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- PDB-1gz1: Mutant D416A of the CELLOBIOHYDROLASE CEL6A FROM HUMICOLA INSOLEN... -

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Basic information

Entry
Database: PDB / ID: 1gz1
TitleMutant D416A of the CELLOBIOHYDROLASE CEL6A FROM HUMICOLA INSOLENS in complex with methyl-cellobiosyl-4-deoxy-4-thio-beta-D-cellobioside
ComponentsCELLOBIOHYDROLASE II
KeywordsHYDROLASE / CELLULOSE DEGRADATION / CELLOBIOHYDROLASE / CELLULASE / GLYCOSIDE HYDROLASE FAMILY 6 / THIOOLIGOSACCHARIDE
Function / homology
Function and homology information


cellulose 1,4-beta-cellobiosidase (non-reducing end) / cellulose 1,4-beta-cellobiosidase activity / cellulose binding / cellulose catabolic process / extracellular region
Similarity search - Function
1, 4-beta cellobiohydrolase / Glycosyl hydrolases family 6 signature 2. / Glycosyl hydrolases family 6 signature 1. / Glycoside hydrolase, family 6, conserved site / 1, 4-beta cellobiohydrolase / 1, 4-beta cellobiohydrolase superfamily / Glycosyl hydrolases family 6 / CBM1 (carbohydrate binding type-1) domain signature. / Cellulose-binding domain, fungal / Cellulose-binding domain superfamily ...1, 4-beta cellobiohydrolase / Glycosyl hydrolases family 6 signature 2. / Glycosyl hydrolases family 6 signature 1. / Glycoside hydrolase, family 6, conserved site / 1, 4-beta cellobiohydrolase / 1, 4-beta cellobiohydrolase superfamily / Glycosyl hydrolases family 6 / CBM1 (carbohydrate binding type-1) domain signature. / Cellulose-binding domain, fungal / Cellulose-binding domain superfamily / Fungal cellulose binding domain / CBM1 (carbohydrate binding type-1) domain profile. / Fungal-type cellulose-binding domain / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesHUMICOLA INSOLENS (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsVarrot, A. / Frandsen, T. / Driguez, H. / Davies, G.J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Structure of the Humicola Insolens Cellobiohydrolase Cel6A D416A Mutant in Complex with a Non-Hydrolysable Substrate Analogue, Methyl Cellobiosyl-4-Thio-Beta-Cellobioside, at 1.9 A
Authors: Varrot, A. / Frandsen, T. / Driguez, H. / Davies, G.J.
History
DepositionMay 13, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 12, 2003Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2011Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / 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.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CELLOBIOHYDROLASE II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8915
Polymers39,9271
Non-polymers9644
Water4,864270
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.257, 68.380, 55.180
Angle α, β, γ (deg.)90.00, 112.39, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein CELLOBIOHYDROLASE II / CELLULASE / CEL6A


Mass: 39927.477 Da / Num. of mol.: 1 / Fragment: CATALYTIC CORE DOMAIN, RESIDUES 89-450 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: N-LINKED N-ACETYLGLUCOSAMINE ON RESIDUE ASN 141 / Source: (gene. exp.) HUMICOLA INSOLENS (fungus)
Description: UNDER CONTROL OF THE FUNGAL AMYLASEURCE 6 PROMOTER AND AMYLOGLUCOSIDASE TERMINATOR
Production host: ASPERGILLUS ORYZAE (mold)
References: UniProt: Q9C1S9*PLUS, cellulose 1,4-beta-cellobiosidase (non-reducing end)
#2: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-4-thio-beta-D-glucopyranose-(1-4)-methyl beta- ...beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-4-thio-beta-D-glucopyranose-(1-4)-methyl beta-D-glucopyranoside


Type: oligosaccharide / Mass: 696.669 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,4,3/[a2122h-1b_1-5_1*OC][a2122h-1b_1-5]/1-2-2-2/a4-b1_b4-c1*S*_c4-d1WURCSPDB2Glycan 1.1.0
[][methyl]{[(1+1)][b-D-Glcp]{[(4+1)][b-D-Glcp4SH]{[(4+S)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}}}LINUCSPDB-CARE
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED MUTATION ASP 416 ALA
Has protein modificationY
Sequence detailsTHIS MUTANT HAS BEEN PRODUCED BY SITE-DIRECTED MUTAGENESIS. THE CLONING WAS PERFORMED SUCH HAS ONLY ...THIS MUTANT HAS BEEN PRODUCED BY SITE-DIRECTED MUTAGENESIS. THE CLONING WAS PERFORMED SUCH HAS ONLY THE PRO-SEQUENCE AND THE CATALYTIC DOMAIN WERE EXPRESSED. THE CELLULOSE BINDING DOMAIN HAS BEEN REMOVED. THE CONSTRUCT IS POST-TRANSLATIONALLY CLEAVED TO YIELD TO A MATURE PROTEIN OF 450 RESIDUES WHICH COMMENCES AT RESIDUE TYR 89.

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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: 2.01 Å3/Da / Density % sol: 42 %
Description: SEARCH MODEL WAS THE D405N MUTANT OF HUMICOLA INSOLENS CELLOBIOHYDROLASE CEL6A IN COMPLEX WITH CELLOTRIOSE
Crystal growpH: 4.6
Details: PROTEIN WAS CONCENTRATED TO 20 MG/ML IN WATER. CRYSTALLISATION IN 200MM MAGNESIUM ACETATE IN 100MM SODIUM ACETATE BUFFER AT PH 4.6. PRECIPITANT WAS 20%. POLYETHYLENE GLYCOL 5500.
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
20-500 mM1dropgradientNaCl
37 mg/mlprotein1drop
420 %PEG5000 MME1reservoir
5100 mM1reservoirpH4.6NaOAc
6200 mM1reservoirMgOAc
720 %glycerol1reservoir
1Tris-HCl1droppH8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 15, 2001 / Details: TORROIDAL MIRROR
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: 1.9→30 Å / Num. obs: 26197 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 21.2
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 4.6 / % possible all: 98
Reflection
*PLUS
Lowest resolution: 30 Å / Redundancy: 3.8 %
Reflection shell
*PLUS
% possible obs: 98 % / Mean I/σ(I) obs: 4.6

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→30 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.935 / SU B: 5.047 / SU ML: 0.152 / Cross valid method: THROUGHOUT / ESU R: 0.165 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.211 1324 5.1 %RANDOM
Rwork0.166 ---
obs0.168 24685 99.2 %-
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: 17.18 Å2
Baniso -1Baniso -2Baniso -3
1--0.8 Å20 Å2-1.06 Å2
2---0.71 Å20 Å2
3---0.7 Å2
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2821 0 62 270 3153
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0212977
X-RAY DIFFRACTIONr_bond_other_d0.0020.022555
X-RAY DIFFRACTIONr_angle_refined_deg1.5731.9474074
X-RAY DIFFRACTIONr_angle_other_deg2.00935942
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0013361
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.75715471
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1050.2441
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023340
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02603
X-RAY DIFFRACTIONr_nbd_refined0.2440.3672
X-RAY DIFFRACTIONr_nbd_other0.2160.32585
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.6550.52
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.5259
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.10.53
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3580.35
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3010.329
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2240.59
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8371.51812
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.46622909
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.20631165
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.5084.51165
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
Rfree0.245 90
Rwork0.194 1803
Refinement
*PLUS
Lowest resolution: 30 Å / Rfactor Rfree: 0.211 / Rfactor Rwork: 0.166
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.014
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.57

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