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- PDB-1xrz: NMR Structure of a Zinc Finger with Cyclohexanylalanine Substitut... -

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Basic information

Entry
Database: PDB / ID: 1xrz
TitleNMR Structure of a Zinc Finger with Cyclohexanylalanine Substituted for the Central Aromatic Residue
ComponentsZinc finger Y-chromosomal protein
KeywordsTRANSCRIPTION / cyclohexanylalanine / zinc finger
Function / homology
Function and homology information


DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin / nucleolus / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm / metal ion binding / nucleus
Similarity search - Function
Transcriptional activator, Zfx / Zfy domain / Zfx / Zfy transcription activation region / C2H2-type zinc-finger domain / Zinc finger, C2H2 type / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type
Similarity search - Domain/homology
Zinc finger Y-chromosomal protein
Similarity search - Component
MethodSOLUTION NMR / Distance geometry, simulated annealing, restrained molecular dynamics
AuthorsLachenmann, M.J. / Ladbury, J.E. / Qian, X. / Huang, K. / Singh, R. / Weiss, M.A.
CitationJournal: Protein Sci. / Year: 2004
Title: Solvation and the hidden thermodynamics of a zinc finger probed by nonstandard repair of a protein crevice
Authors: Lachenmann, M.J. / Ladbury, J.E. / Qian, X. / Huang, K. / Singh, R. / Weiss, M.A.
History
DepositionOct 17, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE LYS A 30 WAS ENGINEERED TO IMPROVE SAMPLE SOLUBILITY WHILE NOT AFFECTING THE STRUCTURE

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Zinc finger Y-chromosomal protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,6712
Polymers3,6051
Non-polymers651
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)34 / 50structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein/peptide Zinc finger Y-chromosomal protein / Zinc Finger 6


Mass: 3605.129 Da / Num. of mol.: 1
Fragment: sequence database residues 570-598: contains C2H2-type 6 Zinc Finger (residues 572-595)
Mutation: P2T, Y10(HAC) / Source method: obtained synthetically
Details: The protein was chemically synthesized using solid-phase peptide synthesis. The ZFY protein is naturally found in Homo Sapiens (Human).
References: UniProt: P08048
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111DQF-COSY
122DQF-COSY
1312D TOCSY
2412D TOCSY
1512D NOESY
2612D NOESY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques. Hydrogen assignments for the cyclohexanyl ring were made by extension from the normal methods.

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Sample preparation

Details
Solution-IDContentsSolvent system
12mM Zfy-6T[Y10(CHA)], 90% H2O, 10% D2O90% H2O/10% D2O
22mM Zfy-6T[Y10(CHA)], 100% D2O100% D2O
Sample conditionsIonic strength: 50mM D11-Tris-HCl, 2.2mM ZnCl2 / pH: 6.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian VXRSVarianVXRS5001
Varian UNITYPLUSVarianUNITYPLUS5002

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Processing

NMR software
NameVersionDeveloperClassification
VNMR4.3Varian, Inc.processing
VNMR5.3Varian, Inc.processing
DGIIStandaloneHavel, T.F.structure solution
X-PLOR3.1Brungerrefinement
NHFITStandaloneRedfield, C.data analysis
RefinementMethod: Distance geometry, simulated annealing, restrained molecular dynamics
Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 50 / Conformers submitted total number: 34

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