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- PDB-2lso: Solution NMR Structure of the Globular Domain of Human Histone H1... -

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Basic information

Entry
Database: PDB / ID: 2lso
TitleSolution NMR Structure of the Globular Domain of Human Histone H1x, Northeast Structural Genomics Consortium (NESG) Target HR7057A
ComponentsHistone H1x
KeywordsNUCLEAR PROTEIN / Structural Genomics / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM / NESG / PSI-Biology / Protein Structure Initiative
Function / homology
Function and homology information


negative regulation of DNA recombination / chromosome condensation / nucleosomal DNA binding / nucleosome assembly / structural constituent of chromatin / nucleosome / chromosome / double-stranded DNA binding / cadherin binding / nucleolus ...negative regulation of DNA recombination / chromosome condensation / nucleosomal DNA binding / nucleosome assembly / structural constituent of chromatin / nucleosome / chromosome / double-stranded DNA binding / cadherin binding / nucleolus / RNA binding / nucleoplasm / nucleus
Similarity search - Function
Linker histone H1/H5 / linker histone H1 and H5 family / Linker histone H1/H5, domain H15 / Linker histone H1/H5 globular (H15) domain profile. / Domain in histone families 1 and 5 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsEletsky, A. / Lee, H. / Lee, D. / Kohan, E. / Janjua, H. / Xiao, R. / Acton, T.B. / Everett, J.K. / Montelione, G.T. / Prestegard, J.H. ...Eletsky, A. / Lee, H. / Lee, D. / Kohan, E. / Janjua, H. / Xiao, R. / Acton, T.B. / Everett, J.K. / Montelione, G.T. / Prestegard, J.H. / Szyperski, T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR Structure of the Globular Domain of Human Histone H1x, Northeast Structural Genomics Consortium (NESG) Target HR7057A
Authors: Eletsky, A. / Lee, H. / Lee, D. / Kohan, E. / Janjua, H. / Xiao, R. / Acton, T.B. / Everett, J.K. / Montelione, G.T. / Prestegard, J.H. / Szyperski, T.
History
DepositionMay 3, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 13, 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 / struct_ref / struct_ref_seq_dif
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 / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone H1x


Theoretical massNumber of molelcules
Total (without water)9,4011
Polymers9,4011
Non-polymers00
Water0
1


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

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Components

#1: Protein Histone H1x


Mass: 9400.785 Da / Num. of mol.: 1 / Fragment: H15 domain residues 44-123
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: H1FX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pMgK / References: UniProt: Q92522

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C CT-HSQC aliphatic
1313D HNCO
1413D CBCA(CO)NH
1513D HN(CA)CB
1613D (H)CCH-TOCSY aliphatic
1713D simutaneous 13C-aromatic,13C-aliphatic,15N edited 1H-1H NOESY
1812D 1H-13C CT-HSQC aromatic
1913D (H)C(CCO)NH-TOCSY
11013D H(CCCO)NH-TOCSY
11113D HBHA(CO)NH
11213D HN(CA)CO
11313D (H)CCH-COSY aliphatic
11413D (H)CCH-COSY aromatic
11522D 1H-13C CT-HSQC methyl
11622D J-resolved 1H-15N HSQC
11732D J-resolved 1H-15N HSQC
11811D 15N T1
11911D 15N T2

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Sample preparation

Details
Solution-IDContentsSolvent system
10.9 mM [U-100% 13C; U-100% 15N] HR7057A.011, 20 mM MES, 100 mM sodium chloride, 5 mM calcium chloride, 50 uM DSS, 0.02 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
20.6 mM [5% 13C; U-100% 15N] HR7057A.011, 20 mM MES, 100 mM sodium chloride, 5 mM calcium chloride, 50 uM DSS, 0.02 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
30.3 mM [5% 13C; U-100% 15N] HR7057A.011, 20 mM MES, 100 mM sodium chloride, 5 mM calcium chloride, 50 uM DSS, 0.02 % sodium azide, 4 % C12E5 PEG, 4 % hexanol, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.9 mMHR7057A.011-1[U-100% 13C; U-100% 15N]1
20 mMMES-21
100 mMsodium chloride-31
5 mMcalcium chloride-41
50 uMDSS-51
0.02 %sodium azide-61
0.6 mMHR7057A.011-7[5% 13C; U-100% 15N]2
20 mMMES-82
100 mMsodium chloride-92
5 mMcalcium chloride-102
50 uMDSS-112
0.02 %sodium azide-122
0.3 mMHR7057A.011-13[5% 13C; U-100% 15N]3
20 mMMES-143
100 mMsodium chloride-153
5 mMcalcium chloride-163
50 uMDSS-173
0.02 %sodium azide-183
4 %C12E5 PEG-193
4 %hexanol-203
Sample conditionspH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA7501
Varian INOVAVarianINOVA6002
Varian INOVAVarianINOVA6003

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readgeometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichrefinement
CYANA3Guntert, Mumenthaler and Wuthrichgeometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
ASDP1Huang, Tejero, Powers and Montelionedata analysis
ASDP1Huang, Tejero, Powers and Montelionerefinement
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
XEASY1.3.13Bartels et al.data analysis
VnmrJ2.2DVariancollection
PINE1Bahrami, Markley, Assadi, and Eghbalniachemical shift assignment
SparkyGoddarddata analysis
TALOS+Shen, Cornilescu, Delaglio and Baxgeometry optimization
PSVS1.4Bhattacharya, Montelionestructure validation
CARA1.8.4Keller and Wuthrichdata analysis
CARA1.8.4Keller and Wuthrichchemical shift assignment
CARA1.8.4Keller and Wuthrichpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Structure determination was performed by running CYANA and ASDP in parallel using NOE-based constraints and PHI and PSI dihedral angle constraints from TALOS+. Consensus peak assignments ...Details: Structure determination was performed by running CYANA and ASDP in parallel using NOE-based constraints and PHI and PSI dihedral angle constraints from TALOS+. Consensus peak assignments were selected and used in iterative refinement with CYANA, with RDC constraints added at later stages. The 20 conformers out of 100 with the lowest target function were further refined by simulated annealing in explicit water bath using the program CNS with PARAM19 force field
NMR constraintsNOE constraints total: 1597 / NOE intraresidue total count: 403 / NOE long range total count: 448 / NOE medium range total count: 413 / NOE sequential total count: 333 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 38 / Protein psi angle constraints total count: 38
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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