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- PDB-6jtf: Complex of MarH and L-Trp -

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Basic information

Entry
Database: PDB / ID: 6jtf
TitleComplex of MarH and L-Trp
ComponentsCupin superfamily protein
KeywordsISOMERASE / Rmlc-like Cupins Superfamily / Complex / Epimerase
Function / homologyRmlC-like cupin domain superfamily / RmlC-like jelly roll fold / metal ion binding / TRYPTOPHAN / Cupin superfamily protein
Function and homology information
Biological speciesStreptomyces sp. B9173 (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsLiu, B. / Hu, K.F. / Zhang, R.D.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China21573258 China
National Natural Science Foundation of China31570720 China
CitationJournal: To Be Published
Title: Structural of MarH in complex with L-Trp
Authors: Liu, B. / Hu, K.F.
History
DepositionApr 10, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_database_status.status_code_nmr_data
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cupin superfamily protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5933
Polymers13,3231
Non-polymers2702
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6840 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Cupin superfamily protein


Mass: 13323.285 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. B9173 (bacteria) / Gene: marH / Production host: Escherichia coli (E. coli) / References: UniProt: X2D812
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-TRP / TRYPTOPHAN


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H12N2O2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D 1H-15N NOESY
121isotropic13D 1H-13C NOESY
131isotropic13D 13C/15N filtered 1H-13C NOESY
141isotropic13D 13C/15N filtered 1H-15N NOESY
1111isotropic12D 1H-15N HSQC
1101isotropic12D 1H-13C HSQC
191isotropic13D HNCA
181isotropic13D HN(CA)CB
171isotropic13D CBCA(CO)NH
161isotropic13D (H)CCH-TOCSY
151isotropic13D CCH-TOCSY
1121isotropic13D HBHA(CO)NH

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Sample preparation

DetailsType: solution
Contents: 0.5 mM [U-13C; U-15N] MarH, 2.0 mM L-Trp, 94% H2O/6% D2O
Details: The complex between MarH and L-Trp was prepared by mixing ~0.5mM 13C/15N-labeled MarH and 2mM unlabeled L-Trp in sodium phosphate buffer (50mM pH 7.0 at room temperature) containing sodium ...Details: The complex between MarH and L-Trp was prepared by mixing ~0.5mM 13C/15N-labeled MarH and 2mM unlabeled L-Trp in sodium phosphate buffer (50mM pH 7.0 at room temperature) containing sodium azide (0.01%) in 94%H2O/6%D2O.
Label: 13C,15N_MarH in complex with L-Trp / Solvent system: 94% H2O/6% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMMarH[U-13C; U-15N]1
2.0 mML-Trpnatural abundance1
Sample conditionsIonic strength: 50 mM / Label: conditions_1 / pH: 7.0 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardpeak picking
SparkyGoddardchemical shift assignment
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 5
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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