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- PDB-1cld: DNA-binding protein -

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Basic information

Entry
Database: PDB / ID: 1cld
TitleDNA-binding protein
ComponentsCD2-LAC9
KeywordsTRANSCRIPTION REGULATION / ZINC-BINDING DOMAIN
Function / homology
Function and homology information


galactose metabolic process / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleus
Similarity search - Function
Gal4 dimerisation domain / Gal4-like dimerisation domain / Fungal specific transcription factor domain / Transcription factor domain, fungi / Fungal specific transcription factor domain / Zn(2)-C6 fungal-type DNA-binding domain signature. / Fungal Zn(2)-Cys(6) binuclear cluster domain / Zn(2)-C6 fungal-type DNA-binding domain superfamily / Zn(2)-C6 fungal-type DNA-binding domain profile. / GAL4-like Zn(II)2Cys6 (or C6 zinc) binuclear cluster DNA-binding domain ...Gal4 dimerisation domain / Gal4-like dimerisation domain / Fungal specific transcription factor domain / Transcription factor domain, fungi / Fungal specific transcription factor domain / Zn(2)-C6 fungal-type DNA-binding domain signature. / Fungal Zn(2)-Cys(6) binuclear cluster domain / Zn(2)-C6 fungal-type DNA-binding domain superfamily / Zn(2)-C6 fungal-type DNA-binding domain profile. / GAL4-like Zn(II)2Cys6 (or C6 zinc) binuclear cluster DNA-binding domain / Zn(2)-C6 fungal-type DNA-binding domain / Basic-leucine zipper domain superfamily
Similarity search - Domain/homology
: / Lactose regulatory protein LAC9
Similarity search - Component
Biological speciesKluyveromyces lactis (yeast)
MethodSOLUTION NMR
AuthorsGardner, K.H. / Coleman, J.E.
Citation
Journal: Nat.Struct.Biol. / Year: 1995
Title: Solution structure of the Kluyveromyces lactis LAC9 Cd2 Cys6 DNA-binding domain.
Authors: Gardner, K.H. / Anderson, S.F. / Coleman, J.E.
#1: Journal: J.Biomol.NMR / Year: 1994
Title: 113Cd-1H Heterotocsy: A Method for Determining Metal-Protein Connectivities
Authors: Gardner, K.H. / Coleman, J.E.
History
DepositionJun 6, 1995Processing site: BNL
Revision 1.0Sep 15, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CD2-LAC9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,3303
Polymers7,1051
Non-polymers2252
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Atom site foot note1: CIS PROLINE - PRO 110 MODEL 1 / 2: CIS PROLINE - PRO 110 MODEL 2 / 3: CIS PROLINE - PRO 110 MODEL 3 / 4: CIS PROLINE - PRO 110 MODEL 4 / 5: CIS PROLINE - PRO 110 MODEL 5 / 6: CIS PROLINE - PRO 110 MODEL 6 / 7: CIS PROLINE - PRO 110 MODEL 7 / 8: CIS PROLINE - PRO 110 MODEL 8 / 9: CIS PROLINE - PRO 110 MODEL 9 / 10: CIS PROLINE - PRO 110 MODEL 10 / 11: CIS PROLINE - PRO 110 MODEL 11 / 12: CIS PROLINE - PRO 110 MODEL 12 / 13: CIS PROLINE - PRO 110 MODEL 13 / 14: CIS PROLINE - PRO 110 MODEL 14 / 15: CIS PROLINE - PRO 110 MODEL 15 / 16: CIS PROLINE - PRO 110 MODEL 16 / 17: CIS PROLINE - PRO 110 MODEL 17 / 18: CIS PROLINE - PRO 110 MODEL 18 / 19: CIS PROLINE - PRO 110 MODEL 19 / 20: CIS PROLINE - PRO 110 MODEL 20 / 21: CIS PROLINE - PRO 110 MODEL 21 / 22: CIS PROLINE - PRO 110 MODEL 22 / 23: CIS PROLINE - PRO 110 MODEL 23 / 24: CIS PROLINE - PRO 110 MODEL 24 / 25: CIS PROLINE - PRO 110 MODEL 25 / 26: CIS PROLINE - PRO 110 MODEL 26 / 27: CIS PROLINE - PRO 110 MODEL 27 / 28: CIS PROLINE - PRO 110 MODEL 28 / 29: CIS PROLINE - PRO 110 MODEL 29
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)29 / -
Representative

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Components

#1: Protein CD2-LAC9


Mass: 7105.403 Da / Num. of mol.: 1 / Mutation: INITIATOR MET
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces lactis (yeast) / Production host: Escherichia coli (E. coli) / References: UniProt: P08657
#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Crystal grow
*PLUS
Method: other / Details: NMR

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR softwareName: X-PLOR / Version: 3.1 / Developer: BRUNGER / Classification: refinement
NMR ensembleConformers submitted total number: 29

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