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- PDB-1gql: Structure of Pseudomonas cellulosa alpha-D-glucuronidase complexe... -

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Basic information

Entry
Database: PDB / ID: 1gql
TitleStructure of Pseudomonas cellulosa alpha-D-glucuronidase complexed with glucuronic acid and xylotriose
ComponentsALPHA-D-GLUCURONIDASE
KeywordsHYDROLASE / GLUCURONIDASE / (ALPHA-BETA)8 BARREL / GLYCOSIDE HYDROLASE / GLUCURONIC ACID / XYLOTRIOSE
Function / homologyAlpha glucuronidase / Beta-hexosaminidase-like, domain 2 / Glycosyl hydrolase family 67 middle domain / Glycosyl hydrolase family 67 C-terminus / Glycosyl hydrolase family 67 N-terminus / Alpha glucuronidase, N-terminal / Glycosyl hydrolase family 67, C-terminal / Glycosyl hydrolase family 67, catalytic domain / Alpha-glucuronidase, C-terminal domain superfamily / Glycoside hydrolase superfamily ...Alpha glucuronidase / Beta-hexosaminidase-like, domain 2 / Glycosyl hydrolase family 67 middle domain / Glycosyl hydrolase family 67 C-terminus / Glycosyl hydrolase family 67 N-terminus / Alpha glucuronidase, N-terminal / Glycosyl hydrolase family 67, C-terminal / Glycosyl hydrolase family 67, catalytic domain / Alpha-glucuronidase, C-terminal domain superfamily / Glycoside hydrolase superfamily / glucuronoxylan catabolic process / xylan alpha-1,2-glucuronosidase / alpha-glucuronidase activity / xylan alpha-1,2-glucuronosidase activity / cell outer membrane / extracellular region / Extracellular xylan exo-alpha-(1->2)-glucuronosidase / Extracellular xylan exo-alpha-(1->2)-glucuronosidase
Function and homology information
Specimen sourceCELLVIBRIO JAPONICUS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / 1.67 Å resolution
AuthorsNurizzo, D. / Nagy, T. / Gilbert, H.J. / Davies, G.J.
CitationJournal: Structure / Year: 2002
Title: The Structural Basis for Catalysis and Specificity of the Pseudomonas Cellulosa Alpha-Glucuronidase, Glca67A
Authors: Nurizzo, D. / Nagy, T. / Gilbert, H.J. / Davies, G.J.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 26, 2001 / Release: Sep 26, 2002
RevisionDateData content typeGroupCategoryItemProviderType
1.0Sep 26, 2002Structure modelrepositoryInitial release
1.1May 8, 2011Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance
1.3Jul 5, 2017Structure modelData collectiondiffrn_source_diffrn_source.type
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" AND "BB" IN EACH CHAIN ON SHEET ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" AND "BB" IN EACH CHAIN ON SHEET RECORDS BELOW ARE ACTUALLY 8-STRANDED BARRELS THESE ARE REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)163,02227
Polyers160,8792
Non-polymers2,14325
Water25,6171422
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)7740
ΔGint (kcal/M)-66.07
Surface area (Å2)46590
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)69.256, 74.323, 87.273
Angle α, β, γ (deg.)115.15, 92.94, 109.24
Int Tables number1
Space group name H-MP 1

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Components

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Protein/peptide , 1 types, 2 molecules AB

#1: Protein/peptide ALPHA-D-GLUCURONIDASE


Mass: 80439.594 Da / Num. of mol.: 2 / Source: (gene. exp.) CELLVIBRIO JAPONICUS (bacteria) / Description: CIMB / Plasmid name: PTN1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TUNER (DE3)
References: UniProt: Q8VP74, UniProt: B3PC73*PLUS, EC: 3.2.1.139

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Non-polymers , 5 types, 1447 molecules

#2: Chemical ChemComp-BDP / BETA-D-GLUCOPYRANURONIC ACID / D-GLUCURONIC ACID


Mass: 194.139 Da / Num. of mol.: 2 / Formula: C6H10O7 / Glucuronic acid
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Formula: C2H6O2 / Ethylene glycol
#4: Chemical
ChemComp-XYP / BETA-D-XYLOPYRANOSE


Mass: 150.130 Da / Num. of mol.: 4 / Formula: C5H10O5
#5: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 8 / Formula: Co / Cobalt
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1422 / 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: 2.4 / Density percent sol: 47.8 %
Crystal growpH: 8
Details: 30MG/ML, 15% PEG3350, 250MM MGCL2, 5MM TRIS PH8.0, 20% ETHYLENE GLYCOL, 50MM GLUCURONIC ACID, 50MM XYLOTRIOSE, pH 8.00
Crystal grow
*PLUS
Temp: 20 ℃ / Method: vapor diffusion, hanging drop
components of the solutions
*PLUS

Crystal ID: 1

IDConcCommon nameSol IDDetailsChemical formula
130 mg/mlproteindrop
25 mMTris-HCldroppH8.0
3250 mMreservoirMgCl2
420 %(v/v)ethylene glycolreservoir
515 %(w/v)PEG3350reservoir

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Data collection

DiffractionMean temperature: 11 kelvins
SourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: MARRESEARCH / Details: OSMICS CONFOCAL MULTILAYER / Detector: IMAGE PLATE / Collection date: Aug 15, 2001
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionD resolution high: 1.67 Å / D resolution low: 2 Å / Number obs: 159491 / Rmerge I obs: 0.049 / NetI over sigmaI: 15.7 / Redundancy: 2.7 % / Percent possible obs: 93.9
Reflection shellRmerge I obs: 0.225 / Highest resolution: 1.67 Å / Lowest resolution: 1.7 Å / MeanI over sigI obs: 3 / Redundancy: 2.5 % / Percent possible all: 86.4
Reflection
*PLUS
Number obs: 149092
Reflection shell
*PLUS
Lowest resolution: 1.7 Å / Number unique obs: 6204 / Percent possible obs: 86.4

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Processing

Software
NameVersionClassification
REFMAC5.0refinement
DENZOdata reduction
SCALEPACKdata scaling
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NATIVE ALPHA-D-GLUCURONIDASE

Correlation coeff Fo to Fc: 0.969 / Correlation coeff Fo to Fc free: 0.963 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS / Overall SU B: 1.5 / Overall SU ML: 0.05 / R Free selection details: RANDOM / Cross valid method: THROUGHOUT / Overall ESU R: 0.087 / Overall ESU R Free: 0.084 / 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: BABINET MODEL WITH MASK
Displacement parametersB iso mean: 14.57 Å2 / Aniso B11: 0.84 Å2 / Aniso B12: -0.05 Å2 / Aniso B13: -0.27 Å2 / Aniso B22: -0.69 Å2 / Aniso B23: -0.48 Å2 / Aniso B33: -0.61 Å2
Least-squares processR factor R free: 0.172 / R factor R work: 0.146 / R factor obs: 0.146 / Highest resolution: 1.67 Å / Lowest resolution: 2 Å / Number reflection R free: 1256 / Number reflection obs: 156986 / Percent reflection R free: 0.8 / Percent reflection obs: 94.1
Refine hist #LASTHighest resolution: 1.67 Å / Lowest resolution: 2 Å
Number of atoms included #LASTProtein: 11262 / Nucleic acid: 0 / Ligand: 100 / Solvent: 1422 / Total: 12784
Refine LS restraints
Refine IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02111858
X-RAY DIFFRACTIONr_bond_other_d0.0040.02010422
X-RAY DIFFRACTIONr_angle_refined_deg1.7241.93416148
X-RAY DIFFRACTIONr_angle_other_deg1.9713.00024196
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7383.0001427
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.14515.0002013
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1220.2001676
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02013296
X-RAY DIFFRACTIONr_gen_planes_other0.0040.0202575
X-RAY DIFFRACTIONr_nbd_refined0.2110.1002544
X-RAY DIFFRACTIONr_nbd_other0.1580.10010451
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0940.2005286
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1060.1001145
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1480.10014
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1870.10054
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1230.10042
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8131.5007022
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.4402.00011346
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.3393.0004836
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.6574.5004802
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
Refine LS shellHighest resolution: 1.67 Å / R factor R free: 0.268 / R factor R work: 0.247 / Lowest resolution: 1.71 Å / Number reflection R free: 97 / Number reflection R work: 11041 / Total number of bins used: 20
Least-squares process
*PLUS
R factor R free: 0.177 / R factor R work: 0.16 / Lowest resolution: 2 Å
Refine LS restraints
*PLUS
Refine IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.017
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.724

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