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- PDB-7nyt: Trichoderma reesei Cel7A E212Q mutant in complex with lactose. -

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Basic information

Entry
Database: PDB / ID: 7nyt
TitleTrichoderma reesei Cel7A E212Q mutant in complex with lactose.
ComponentsExoglucanase 1Cellulose 1,4-beta-cellobiosidase
KeywordsHYDROLASE / GLYCOSIDE HYDROLASE / CELLULASE / ENZYME KINETICS / NON-PRODUCTIVE BINDING
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
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 / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
beta-lactose / beta-D-glucopyranose / : / beta-D-galactopyranose / P-NITROPHENOL / Exoglucanase 1
Similarity search - Component
Biological speciesHypocrea jecorina (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.09 Å
AuthorsHaataja, T. / Sandgren, M. / Stahlberg, J.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Energy Agency42035-1 Sweden
CitationJournal: Febs J. / Year: 2023
Title: Enzyme kinetics by GH7 cellobiohydrolases on chromogenic substrates is dictated by non-productive binding: insights from crystal structures and MD simulation.
Authors: Haataja, T. / Gado, J.E. / Nutt, A. / Anderson, N.T. / Nilsson, M. / Momeni, M.H. / Isaksson, R. / Valjamae, P. / Johansson, G. / Payne, C.M. / Stahlberg, J.
History
DepositionMar 23, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 9, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 7, 2022Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.3Feb 1, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.4Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Exoglucanase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2498
Polymers46,0681
Non-polymers1,1817
Water10,070559
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2190 Å2
ΔGint4 kcal/mol
Surface area16160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.540, 82.210, 110.734
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-505-

CO

21A-612-

HOH

31A-1077-

HOH

41A-1090-

HOH

51A-1128-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Exoglucanase 1 / Cellulose 1,4-beta-cellobiosidase / 1 / 4-beta-cellobiohydrolase / Cellobiohydrolase 7A / Cel7A / Exocellobiohydrolase I / CBHI / Exoglucanase I


Mass: 46067.754 Da / Num. of mol.: 1 / Mutation: E212Q
Source method: isolated from a genetically manipulated source
Details: CATALYTIC MODULE, RESIDUES 18-451. / Source: (gene. exp.) Hypocrea jecorina (fungus) / Gene: cbh1 / Plasmid: PEM-F5 / Production host: Trichoderma reesei QM9414 (fungus) / Strain (production host): VTT-D-93201
References: UniProt: P62694, cellulose 1,4-beta-cellobiosidase (non-reducing end)

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Sugars , 4 types, 4 molecules

#2: Polysaccharide beta-D-galactopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: oligosaccharide / References: beta-lactose
DescriptorTypeProgram
DGalpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5][a2112h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{}}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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / 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.: 1 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
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
#5: Sugar ChemComp-GAL / beta-D-galactopyranose / beta-D-galactose / D-galactose / galactose / Galactose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGalpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactopyranoseCOMMON NAMEGMML 1.0
b-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 562 molecules

#6: Chemical ChemComp-NPO / P-NITROPHENOL / 4-Nitrophenol


Mass: 139.109 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5NO3 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Co
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 559 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.06 Å3/Da / Density % sol: 40.39 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 50 mM morpholinoethane sulphonic acid (pH 6.0), 21.25% polyethylene glycol 5000 monomethyl ether, 12.5% glycerol, 5 mM cobalt chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.979957 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 14, 2018 / Details: KB mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979957 Å / Relative weight: 1
ReflectionResolution: 1.09→41.77 Å / Num. obs: 137896 / % possible obs: 88.5 % / Redundancy: 6.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.032 / Rrim(I) all: 0.081 / Net I/σ(I): 13.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.09-1.132.70.6831696362540.70.4420.821.341.4
4.24-41.776.40.0351843328670.9990.0150.03844.299.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
REFMAC5.8.0258phasing
pointless1.11.21data processing
Aimless0.5.21data scaling
pointless1.10.18data processing
XDSJan 26, 2018data reduction
EDNAdata processing
MxCuBE3data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4C4C

4c4c


Resolution: 1.09→41.77 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.978 / SU B: 0.802 / SU ML: 0.017 / Cross valid method: THROUGHOUT / ESU R: 0.03 / ESU R Free: 0.03 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1425 6802 4.9 %RANDOM
Rwork0.1234 ---
obs0.1243 131092 88.31 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.3 Å / Solvent model: MASK
Displacement parametersBiso max: 52.31 Å2 / Biso mean: 11.287 Å2 / Biso min: 5.84 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å2-0 Å20 Å2
2--0.23 Å20 Å2
3---0.05 Å2
Refinement stepCycle: final / Resolution: 1.09→41.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3224 0 82 563 3869
Biso mean--14.3 22.55 -
Num. residues----434
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0183780
X-RAY DIFFRACTIONr_bond_other_d0.0010.0193172
X-RAY DIFFRACTIONr_angle_refined_deg1.4971.865216
X-RAY DIFFRACTIONr_angle_other_deg1.2012.7237431
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5665521
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.89125.119168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.02315538
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.267157
X-RAY DIFFRACTIONr_chiral_restr0.0970.2563
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025011
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02874
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.15736950
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.094→1.123 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.39 219 -
Rwork0.409 4008 -
all-4227 -
obs--36.86 %

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