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- PDB-1h41: Pseudomonas cellulosa E292A alpha-D-glucuronidase mutant complexe... -

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Basic information

Entry
Database: PDB / ID: 1h41
TitlePseudomonas cellulosa E292A alpha-D-glucuronidase mutant complexed with aldotriuronic acid
ComponentsALPHA-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
: / 4-O-methyl-alpha-D-glucopyranuronic acid / Extracellular xylan exo-alpha-(1->2)-glucuronosidase / Extracellular xylan exo-alpha-(1->2)-glucuronosidase
Similarity search - Component
Biological speciesPSEUDOMONAS CELLULOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsNurizzo, D. / Nagy, T. / Gilbert, H.J. / Davies, G.J.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: The Alpha-Glucuronidase,Glca67A,of Cellvibrio Japonicus Utilizes the Carboxylate and Methyl Groups of Aldobiouronic Acid as Important Substrate Recognition Determinants
Authors: Nagy, T. / Nurizzo, D. / Davies, G.J. / Biely, P. / Lakey, J.H. / Bolam, D.N. / Gilbert, H.J.
History
DepositionSep 25, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 1, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 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 / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Dec 13, 2023Group: 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 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)163,50742
Polymers160,7632
Non-polymers2,74440
Water30,0311667
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)69.412, 74.393, 87.462
Angle α, β, γ (deg.)115.09, 93.04, 109.44
Int Tables number1
Space group name H-MP1

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Components

#1: Protein ALPHA-GLUCURONIDASE /


Mass: 80381.562 Da / Num. of mol.: 2 / Mutation: YES
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: Q8VP74, UniProt: B3PC73*PLUS, EC: 3.2.1.139
#2: Sugar ChemComp-GCV / 4-O-methyl-alpha-D-glucopyranuronic acid / 4-O-METHYL-ALPHA-D-GLUCURONIC ACID / 4-O-methyl-D-glucuronic acid / 4-O-methyl-glucuronic acid


Type: D-saccharide, alpha linking / Mass: 208.166 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C7H12O7
IdentifierTypeProgram
a-D-GlcpA4OMeIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Co
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1667 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED MUTATION GLU 312 ALA

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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: 48.5 %
Crystal growpH: 8
Details: 15% PEG3350, 250MM MGCL2, 5MM TRIS-HCL PH8.0, 20% GLYCEROL, pH 8.00
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop / Details: Nurizzo, D., (2002) Structure, 10, 547.
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: ID14-4 / Wavelength: 0.9392
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 15, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9392 Å / Relative weight: 1
ReflectionResolution: 1.5→20 Å / Num. obs: 212953 / % possible obs: 91.2 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 20.06
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.215 / Mean I/σ(I) obs: 4.23 / % possible all: 52.9
Reflection
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 20 Å / Rmerge(I) obs: 0.047
Reflection shell
*PLUS
% possible obs: 52.9 % / Redundancy: 2.6 % / Num. unique obs: 8276 / Rmerge(I) obs: 0.237 / Mean I/σ(I) obs: 4.2

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Processing

Software
NameVersionClassification
REFMAC5.1.08refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GQI

1gqi


Resolution: 1.5→20 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.968 / SU B: 0.943 / SU ML: 0.035 / Cross valid method: THROUGHOUT / ESU R: 0.069 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.153 1679 0.8 %RANDOM
Rwork0.118 ---
obs0.118 211429 91.2 %-
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: 12.76 Å2
Baniso -1Baniso -2Baniso -3
1-1.03 Å2-0.05 Å2-0.45 Å2
2---0.71 Å2-0.48 Å2
3----0.8 Å2
Refinement stepCycle: LAST / Resolution: 1.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11233 0 150 1667 13050
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d
X-RAY DIFFRACTIONr_bond_other_d0.0030.0210420
X-RAY DIFFRACTIONr_angle_refined_deg
X-RAY DIFFRACTIONr_angle_other_deg2.205324233
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.89751397
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.37523.428601
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.645151922
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.951594
X-RAY DIFFRACTIONr_chiral_restr0.1240.21657
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213133
X-RAY DIFFRACTIONr_gen_planes_other0.0040.022529
X-RAY DIFFRACTIONr_nbd_refined0.2290.22507
X-RAY DIFFRACTIONr_nbd_other0.2630.212538
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.1070.26127
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.120.21016
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0690.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1390.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.330.273
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1390.234
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3631.56977
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.968211243
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.74434854
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.9554.54759
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: 1.5→1.54 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.161 73
Rwork0.127 9061
Refinement
*PLUS
Rfactor Rfree: 0.153 / Rfactor Rwork: 0.118
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.017
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.936

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