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- PDB-2m5h: NMR structure note: solution structure of monomeric human FAM96A -

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Basic information

Entry
Database: PDB / ID: 2m5h
TitleNMR structure note: solution structure of monomeric human FAM96A
ComponentsMIP18 family protein FAM96A
KeywordsIMMUNE SYSTEM / FAM96A / DUF59 / 3D Domain Swapping
Function / homology
Function and homology information


cytosolic [4Fe-4S] assembly targeting complex / protein maturation / chromosome segregation / nucleoplasm / metal ion binding / cytosol
Similarity search - Function
MIP18 family / MIP18 family-like / Iron-sulfur cluster assembly protein / Fe-S cluster assembly domain superfamily
Similarity search - Domain/homology
Cytosolic iron-sulfur assembly component 2A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
Model detailslowest energy, model1
AuthorsOuyang, B. / Xia, B.
CitationJournal: J.Biomol.Nmr / Year: 2013
Title: Solution structure of monomeric human FAM96A
Authors: Ouyang, B. / Wang, L. / Wan, S. / Luo, Y. / Wang, L. / Lin, J. / Xia, B.
History
DepositionFeb 25, 2013Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Sep 25, 2013Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MIP18 family protein FAM96A


Theoretical massNumber of molelcules
Total (without water)16,2551
Polymers16,2551
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein MIP18 family protein FAM96A


Mass: 16254.600 Da / Num. of mol.: 1 / Fragment: UNP residues 28-160
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FAM96A / Production host: Escherichia coli (E. coli) / Strain (production host): K12 / Variant (production host): BL21(DE3) / References: UniProt: Q9H5X1

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D 1H-15N NOESY
1313D 1H-13C NOESY
1413D HN(CA)CB
1513D CBCA(CO)NH
1613D HBHA(CO)NH
1713D (H)CCH-COSY
1813D (H)CCH-TOCSY

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Sample preparation

DetailsContents: 0.4 mM [U-100% 13C; U-100% 15N] Fam96a-1, 50 mM sodium phosphate-2, 50 mM sodium chloride-3, 1 mM EDTA-4, 50 mM DTT-5, 50 mM ARG-6, 50 mM GLU-7, 5 % D2O-8, 95 % H2O-9, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.4 mMFam96a-1[U-100% 13C; U-100% 15N]1
50 mMsodium phosphate-21
50 mMsodium chloride-31
1 mMEDTA-41
50 mMDTT-51
50 mMARG-61
50 mMGLU-71
5 %D2O-81
95 %H2O-91
Sample conditionsIonic strength: 100 / pH: 7 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE7002
Bruker AvanceBrukerAVANCE6003

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Processing

NMR software
NameVersionDeveloperClassification
Amber9Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
DYANA2.1Guntert, Braun and Wuthrichrefinement
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
SANEDuggan, Legge, Dyson & Wrightchemical shift assignment
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 4225 / NOE intraresidue total count: 1723 / NOE long range total count: 366 / NOE medium range total count: 300 / NOE sequential total count: 636 / Hydrogen bond constraints total count: 50 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 523 / Protein phi angle constraints total count: 80 / Protein psi angle constraints total count: 79
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum torsion angle constraint violation: 0 ° / Maximum upper distance constraint violation: 0.194 Å / Representative conformer: 1

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