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- PDB-4c91: Evidence that GH115 alpha-glucuronidase activity is dependent on ... -

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Basic information

Entry
Database: PDB / ID: 4c91
TitleEvidence that GH115 alpha-glucuronidase activity is dependent on conformational flexibility
ComponentsALPHA-GLUCURONIDASE GH115
KeywordsHYDROLASE / XYLOSE / GLUCURONIC ACID
Function / homology
Function and homology information


carbohydrate metabolic process
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #2150 / Jelly Rolls - #1620 / Glycosyl hydrolase family 115 / Glycosyl hydrolase family 115 / Gylcosyl hydrolase 115 C-terminal domain / Glycosyl hydrolase 115 superfamily / Glycosyl hydrolase family 115 / Gylcosyl hydrolase family 115 C-terminal domain / Chitobiase/beta-hexosaminidase domain 2-like / Chitobiase; domain 2 ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #2150 / Jelly Rolls - #1620 / Glycosyl hydrolase family 115 / Glycosyl hydrolase family 115 / Gylcosyl hydrolase 115 C-terminal domain / Glycosyl hydrolase 115 superfamily / Glycosyl hydrolase family 115 / Gylcosyl hydrolase family 115 C-terminal domain / Chitobiase/beta-hexosaminidase domain 2-like / Chitobiase; domain 2 / Beta-hexosaminidase-like, domain 2 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Jelly Rolls / TIM Barrel / Alpha-Beta Barrel / Up-down Bundle / Sandwich / 2-Layer Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
CITRATE ANION / D-glucuronic acid / Gylcosyl hydrolase 115 C-terminal domain-containing protein
Similarity search - Component
Biological speciesBACTEROIDES OVATUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å
AuthorsRogowski, A. / Basle, A. / Farinas, C.S. / Solovyova, A. / Mortimer, J.C. / Dupree, P. / Gilbert, H.J. / Bolam, D.N.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Evidence that Gh115 Alpha-Glucuronidase Activity is Dependent on Conformational Flexibility
Authors: Rogowski, A. / Basle, A. / Farinas, C.S. / Solovyova, A. / Mortimer, J.C. / Dupree, P. / Gilbert, H.J. / Bolam, D.N.
History
DepositionOct 2, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 13, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2013Group: Database references
Revision 1.2Jan 15, 2014Group: Database references
Revision 1.3Sep 13, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ALPHA-GLUCURONIDASE GH115
B: ALPHA-GLUCURONIDASE GH115
hetero molecules


Theoretical massNumber of molelcules
Total (without water)197,0834
Polymers196,7002
Non-polymers3832
Water10,845602
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8230 Å2
ΔGint-32.7 kcal/mol
Surface area54190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.040, 130.290, 190.170
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ALPHA-GLUCURONIDASE GH115


Mass: 98350.102 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACTEROIDES OVATUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: A7M022
#2: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#3: Sugar ChemComp-REL / D-glucuronic acid / D-Glucuronate, alpha-D-glucofuranuronic acid / Glucuronic acid


Type: D-saccharide / Mass: 194.139 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H10O7
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 602 / 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: 2.37 Å3/Da / Density % sol: 48 % / Description: NONE
Crystal growDetails: 19% PEG3350, 0.2M SODIUM CITRATE PH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 16, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 2.14→45.43 Å / Num. obs: 93249 / % possible obs: 94.4 % / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 9.3
Reflection shellResolution: 2.14→2.26 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.5 / % possible all: 91.5

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: APO FORM SEE PAPER

Resolution: 2.14→44.74 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.922 / SU B: 5.11 / SU ML: 0.129 / Cross valid method: THROUGHOUT / ESU R: 0.238 / ESU R Free: 0.189 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED ATOMS WERE NOT MODELED
RfactorNum. reflection% reflectionSelection details
Rfree0.21878 4649 5 %RANDOM
Rwork0.17398 ---
obs0.17618 88546 93.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.906 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å20 Å20 Å2
2---0.06 Å20 Å2
3---0.28 Å2
Refinement stepCycle: LAST / Resolution: 2.14→44.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12687 0 26 602 13315
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.01913064
X-RAY DIFFRACTIONr_bond_other_d0.0050.0211764
X-RAY DIFFRACTIONr_angle_refined_deg1.6221.9417815
X-RAY DIFFRACTIONr_angle_other_deg1.052326944
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.55651617
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.42724.457608
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.023152005
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3741557
X-RAY DIFFRACTIONr_chiral_restr0.1030.21907
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02115080
X-RAY DIFFRACTIONr_gen_planes_other0.0050.023093
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_it1.972.6136477
X-RAY DIFFRACTIONr_mcbond_other1.9692.6136476
X-RAY DIFFRACTIONr_mcangle_it2.9323.9168088
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.2892.7176587
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.14→2.196 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 387 -
Rwork0.249 6434 -
obs--93.82 %

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