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- PDB-2mwj: Solution structure of Family 1 Carbohydrate-Binding Module from T... -

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Basic information

Entry
Database: PDB / ID: 2mwj
TitleSolution structure of Family 1 Carbohydrate-Binding Module from Trichoderma reesei Cel7A with O-mannose residues at Thr1 and Ser3
ComponentsExoglucanase 1Cellulose 1,4-beta-cellobiosidase
KeywordsHYDROLASE / O-glycosylation
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
alpha-D-mannopyranose / Exoglucanase 1
Similarity search - Component
Biological speciesTrichoderma reesei (fungus)
MethodSOLUTION NMR / simulated annealing, molecular dynamics
Model detailsfewest violations, model1
AuthorsHapps, R.M. / Chen, L. / Resch, M.G. / Davis, M.F. / Beckham, G.T. / Tan, Z. / Crowley, M.F.
CitationJournal: Febs J. / Year: 2015
Title: O-glycosylation effects on family 1 carbohydrate-binding module solution structures.
Authors: Happs, R.M. / Guan, X. / Resch, M.G. / Davis, M.F. / Beckham, G.T. / Tan, Z. / Crowley, M.F.
History
DepositionNov 12, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 2, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2015Group: Database references
Revision 1.2Sep 16, 2015Group: Database references
Revision 1.3Feb 3, 2016Group: Database references
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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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)4,1063
Polymers3,7461
Non-polymers3602
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 30molecular dynamics
RepresentativeModel #1fewest violations

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Components

#1: Protein/peptide Exoglucanase 1 / Cellulose 1,4-beta-cellobiosidase / 1 / 4-beta-cellobiohydrolase / Exocellobiohydrolase I / CBHI / Exoglucanase I


Mass: 3746.126 Da / Num. of mol.: 1 / Fragment: CBM1 DOMAIN RESIDUES 478-513; / Source method: obtained synthetically / Source: (synth.) Trichoderma reesei (fungus)
References: UniProt: P62694, cellulose 1,4-beta-cellobiosidase (non-reducing end)
#2: Sugar ChemComp-MAN / alpha-D-mannopyranose / Mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2
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

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H TOCSY
1212D DQF-COSY
1312D 1H-1H NOESY
1422D 1H-1H TOCSY
2512D DQF-COSY
2612D 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.7 mg CBM_2M, 90% H2O/10% D2O90% H2O/10% D2O
21.7 mg CBM_2M, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
1.7 mg/mLCBM_2M-11
1.7 mg/mLCBM_2M-22
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
130 5 ambient 300 K
230 5 ambient 288 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.2Bruker Biospincollection
TopSpin3.2Bruker Biospinprocessing
TopSpin3.2Bruker Biospindata analysis
TopSpin3.2Bruker Biospinchemical shift assignment
TopSpin3.2Bruker Biospinpeak picking
XPLOR-NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
CHARMM_DOMDECBrooks, Bruccoleri, Olafson, States, Swaminathan, and Karplusrefinement
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
Details: 30 conformers initially calculated were refined with 4 rounds of SA, Final selection of structures for submission was done based on the behavior of the models during the 200 ns trajectories: ...Details: 30 conformers initially calculated were refined with 4 rounds of SA, Final selection of structures for submission was done based on the behavior of the models during the 200 ns trajectories: only models which stayed within 3 RMSD of the starting structures were selected.
NMR constraintsNOE constraints total: 466 / NOE intraresidue total count: 217 / NOE long range total count: 147 / NOE sequential total count: 102 / Hydrogen bond constraints total count: 22 / Protein phi angle constraints total count: 22
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: molecular dynamics / Conformers calculated total number: 30 / Conformers submitted total number: 10 / Maximum torsion angle constraint violation: 5.7 ° / Maximum upper distance constraint violation: 0.5 Å

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