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- PDB-2lqt: Solution structure of CHCHD7 -

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Basic information

Entry
Database: PDB / ID: 2lqt
TitleSolution structure of CHCHD7
ComponentsCoiled-coil-helix-coiled-coil-helix domain-containing protein 7
KeywordsUNKNOWN FUNCTION / CHCH domain / mitochondrial import / alpha-hairpin / Mia40-dependent disulfide relay system
Function / homologyCysteine alpha-hairpin motif superfamily / Mitochondrial protein import / Coiled coil-helix-coiled coil-helix (CHCH) domain profile. / mitochondrial intermembrane space / Coiled-coil-helix-coiled-coil-helix domain-containing protein 7
Function and homology information
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
Model detailsfewest violations, model 1
AuthorsWinkelmann, J. / Ciofi-Baffoni, S. / Banci, L. / Bertini, I.
CitationJournal: J.Struct.Biol. / Year: 2012
Title: Structural characterization of CHCHD5 and CHCHD7: Two atypical human twin CX(9)C proteins.
Authors: Banci, L. / Bertini, I. / Ciofi-Baffoni, S. / Jaiswal, D. / Neri, S. / Peruzzini, R. / Winkelmann, J.
History
DepositionMar 14, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 24, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Coiled-coil-helix-coiled-coil-helix domain-containing protein 7


Theoretical massNumber of molelcules
Total (without water)10,1111
Polymers10,1111
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 / 200target function
RepresentativeModel #1fewest violations

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Components

#1: Protein Coiled-coil-helix-coiled-coil-helix domain-containing protein 7


Mass: 10110.507 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CHCHD7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Origami(DE3) / References: UniProt: Q9BUK0

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-13C HSQC
1323D HNCO
1423D HNCA
1523D HN(CA)CB
1623D HN(CO)CA
1723D (H)CCH-TOCSY
1823D HN(CA)CO
1923D CBCA(CO)NH
11012D 1H-1H NOESY
11113D 1H-15N NOESY
11223D 1H-13C NOESY aliphatic

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5-1 mM [U-100% 15N] protein, 50 mM potassium phosphate, 90% H2O/10% D2O90% H2O/10% D2O
20.5-1 mM [U-100% 13C; U-100% 15N] protein, 50 mM potassium phosphate, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMentity-1[U-100% 15N]0.5-11
50 mMpotassium phosphate-21
mMentity-3[U-100% 13C; U-100% 15N]0.5-12
50 mMpotassium phosphate-42
Sample conditionsIonic strength: 50 / pH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE9001
Bruker AvanceBrukerAVANCE5002
Bruker AvanceBrukerAVANCE7003

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
CARAKeller and Wuthrichdata analysis
PECANEghbalnia, Wang, Bahrami, Assadi, and Markleydata analysis
TALOSCornilescu, Delaglio and Baxdata analysis
ATNOSHerrmann, Guntert and Wuthrichpeak picking
CANDIDHerrmann, Guntert and Wuthrichnoes assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
XEASYBartels et al.data analysis
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmrefinement
ProcheckNMRLaskowski and MacArthurstructure validation
PSVSBhattacharya and Montelionestructure validation
WHAT IFVriendstructure validation
MOLMOLKoradi, Billeter and Wuthrichdata analysis
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 20

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