid name: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21gold (DE3) / References: UniProt: C1F2K5, beta-glucuronidase
#2: Chemical ChemComp-BDP / BETA-D-GLUCOPYRANURONIC ACID / D-GLUCURONIC ACID


Mass: 194.139 Da / Num. of mol.: 1 / Formula: C6H10O7 / Glucuronic acid
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Formula: PO4 / Phosphate
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Formula: C3H8O3 / Glycerol
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 349 / Formula: H2O / Water

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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: 2.67 / Density percent sol: 53.88 %
Crystal growTemp: 293 K / Method: vapor diffusion, sitting drop
Details: 2.0M sodium phosphate monobasic monohydrate/potassium phosphate dibasic (0.5/9.5 [v/v]), VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 kelvins
SourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Collection date: Jan 29, 2010
RadiationMonochromator: Si111 / Diffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 19.8 Å2 / D resolution high: 1.8 Å / D resolution low: 40.01 Å / Number obs: 52642 / Observed criterion sigma I: 0 / Rmerge I obs: 0.061 / NetI over sigmaI: 51.7 / Redundancy: 14 % / Percent possible obs: 99.9
Reflection shellRmerge I obs: 0.291 / Highest resolution: 1.8 Å / Lowest resolution: 1.83 Å / MeanI over sigI obs: 10.4 / Number unique all: 2594 / Redundancy: 14 % / Percent possible all: 1

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.5.0109phasing
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3VNY
Correlation coeff Fo to Fc: 0.949 / Correlation coeff Fo to Fc free: 0.936 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS / Overall SU B: 2.656 / Overall SU ML: 0.083 / R Free selection details: RANDOM / Cross valid method: THROUGHOUT / Overall ESU R: 0.125 / Overall ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Solvent computationSolvent ion probe radii: 0.8 Å / Solvent shrinkage radii: 0.8 Å / Solvent vdw probe radii: 1.4 Å / Solvent model details: MASK
Displacement parametersB iso mean: 21.954 Å2 / Aniso B11: 0.1 Å2 / Aniso B12: 0 Å2 / Aniso B13: 0 Å2 / Aniso B22: 0.1 Å2 / Aniso B23: 0 Å2 / Aniso B33: -0.2 Å2
Least-squares processR factor R free: 0.23015 / R factor R work: 0.19894 / R factor obs: 0.20054 / Highest resolution: 1.8 Å / Lowest resolution: 38.42 Å / Number reflection R free: 2676 / Number reflection obs: 49797 / Percent reflection R free: 5.1 / Percent reflection obs: 99.65
Refine hist #LASTHighest resolution: 1.8 Å / Lowest resolution: 38.42 Å
Number of atoms included #LASTProtein: 3531 / Nucleic acid: 0 / Ligand: 24 / Solvent: 349 / Total: 3904
Refine LS restraints
Refine IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223733
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2511.9565091
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9825.000481
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.11023.690168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.43415.000537
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.88315.00022
X-RAY DIFFRACTIONr_chiral_restr0.0860.200542
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212942
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_it0.6731.5002359
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.1612.0003750
X-RAY DIFFRACTIONr_scbond_it1.9693.0001374
X-RAY DIFFRACTIONr_scangle_it3.2034.5001337
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS shellHighest resolution: 1.801 Å / R factor R free: 0.302 / R factor R work: 0.263 / Lowest resolution: 1.847 Å / Number reflection R free: 196 / Number reflection R work: 3608 / Number reflection obs: 3608 / Total number of bins used: 20 / Percent reflection obs: 99.22

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