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- PDB-2lql: Solution structure of CHCH5 -

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Basic information

Entry
Database: PDB / ID: 2lql
TitleSolution structure of CHCH5
ComponentsCoiled-coil-helix-coiled-coil-helix domain-containing protein 5
KeywordsPROTEIN BINDING / CHCH domain / mitochondrial import / Mia40-dependent disulfide relay system / alpha-hairpin domain
Function / homology
Function and homology information


Mitochondrial protein import / mitochondrial intermembrane space
Similarity search - Function
IMS import disulfide relay-system, CHCH-CHCH-like Cx9C / CHCH-CHCH-like Cx9C, IMS import disulfide relay-system, / Helix Hairpins - #2900 / CHCH domain / Coiled coil-helix-coiled coil-helix (CHCH) domain profile. / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Coiled-coil-helix-coiled-coil-helix domain-containing protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
Model detailsfewest violations, model 4
AuthorsPeruzzini, R. / 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 9, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 24, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_conn / struct_conn_type / 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: Coiled-coil-helix-coiled-coil-helix domain-containing protein 5


Theoretical massNumber of molelcules
Total (without water)12,6911
Polymers12,6911
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 #1

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Components

#1: Protein Coiled-coil-helix-coiled-coil-helix domain-containing protein 5


Mass: 12691.363 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C2orf9, CHCHD5 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Origami(DE3) / References: UniProt: Q9BSY4

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: Solution structure of CHCH5 by NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-13C HSQC
1312D 1H-1H NOESY
1423D CBCA(CO)NH
1523D HN(CA)CB
1623D HNCO
1723D HNCA
1823D HBHA(CO)NH
1923D HN(CO)CA
11023D HN(CA)CO
11123D (H)CCH-TOCSY
11223D 1H-15N NOESY
11323D 1H-13C NOESY aliphatic
NMR detailsText: The structure was determined using a combination of NOE and dihedral angle data.

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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: 308 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Bruker AvanceBrukerAVANCE7002
Bruker AvanceBrukerAVANCE9003

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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
CANDIDHerrmann, Guntert and Wuthrichchemical shift assignment
ATNOSHerrmann, Guntert and Wuthrichpeak picking
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmrefinement
WHAT IFVrienddata analysis
ProcheckNMRLaskowski and MacArthurdata analysis
PSVSBhattacharya and Montelionedata analysis
MOLMOLKoradi, Billeter and Wuthrichdata analysis
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 20

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