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

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Basic information

Entry
Database: PDB / ID: 1gqk
TitleStructure of Pseudomonas cellulosa alpha-D-glucuronidase complexed with glucuronic acid
ComponentsALPHA-D-GLUCURONIDASE
KeywordsHYDROLASE / GLUCURONIDASE / (ALPHA-BETA)8 BARREL / GLYCOSIDE HYDROLASE / GLUCURONIC ACID
Function / homology
Function and homology information


glucuronoxylan catabolic process / xylan alpha-1,2-glucuronosidase / xylan alpha-1,2-glucuronosidase activity / alpha-glucuronidase activity / cell outer membrane / extracellular region
Similarity search - Function
Alpha-d-glucuronidase, C-terminal Domain / Alpha-glucuronidase, C-terminal domain / Alpha glucuronidase, N-terminal / Glycosyl hydrolase family 67, C-terminal / Glycosyl hydrolase family 67, catalytic domain / Alpha glucuronidase / Alpha-glucuronidase, C-terminal domain superfamily / Glycosyl hydrolase family 67 N-terminus / Glycosyl hydrolase family 67 C-terminus / Glycosyl hydrolase family 67 middle domain ...Alpha-d-glucuronidase, C-terminal Domain / Alpha-glucuronidase, C-terminal domain / Alpha glucuronidase, N-terminal / Glycosyl hydrolase family 67, C-terminal / Glycosyl hydrolase family 67, catalytic domain / Alpha glucuronidase / Alpha-glucuronidase, C-terminal domain superfamily / Glycosyl hydrolase family 67 N-terminus / Glycosyl hydrolase family 67 C-terminus / Glycosyl hydrolase family 67 middle domain / Chitobiase/beta-hexosaminidase domain 2-like / Chitobiase; domain 2 / Beta-hexosaminidase-like, domain 2 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
beta-D-glucopyranuronic acid / : / Extracellular xylan exo-alpha-(1->2)-glucuronosidase / Extracellular xylan exo-alpha-(1->2)-glucuronosidase
Similarity search - Component
Biological speciesCELLVIBRIO JAPONICUS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
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.
History
DepositionNov 26, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 26, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)162,48424
Polymers160,8792
Non-polymers1,60522
Water23,1491285
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8160 Å2
ΔGint-49.77 kcal/mol
Surface area46840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.707, 74.879, 87.481
Angle α, β, γ (deg.)115.34, 93.06, 109.20
Int Tables number1
Space group name H-MP1

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Components

#1: Protein ALPHA-D-GLUCURONIDASE


Mass: 80439.594 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CELLVIBRIO JAPONICUS (bacteria) / Strain: NCIMB-10462 / Description: NCIMB / Plasmid: PTN1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TUNER (DE3)
References: UniProt: Q8VP74, UniProt: B3PC73*PLUS, EC: 3.2.1.139
#2: Sugar ChemComp-BDP / beta-D-glucopyranuronic acid / beta-D-glucuronic acid / D-glucuronic acid / glucuronic acid


Type: D-saccharide, beta linking / Mass: 194.139 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H10O7
IdentifierTypeProgram
DGlcpAbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranuronic acidCOMMON NAMEGMML 1.0
b-D-GlcpAIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcASNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Co
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1285 / 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: 2.4 Å3/Da / Density % sol: 47.8 %
Crystal growpH: 8
Details: 30MG/ML, 15% PEG3350, 250MM MGCL2, 5MM TRIS PH8.0, 20% ETHYLENE GLYCOL 100MM GLUCURONIC ACID, pH 8.00
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
130 mg/mlprotein1drop
25 mMTris-HCl1droppH8.0
3250 mM1reservoirMgCl2
420 %(v/v)ethylene glycol1reservoir
515 %(w/v)PEG33501reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 15, 2001 / Details: OSMICS CONFOCAL MULTILAYER
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 113754 / % possible obs: 97.3 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 9.8
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.353 / Mean I/σ(I) obs: 2.2 / % possible all: 94.1
Reflection shell
*PLUS
% possible obs: 94.1 % / Num. unique obs: 5509

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NATIVE ALPHA-D-GLUCURONIDASE

Resolution: 1.9→19.73 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.953 / SU B: 4.179 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.134 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.186 869 0.8 %RANDOM
Rwork0.151 ---
obs0.152 111807 97.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 16.67 Å2
Baniso -1Baniso -2Baniso -3
1-1.26 Å20.53 Å2-0.1 Å2
2--0.02 Å2-0.53 Å2
3----1.4 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11376 0 82 1285 12743
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02111862
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210430
X-RAY DIFFRACTIONr_angle_refined_deg1.4851.93116100
X-RAY DIFFRACTIONr_angle_other_deg1.812324214
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.30131414
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.88152025
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1080.21666
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213307
X-RAY DIFFRACTIONr_gen_planes_other0.0040.022568
X-RAY DIFFRACTIONr_nbd_refined0.2240.32475
X-RAY DIFFRACTIONr_nbd_other0.1950.310199
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.2440.513
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1190.51055
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0690.53
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1560.39
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1920.341
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0830.523
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7991.57057
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.335211360
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.23834805
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3984.54740
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: 1.9→1.95 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.28 55
Rwork0.224 7963
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor Rfree: 0.186 / Rfactor Rwork: 0.152
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.016
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.485

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