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- PDB-3vny: Crystal structure of beta-glucuronidase from Acidobacterium capsulatum -

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Basic information

Entry
Database: PDB / ID: 3vny
TitleCrystal structure of beta-glucuronidase from Acidobacterium capsulatum
Componentsbeta-GLUCURONIDASE
KeywordsHYDROLASE / TIM Barrel / Greek-key / Glycoside hydrolase family 79
Function / homology
Function and homology information


hydrolase activity, acting on glycosyl bonds / membrane
Similarity search - Function
Beta-glucuronidase, C-terminal / Glycosyl hydrolase family 79 C-terminal beta domain / Glycoside hydrolase, family 79 / Glycosyl hydrolase family 79, N-terminal domain / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel ...Beta-glucuronidase, C-terminal / Glycosyl hydrolase family 79 C-terminal beta domain / Glycoside hydrolase, family 79 / Glycosyl hydrolase family 79, N-terminal domain / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Beta-glucuronidase C-terminal domain-containing protein
Similarity search - Component
Biological speciesAcidobacterium capsulatum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å
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.
History
DepositionJan 18, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 22, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2015Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: beta-GLUCURONIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6194
Polymers52,3401
Non-polymers2793
Water9,062503
1


  • Idetical with deposited unit
  • defined by author
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)105,2398
Polymers104,6812
Non-polymers5586
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_545y+1/2,x-1/2,-z+1/21
Buried area3800 Å2
ΔGint-26 kcal/mol
Surface area34040 Å2
MethodPISA
3
A: beta-GLUCURONIDASE
hetero molecules

A: beta-GLUCURONIDASE
hetero molecules

A: beta-GLUCURONIDASE
hetero molecules

A: beta-GLUCURONIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)210,47816
Polymers209,3614
Non-polymers1,11712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_545y+1/2,x-1/2,-z+1/21
crystal symmetry operation10_655-x+1,-y,z1
crystal symmetry operation16_555-y+1/2,-x+1/2,-z+1/21
Buried area9450 Å2
ΔGint-59 kcal/mol
Surface area66210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.126, 101.126, 217.881
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-1095-

HOH

21A-1096-

HOH

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Components

#1: Protein beta-GLUCURONIDASE /


Mass: 52340.289 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acidobacterium capsulatum (bacteria) / Strain: ATCC 51196 / Gene: ACP_2665 / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21gold (DE3) / References: UniProt: C1F2K5, beta-glucuronidase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 503 / 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: 2.66 Å3/Da / Density % sol: 53.77 %
Crystal growTemperature: 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

Diffraction
IDMean temperature (K)Crystal-ID
1951
2951
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory AR-NE3A11
SYNCHROTRONPhoton Factory AR-NE3A20.97946, 0.97967, 0.96000
Detector
TypeIDDetectorDate
ADSC QUANTUM 2701CCDJan 29, 2010
ADSC QUANTUM 2702CCDJan 29, 2010
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si111SINGLE WAVELENGTHMx-ray1
2Si111MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.979461
30.979671
40.961
ReflectionResolution: 1.5→30.684 Å / Num. obs: 90146 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 14.6 % / Biso Wilson estimate: 14.5 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 47
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 14.4 % / Rmerge(I) obs: 0.392 / Mean I/σ(I) obs: 6.8 / Num. unique all: 4427 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.5→30.58 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.954 / SU B: 0.962 / SU ML: 0.037 / Cross valid method: THROUGHOUT / ESU R: 0.065 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18987 4504 5 %RANDOM
Rwork0.17173 ---
obs0.17264 85363 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.946 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2--0.05 Å20 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 1.5→30.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3531 0 17 503 4051
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0223852
X-RAY DIFFRACTIONr_angle_refined_deg1.0661.9545269
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5765514
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.54423.371178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.77115576
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8071527
X-RAY DIFFRACTIONr_chiral_restr0.0730.2557
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213056
X-RAY DIFFRACTIONr_mcbond_it0.4811.52412
X-RAY DIFFRACTIONr_mcangle_it0.90523856
X-RAY DIFFRACTIONr_scbond_it1.41131440
X-RAY DIFFRACTIONr_scangle_it2.2954.51393
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.229 327 -
Rwork0.205 6229 -
obs-6229 99.67 %

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