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- PDB-1hze: SOLUTION STRUCTURE OF THE N-TERMINAL DOMAIN OF RIBOFLAVIN SYNTHAS... -

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Basic information

Entry
Database: PDB / ID: 1hze
TitleSOLUTION STRUCTURE OF THE N-TERMINAL DOMAIN OF RIBOFLAVIN SYNTHASE FROM E. COLI
ComponentsRIBOFLAVIN SYNTHASE ALPHA CHAIN
KeywordsTRANSFERASE / greek-key-barrel
Function / homology
Function and homology information


riboflavin synthase / riboflavin synthase activity / riboflavin biosynthetic process / cytosol
Similarity search - Function
Lumazine-binding protein / Lumazine-binding domain / Lumazine binding domain / Riboflavin synthase alpha chain lumazine-binding repeat profile. / Elongation Factor Tu (Ef-tu); domain 3 - #20 / ATP synthase subunit alpha, N-terminal domain-like superfamily / Elongation Factor Tu (Ef-tu); domain 3 / Riboflavin synthase-like beta-barrel / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
RIBOFLAVIN / Riboflavin synthase / Riboflavin synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / simulated annealing
Model type detailsminimized average
AuthorsTruffault, V. / Coles, M. / Diercks, T. / Abelmann, K. / Eberhardt, S. / Luettgen, H. / Bacher, A. / Kessler, H.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: The solution structure of the N-terminal domain of riboflavin synthase.
Authors: Truffault, V. / Coles, M. / Diercks, T. / Abelmann, K. / Eberhardt, S. / Luttgen, H. / Bacher, A. / Kessler, H.
History
DepositionJan 24, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RIBOFLAVIN SYNTHASE ALPHA CHAIN
B: RIBOFLAVIN SYNTHASE ALPHA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9054
Polymers21,1522
Non-polymers7532
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
Representativeminimized average structure

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Components

#1: Protein RIBOFLAVIN SYNTHASE ALPHA CHAIN


Mass: 10575.960 Da / Num. of mol.: 2 / Fragment: N-TERMINAL DOMAIN, RESIDUES 1-97
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
References: UniProt: P29015, UniProt: P0AFU8*PLUS, riboflavin synthase
#2: Chemical ChemComp-RBF / RIBOFLAVIN / RIBOFLAVINE / VITAMIN B2


Mass: 376.364 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H20N4O6

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
121NCH-NOESY
131CCH-NOESY
141CNH-NOESY
1523D 15N-separated NOESY
162NNH-NOESY
1732D 12C-filtered, 13C edited NOESY
182HNHA

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM U-15N,13C ; excess riboflavin90% H2O, 10% D2O 50 mM phosphate buffer 50 mM HCl
21 mM U-15N ; excess riboflavin90% H2O, 10% D2O 50 mM phosphate buffer 50 mM HCl
31 mM U-15N ; excess U-15N,13C riboflavin 50 mM phosphate buffer 50 mM HCl90% H2O, 10% D2O 50 mM phosphate buffer 50 mM HCl
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
150 mM 7.3ambient 300 K
250 mM 7.3ambient 300 K
350 mM 7.3ambient 300 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX6001
Bruker DMXBrukerDMX7502

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Processing

NMR software
NameClassification
XwinNMRcollection
AURELIAdata analysis
X-PLORstructure solution
X-PLORrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Structures based on 2569 NOE restraints (353*2 intrares., 365*2 sequential, 159*2 medium-range, 372*2 long-range, 71 intermolecular) 56*2 dihedral restraints, 42*2 h-bonds
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformers submitted total number: 1

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