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- PDB-2bvk: Hyaluronan: the local solution conformation determined by NMR and... -

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Entry
Database: PDB / ID: 2bvk
TitleHyaluronan: the local solution conformation determined by NMR and computer modelling is close to a contracted left-handed four-fold helix
Components(0) x 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid
KeywordsCELL ADHESION / HYALURONAN / GLYCOSAMINOGLYCAN / CARBOHYDRATE / N-ACETYL- GLUCOSAMINE / GLUCURONIC ACID / EXTRACELLULAR MATRIX / SIMLUATION / AQUEOUS MOLECULAR DYNAMICS / HYALURONIC ACID / SODIUM HYALURONATE
MethodSOLUTION NMR / THEORETICAL MODEL / MOLECULAR DYNAMICS CONFIRMED BY BA CALCULATION OF EXPERIMENTAL NMR PA
Model details50 NANOSECOND FREE MOLECULAR DYNAMICS SIMULATION WITH EXPLIC INCLUSION OF WATER MOLECULES AND IONS ...50 NANOSECOND FREE MOLECULAR DYNAMICS SIMULATION WITH EXPLIC INCLUSION OF WATER MOLECULES AND IONS AND A FORCE-FIELD DERIVED FOR CARBOHYRDRATES. THE DERIVED PDB STRUCTURE WAS THE AVERAGE CONFORMAT OBSERVED DURING THE MOLECULAR DYNAMICS SIMULATION
Model type detailsMINIMIZED AVERAGE
AuthorsAlmond, A. / DeAngelis, P.L. / Blundell, C.D.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Hyaluronan: The Local Solution Conformation Determined by NMR and Computer Modeling is Close to a Contracted Left-Handed 4-Fold Helix.
Authors: Almond, A. / Deangelis, P.L. / Blundell, C.D.
History
DepositionJun 30, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 30, 2006Provider: repository / Type: Initial release
Revision 1.1Jun 2, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 3, 2018Group: Data collection / Category: pdbx_nmr_spectrometer
Item: _pdbx_nmr_spectrometer.manufacturer / _pdbx_nmr_spectrometer.model
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / 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 / struct_asym / struct_conn
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _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.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,5351
Polymers0
Non-polymers1,5351
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 250000AVERAGE CONFORMATION FROM A 50 NAN MOLECULAR DYNAMICS TRAJECTORY THAT EXPLICIT SOLVENT WATER AND CHARGE SODIUM IONS. THE 1-3 AND 1-4 LINKA FIXED AT (50.78, 9.78) AND (47.98, RESPECTIVELY USING THE H1-C1-OX-HX NOMENCLATURE
Representative

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Components

#1: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid


Type: oligosaccharide / Mass: 1535.282 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpAb1-3DGlcpNAcb1-4DGlcpAb1-3DGlcpNAcb1-4DGlcpAb1-3DGlcpNAcb1-4DGlcpAb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,8,7/[a2122A-1b_1-5][a2122h-1b_1-5_2*NCC/3=O]/1-2-1-2-1-2-1-2/a4-b1_b3-c1_c4-d1_d3-e1_e4-f1_f3-g1_g4-h1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpA]{[(4+1)][b-D-GlcpNAc]{[(3+1)][b-D-GlcpA]{[(4+1)][b-D-GlcpNAc]{[(3+1)][b-D-GlcpA]{[(4+1)][b-D-GlcpNAc]{[(3+1)][b-D-GlcpA]{[(4+1)][b-D-GlcpNAc]{}}}}}}}}LINUCSPDB-CARE

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Experimental details

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Experiment

Experiment
Method
SOLUTION NMR
THEORETICAL MODEL
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111[1H-15N] HSQC
121[1H-1H-15N] NOESY-H
NMR detailsText: IONS AND WATER WERE REMOVED TO GENERATE ATOMIC COORDINATES

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Sample preparation

Sample conditionspH: 6.0 / Temperature: 298 K

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Data collection

NMR spectrometerType: GE OMEGA / Manufacturer: GE / Model: OMEGA / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
CHARMMBROOKS,BRUCCOLERI,OLAFSEN,STATES, SWAMINATHAN, KARPLUSrefinement
CHARMMstructure solution
RefinementMethod: MOLECULAR DYNAMICS CONFIRMED BY BA CALCULATION OF EXPERIMENTAL NMR PA
Software ordinal: 1
NMR ensembleConformer selection criteria: AVERAGE CONFORMATION FROM A 50 NAN MOLECULAR DYNAMICS TRAJECTORY THAT EXPLICIT SOLVENT WATER AND CHARGE SODIUM IONS. THE 1-3 AND 1-4 LINKA FIXED AT (50.78, 9.78) AND (47. ...Conformer selection criteria: AVERAGE CONFORMATION FROM A 50 NAN MOLECULAR DYNAMICS TRAJECTORY THAT EXPLICIT SOLVENT WATER AND CHARGE SODIUM IONS. THE 1-3 AND 1-4 LINKA FIXED AT (50.78, 9.78) AND (47.98, RESPECTIVELY USING THE H1-C1-OX-HX NOMENCLATURE
Conformers calculated total number: 250000 / Conformers submitted total number: 1

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