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- PDB-1gqi: Structure of Pseudomonas cellulosa alpha-D-glucuronidase -

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Basic information

Entry
Database: PDB / ID: 1gqi
TitleStructure of Pseudomonas cellulosa alpha-D-glucuronidase
ComponentsALPHA-GLUCURONIDASE
KeywordsGLUCURONIDASE / (ALPHA-BETA)8 BARREL / GLYCOSIDE HYDROLASE
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
: / Extracellular xylan exo-alpha-(1->2)-glucuronosidase
Similarity search - Component
Biological speciesPSEUDOMONAS CELLULOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.48 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 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
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 IS ACTUALLY AN 8-STRANDED BARREL THIS IS 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-GLUCURONIDASE
B: ALPHA-GLUCURONIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,14424
Polymers160,8792
Non-polymers1,26522
Water31,8141766
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)69.912, 74.682, 87.587
Angle α, β, γ (deg.)115.18, 93.14, 109.33
Int Tables number1
Space group name H-MP1

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Components

#1: Protein ALPHA-GLUCURONIDASE


Mass: 80439.594 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS CELLULOSA (bacteria) / Plasmid: PTN1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TUNER (DE3) / References: UniProt: B3PC73*PLUS, EC: 3.2.1.139
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 58.933 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Co
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1766 / 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, 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: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 13, 2001 / Details: MIRRORS
RadiationMonochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.484→20 Å / Num. obs: 235655 / % possible obs: 97.6 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 7.1
Reflection shellResolution: 1.48→1.56 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.345 / Mean I/σ(I) obs: 1.6 / % possible all: 90.4
Reflection
*PLUS
Highest resolution: 1.48 Å / Lowest resolution: 20 Å / Num. obs: 236943
Reflection shell
*PLUS
Highest resolution: 1.48 Å / % possible obs: 90.4 % / Num. unique obs: 32167

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SIRAS / Resolution: 1.48→20 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.964 / SU B: 2.779 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.069 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.168 1894 0.8 %RANDOM
Rwork0.133 ---
obs0.133 233691 96.8 %-
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: 10.86 Å2
Baniso -1Baniso -2Baniso -3
1-0.46 Å20.11 Å2-0.16 Å2
2---0.1 Å2-0.3 Å2
3----0.56 Å2
Refinement stepCycle: LAST / Resolution: 1.48→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11376 0 58 1766 13200
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02111884
X-RAY DIFFRACTIONr_bond_other_d0.0010.0210507
X-RAY DIFFRACTIONr_angle_refined_deg1.5891.9316126
X-RAY DIFFRACTIONr_angle_other_deg2.019324413
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.91931414
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.102152059
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1220.21667
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213311
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022572
X-RAY DIFFRACTIONr_nbd_refined0.2510.32650
X-RAY DIFFRACTIONr_nbd_other0.2070.310640
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.1940.520
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.51192
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0820.56
X-RAY DIFFRACTIONr_metal_ion_refined0.1230.51
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1830.320
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2110.350
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2130.552
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2711.57057
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.833211382
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.57734827
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.7244.54744
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: 1.48→1.52 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.284 134
Rwork0.203 14735
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor Rfree: 0.168 / Rfactor Rwork: 0.133
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_deg1.589

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