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- PDB-1z3t: Structure of Phanerochaete chrysosporium cellobiohydrolase Cel7D ... -

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Basic information

Entry
Database: PDB / ID: 1z3t
TitleStructure of Phanerochaete chrysosporium cellobiohydrolase Cel7D (CBH58) in complex with cellobiose
Componentscellulase
KeywordsHYDROLASE / Beta sandwich
Function / homology
Function and homology information


Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / cellulose binding / cellulose catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / extracellular region
Similarity search - Function
1,4-Beta-D-Glucan Cellobiohydrolase I; Chain A / Glycoside hydrolase, family 7, domain / Glycoside hydrolase, family 7 / Glycoside hydrolase family 7, catalytic domain superfamily / Glycosyl hydrolase family 7 / 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. ...1,4-Beta-D-Glucan Cellobiohydrolase I; Chain A / Glycoside hydrolase, family 7, domain / Glycoside hydrolase, family 7 / Glycoside hydrolase family 7, catalytic domain superfamily / Glycosyl hydrolase family 7 / 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 / Distorted Sandwich / Concanavalin A-like lectin/glucanase domain superfamily / Mainly Beta
Similarity search - Domain/homology
beta-cellobiose / Glucanase
Similarity search - Component
Biological speciesPhanerochaete chrysosporium (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsUbhayasekera, W. / Stahlberg, J. / Mowbray, S.L.
Citation
Journal: Febs J. / Year: 2005
Title: Structures of Phanerochaete chrysosporium Cel7D in complex with product and inhibitors
Authors: Ubhayasekera, W. / Munoz, I.G. / Vasella, A. / Stahlberg, J. / Mowbray, S.L.
#1: Journal: J.Mol.Biol. / Year: 2001
Title: Family 7 cellobiohydrolases from Phanerochaete chrysosporium: crystal structure of the catalytic module of Cel7D (CBH58) at 1.32 A resolution and homology models of the isozymes
Authors: Munoz, I.G. / Ubhayasekera, W. / Henriksson, H. / Szabo, I. / Pettersson, G. / Johansson, G. / Mowbray, S.L. / Stahlberg, J.
#2: Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2003
Title: The catalytic module of Cel7D from Phanerochaete chrysosporium as a chiral selector: structural studies of its complex with the beta blocker (R)-propranolol
Authors: Munoz, I.G. / Mowbray, S.L. / Stahlberg, J.
History
DepositionMar 14, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 26, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Dec 25, 2019Group: Database references / Derived calculations / Polymer sequence
Category: entity_poly / pdbx_struct_mod_residue ...entity_poly / pdbx_struct_mod_residue / struct_conn / struct_ref_seq_dif
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag
Revision 3.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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 / 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_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Oct 25, 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 3.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: cellulase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3413
Polymers45,7771
Non-polymers5642
Water1,892105
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.414, 46.842, 99.488
Angle α, β, γ (deg.)90.00, 102.99, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein cellulase / Cellobiohydrolase


Mass: 45777.141 Da / Num. of mol.: 1 / Fragment: Catalytic module / Source method: isolated from a natural source / Source: (natural) Phanerochaete chrysosporium (fungus) / Strain: K3
References: UniProt: Q7LIJ0, cellulose 1,4-beta-cellobiosidase (non-reducing end)
#2: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-cellobiose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-cellobiose
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.2 Å3/Da / Density % sol: 42.8 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7
Details: TRIS-HCl, calcium chloride, PEG 5000, glycerol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.937 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 7, 1999
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.937 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 43328 / Num. obs: 43328 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 11
Reflection shellResolution: 1.7→1.73 Å / Rmerge(I) obs: 0.321 / Mean I/σ(I) obs: 5.8 / Num. unique all: 2867 / % possible all: 93.1

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1GPI

1gpi


Resolution: 1.7→40 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.956 / SU B: 5.88 / SU ML: 0.101 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.191 / ESU R Free: 0.104 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19866 2541 5.9 %RANDOM
Rwork0.15879 ---
all0.172 40782 --
obs0.16125 40782 100 %-
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: 20.816 Å2
Baniso -1Baniso -2Baniso -3
1-2.53 Å20 Å2-0.74 Å2
2---1.17 Å20 Å2
3----1.7 Å2
Refinement stepCycle: LAST / Resolution: 1.7→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3198 0 37 105 3340
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0213311
X-RAY DIFFRACTIONr_bond_other_d0.0010.022740
X-RAY DIFFRACTIONr_angle_refined_deg2.0621.9484512
X-RAY DIFFRACTIONr_angle_other_deg0.98336438
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2993430
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.15215523
X-RAY DIFFRACTIONr_chiral_restr0.1350.2505
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023776
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02628
X-RAY DIFFRACTIONr_nbd_refined0.350.3675
X-RAY DIFFRACTIONr_nbd_other0.2110.32580
X-RAY DIFFRACTIONr_nbtor_other0.6940.51
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3620.5414
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0530.52
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3570.313
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3010.320
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.6060.522
X-RAY DIFFRACTIONr_mcbond_it2.1251.52123
X-RAY DIFFRACTIONr_mcangle_it3.20423403
X-RAY DIFFRACTIONr_scbond_it4.35731188
X-RAY DIFFRACTIONr_scangle_it6.124.51109
X-RAY DIFFRACTIONr_rigid_bond_restr2.59923311
X-RAY DIFFRACTIONr_sphericity_free6.6342447
X-RAY DIFFRACTIONr_sphericity_bonded4.67723235
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.251 178
Rwork0.153 2867
obs-2867

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