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

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Basic information

Entry
Database: PDB / ID: 1ocn
TitleMutant D416A of the CELLOBIOHYDROLASE CEL6A FROM HUMICOLA INSOLENS in complex with a cellobio-derived isofagomine at 1.3 angstrom resolution
ComponentsCELLOBIOHYDROLASE II
KeywordsHYDROLASE / CELLULOSE DEGRADATION / CELLOBIOHYDROLASE / CELLULASE / GLYCOSIDE HYDROLASE FAMILY 6
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
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 / 1, 4-beta cellobiohydrolase / CBM1 (carbohydrate binding type-1) domain signature. / Cellulose-binding domain, fungal / Cellulose-binding domain superfamily ...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 / 1, 4-beta cellobiohydrolase / 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
beta-D-glucopyranose / 5-HYDROXYMETHYL-3,4-DIHYDROXYPIPERIDINE / Exoglucanase-6A
Similarity search - Component
Biological speciesHUMICOLA INSOLENS (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.31 Å
AuthorsVarrot, A. / Macdonald, J. / Stick, R.V. / Pell, G. / Gilbert, H.J. / Davies, G.J.
CitationJournal: Chem.Commun.(Camb.) / Year: 2003
Title: Distortion of a Cellobio-Derived Isofagomine Highlights the Potential Conformational Itinerary of Inverting Beta-Glucosidases
Authors: Varrot, A. / Macdonald, J. / Stick, R.V. / Pell, G. / Gilbert, H.J. / Davies, G.J.
History
DepositionFeb 9, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 22, 2003Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2015Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 1.2Jul 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.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _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.ptnr2_auth_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_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.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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 1.3Dec 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 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

Downloads & links

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Assembly

Deposited unit
A: CELLOBIOHYDROLASE II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9278
Polymers39,9711
Non-polymers9567
Water9,386521
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)49.357, 69.842, 51.950
Angle α, β, γ (deg.)90.00, 113.52, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein CELLOBIOHYDROLASE II / CELLULASE / CEL6A


Mass: 39970.504 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)
Plasmid: UNDER CONTROL OF THE FUNGAL AMYLASE PROMOTER AND AMYLOGLUCOSIDASE TERMINATOR
Production host: ASPERGILLUS ORYZAE (mold)
References: UniProt: Q9C1S9*PLUS, cellulose 1,4-beta-cellobiosidase (non-reducing end)

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Sugars , 2 types, 3 molecules

#2: 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 / N-Acetylglucosamine


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: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose / Glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 525 molecules

#3: Chemical ChemComp-IFM / 5-HYDROXYMETHYL-3,4-DIHYDROXYPIPERIDINE / Afegostat / isofagomine / (3R,4R,5R)-5-(HYDROXYMETHYL)PIPERIDINE-3,4-DIOL / Afegostat


Mass: 147.172 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO3
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 521 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED MUTATION ASP 416 ALA CHAIN A
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. THIS PROTEIN IS CLOSELY RELATED TO AVICELASE 2 (SWISS-PROT ACCESSION ID:Q9C1S9) WITH WHICH IT HAS 96% SEQUENCE IDENTITY.

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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: MOLECULE A
Crystal growpH: 7.5
Details: PROTEIN WAS CONCENTRATED TO 10MG/ML IN WATER.CRYSTALLISATION IN 200MM CALCIUM ACETATE, 100MM HEPES PH 7.5 AND 21% POLYETHYLENE GLYCOL 5KMME.20 % GLYCEROL WAS ADDED FOR CRYOPROTECTION

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 15, 2002 / Details: TORROIDAL MIRROR
RadiationMonochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.31→15 Å / Num. obs: 77018 / % possible obs: 91.7 % / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 17.9
Reflection shellResolution: 1.31→1.33 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.275 / Mean I/σ(I) obs: 7.6 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BVW

2bvw


Resolution: 1.31→15 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.973 / SU B: 0.638 / SU ML: 0.028 / Cross valid method: THROUGHOUT / ESU R: 0.056 / ESU R Free: 0.051 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.162 3485 5 %RANDOM
Rwork0.13 ---
obs0.132 65959 90.2 %-
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: 12.29 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20 Å20.28 Å2
2---0.2 Å20 Å2
3---0.3 Å2
Refinement stepCycle: LAST / Resolution: 1.31→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2804 0 58 521 3383
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0212972
X-RAY DIFFRACTIONr_bond_other_d0.0080.022575
X-RAY DIFFRACTIONr_angle_refined_deg1.6861.9464072
X-RAY DIFFRACTIONr_angle_other_deg1.01935992
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3285366
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1120.2441
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023343
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02600
X-RAY DIFFRACTIONr_nbd_refined0.2590.2598
X-RAY DIFFRACTIONr_nbd_other0.2620.23037
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0850.21508
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1240.2256
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1430.26
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0770.24
X-RAY DIFFRACTIONr_symmetry_vdw_other0.330.253
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1470.241
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5011.51818
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.13322922
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.68631154
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.8424.51147
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: 1.31→1.35 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.198 271
Rwork0.146 5079

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