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- PDB-3n9k: F229A/E292S Double Mutant of Exo-beta-1,3-glucanase from Candida ... -

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Basic information

Entry
Database: PDB / ID: 3n9k
TitleF229A/E292S Double Mutant of Exo-beta-1,3-glucanase from Candida albicans in Complex with Laminaritriose at 1.7 A
ComponentsGlucan 1,3-beta-glucosidase
KeywordsHYDROLASE / Aromatic entranceway/clamp / Exoglucanase / Glycoside hydrolase / Protein-carbohydrate interaction / Site-directed mutagenesis / Laminaritriose
Function / homology
Function and homology information


single-species biofilm formation in or on host organism / glucan metabolic process / glucan 1,3-beta-glucosidase / single-species biofilm formation on inanimate substrate / adhesion of symbiont to host cell / glucan exo-1,3-beta-glucosidase activity / fungal-type cell wall organization / glucan catabolic process / Transferases; Glycosyltransferases; Hexosyltransferases / cell-substrate adhesion ...single-species biofilm formation in or on host organism / glucan metabolic process / glucan 1,3-beta-glucosidase / single-species biofilm formation on inanimate substrate / adhesion of symbiont to host cell / glucan exo-1,3-beta-glucosidase activity / fungal-type cell wall organization / glucan catabolic process / Transferases; Glycosyltransferases; Hexosyltransferases / cell-substrate adhesion / cell adhesion molecule binding / extracellular vesicle / transferase activity / cell surface / extracellular region
Similarity search - Function
: / Glycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
beta-laminaribiose / Glucan 1,3-beta-glucosidase
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsNakatani, Y. / Cutfield, S.M. / Cutfield, J.F.
CitationJournal: Febs J. / Year: 2010
Title: Carbohydrate binding sites in Candida albicans exo-beta-1,3-glucanase and the role of the Phe-Phe 'clamp' at the active site entrance
Authors: Patrick, W.M. / Nakatani, Y. / Cutfield, S.M. / Sharpe, M.L. / Ramsay, R.J. / Cutfield, J.F.
History
DepositionMay 30, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 1, 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
Revision 2.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glucan 1,3-beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5044
Polymers45,6171
Non-polymers8873
Water7,278404
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.725, 64.397, 94.866
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 Glucan 1,3-beta-glucosidase / Exo-1 / 3-beta-glucanase


Mass: 45617.219 Da / Num. of mol.: 1 / Mutation: F229A,E292S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans (yeast) / Strain: ATCC 10261 / Gene: XOG / Plasmid: PPIC9K / Production host: Pichia pastoris (fungus) / Strain (production host): KM71 / References: UniProt: P29717, glucan 1,3-beta-glucosidase
#2: Polysaccharide beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-3DGlcpb1-3DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1b_1-5]/1-1-1/a3-b1_b3-c1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(3+1)][b-D-Glcp]{[(3+1)][b-D-Glcp]{}}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-glucopyranose-(1-3)-beta-D-glucopyranose / beta-laminaribiose


Type: oligosaccharide, Oligosaccharide / Class: Antimicrobial / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-laminaribiose
DescriptorTypeProgram
DGlcpb1-3DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5]/1-1/a3-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(3+1)][b-D-Glcp]{}}LINUCSPDB-CARE
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 404 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsDUE TO ALTERNATIVE CODON USAGE BY CANDIDA ALBICANS, THIS POSITION IS A SER WHEN FROM NATURAL ...DUE TO ALTERNATIVE CODON USAGE BY CANDIDA ALBICANS, THIS POSITION IS A SER WHEN FROM NATURAL SOURCES, AND A LEU WHEN EXPRESSED IN SACCHAROMYCES CEREVISIAE.

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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: 1.97 Å3/Da / Density % sol: 37.44 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 0.1M HEPES-KOH, 0.2M CACL2, 19% PEG 8000, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 10, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→38.19 Å / Num. all: 40339 / Num. obs: 40247 / % possible obs: 99.8 % / Redundancy: 4.2 % / Biso Wilson estimate: 17.8 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 14.1
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.636 / Mean I/σ(I) obs: 2.2 / Num. unique all: 5803 / Rsym value: 0.636 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
REFMAC5.5.0088refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CZ1

1cz1


Resolution: 1.7→38.19 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.077 / SU ML: 0.068 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19681 2014 5 %RANDOM
Rwork0.15168 ---
obs0.15397 38177 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.546 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å20 Å2
2--0.08 Å20 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.7→38.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3205 0 58 404 3667
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0213430
X-RAY DIFFRACTIONr_angle_refined_deg1.9431.9184709
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4265413
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.50825.052192
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.9715499
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0421513
X-RAY DIFFRACTIONr_chiral_restr0.1430.2490
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0212735
X-RAY DIFFRACTIONr_mcbond_it1.2191.51981
X-RAY DIFFRACTIONr_mcangle_it1.91123196
X-RAY DIFFRACTIONr_scbond_it2.97931449
X-RAY DIFFRACTIONr_scangle_it4.3824.51503
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 141 -
Rwork0.249 2792 -
obs--99.93 %

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