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- PDB-1qk2: WILD TYPE CEL6A WITH A NON-HYDROLYSABLE CELLOTETRAOSE -

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Basic information

Entry
Database: PDB / ID: 1qk2
TitleWILD TYPE CEL6A WITH A NON-HYDROLYSABLE CELLOTETRAOSE
ComponentsCELLOBIOHYDROLASE CEL6A (FORMERLY CALLED CBH II)
KeywordsHYDROLASE / GLYCOSIDASE / GLYCOPROTEIN
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 / identical protein binding
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
alpha-D-mannopyranose / Exoglucanase 2
Similarity search - Component
Biological speciesTRICHODERMA REESEI (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsZou, J.-Y. / Jones, T.A.
Citation
Journal: Structure / Year: 1999
Title: Crystallographic Evidence for Substrate Ring Distortion and Protein Conformational Changes During Catalysis in Cellobiohydrolase Cel6A from Trichoderma Reesei
Authors: Zou, J.-Y. / Kleywegt, G.J. / Stahlberg, J. / Driguez, H. / Nerinckx, W. / Claeyssens, M. / Koivula, A. / Teeri, T.T. / Jones, T.A.
#1: Journal: Science / Year: 1990
Title: Three-Dimensional Structure of Cellobiohydrolase II from Trichoderma Reesei
Authors: Rouvinen, J. / Bergfors, T. / Teeri, T. / Knowles, J.K. / Jones, T.A.
History
DepositionJul 9, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 18, 1999Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2016Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Version format compliance
Revision 1.2Oct 23, 2019Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Derived calculations / Experimental preparation / Other / Structure summary
Category: chem_comp / exptl_crystal_grow ...chem_comp / exptl_crystal_grow / pdbx_database_status / pdbx_entity_instance_feature / pdbx_entry_details / struct_conn
Item: _chem_comp.type / _exptl_crystal_grow.method ..._chem_comp.type / _exptl_crystal_grow.method / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_ligand_of_interest / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / 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_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_chiral / 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_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _struct_conn.pdbx_dist_value / _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_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
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 / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CELLOBIOHYDROLASE CEL6A (FORMERLY CALLED CBH II)
B: CELLOBIOHYDROLASE CEL6A (FORMERLY CALLED CBH II)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,62322
Polymers77,8222
Non-polymers4,80020
Water9,818545
1
A: CELLOBIOHYDROLASE CEL6A (FORMERLY CALLED CBH II)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,31111
Polymers38,9111
Non-polymers2,40010
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: CELLOBIOHYDROLASE CEL6A (FORMERLY CALLED CBH II)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,31111
Polymers38,9111
Non-polymers2,40010
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)48.830, 74.700, 91.840
Angle α, β, γ (deg.)90.00, 104.12, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.994054, -0.099704, -0.04377), (0.100364, 0.994864, 0.013134), (0.042236, -0.017449, 0.998955)
Vector: -25.794, -42.109, -43.941)

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Components

#1: Protein CELLOBIOHYDROLASE CEL6A (FORMERLY CALLED CBH II) / CEL6A


Mass: 38911.164 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, RESIDUES 85-447
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TRICHODERMA REESEI (fungus) / Gene: CBH2 / Production host: TRICHODERMA REESEI (fungus)
References: UniProt: P07987, cellulose 1,4-beta-cellobiosidase (non-reducing end)
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-4-thio-beta-D-glucopyranose-(1-4)-methyl ...alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-4-thio-beta-D-glucopyranose-(1-4)-methyl beta-D-glucopyranoside


Type: oligosaccharide / Mass: 696.669 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/3,4,3/[a2122h-1b_1-5_1*OC][a2122h-1b_1-5][a2122h-1a_1-5]/1-2-3-3/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.: 4
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-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 545 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY
Sequence detailsA SWS P07987 1 - 108 NOT IN ATOMS LIST B SWS P07987 1 - 108 NOT IN ATOMS LIST

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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: 2.09 Å3/Da / Density % sol: 41.07 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6
Details: 20% PEG6000, 20MM MES BUFFER PH6.0, 10MM COCL2., pH 6.00
Crystal grow
*PLUS
Method: unknown / Details: used to seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 %PEG600011can be replaced by mPEG5000
220 mMMES11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Jun 10, 1996 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→39.8 Å / Num. obs: 41716 / % possible obs: 94.9 % / Redundancy: 2.9 % / Biso Wilson estimate: 17.1 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 15.1
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.266 / Mean I/σ(I) obs: 3.8 / % possible all: 79.2
Reflection shell
*PLUS
% possible obs: 79.2 %

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Processing

Software
NameVersionClassification
CNS0.5refinement
DENZOdata reduction
SCALEPACKdata scaling
CNS0.5phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→20 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1626766.68 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: BULK SOLVENT MODEL USED THE CATALYTIC CORE STARTS AT RESIDUE 83.
RfactorNum. reflection% reflectionSelection details
Rfree0.222 1278 3.1 %RANDOM
Rwork0.189 ---
obs0.189 41476 95.6 %-
Solvent computationSolvent model: FLAT MODEL / ksol: 0.361336 e/Å3
Displacement parametersBiso mean: 17.5 Å2
Baniso -1Baniso -2Baniso -3
1--1.33 Å20 Å21.08 Å2
2---1.71 Å20 Å2
3---3.04 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.21 Å
Luzzati d res low-20 Å
Luzzati sigma a0.23 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5494 0 302 545 6341
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.731.5
X-RAY DIFFRACTIONc_mcangle_it1.212
X-RAY DIFFRACTIONc_scbond_it1.062
X-RAY DIFFRACTIONc_scangle_it1.582.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.276 182 2.8 %
Rwork0.229 6323 -
obs--89.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.78

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