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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 N-ACETYL-D-GLUCOSAMINE
  • (1) x 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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jun 30, 2005 / Release: Oct 30, 2006
RevisionDateData content typeGroupCategoryItemProviderType
1.0Oct 30, 2006Structure modelrepositoryInitial release
1.1Jun 2, 2011Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance
1.3Oct 3, 2018Structure modelData collectionpdbx_nmr_spectrometer_pdbx_nmr_spectrometer.manufacturer / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,6618
Polyers0
Non-polymers1,6618
Water0
1


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: Chemical
ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


Mass: 221.208 Da / Num. of mol.: 4 / Formula: C8H15NO6 / N-Acetylglucosamine
#2: Chemical
ChemComp-BDP / BETA-D-GLUCOPYRANURONIC ACID / D-GLUCURONIC ACID


Mass: 194.139 Da / Num. of mol.: 4 / Formula: C6H10O7 / Glucuronic acid

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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 (47.98, RESPECTIVELY USING THE H1-C1-OX-HX NOMENCLATURE
Conformers calculated total number: 250000 / Conformers submitted total number: 1

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