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- PDB-1h7v: Rubredoxin from Guillardia Theta -

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Basic information

Entry
Database: PDB / ID: 1h7v
TitleRubredoxin from Guillardia Theta
ComponentsRUBREDOXIN
KeywordsELECTRON TRANSPORT / RUBREDOXIN / GUILLARDIA THETA / ZINC- SUBSTITUTION / DIPOLAR COUPLINGS
Function / homology
Function and homology information


alkane catabolic process / DNA-directed RNA polymerase complex / electron transfer activity / iron ion binding / membrane
Similarity search - Function
: / Rubrerythrin, domain 2 - #10 / Rubredoxin domain / Rubredoxin / Rubredoxin-like domain / Rubredoxin-like domain profile. / Rubrerythrin, domain 2 / Single Sheet / Mainly Beta
Similarity search - Domain/homology
Biological speciesGUILLARDIA THETA (eukaryote)
MethodSOLUTION NMR / simulated annealing
AuthorsSchweimer, K. / Hoffmann, S. / Wastl, J. / Maier, U.G. / Roesch, P. / Sticht, H.
CitationJournal: Protein Sci. / Year: 2000
Title: Solution structure of a zinc substituted eukaryotic rubredoxin from the cryptomonad alga Guillardia theta.
Authors: Schweimer, K. / Hoffmann, S. / Wastl, J. / Maier, U.G. / Rosch, P. / Sticht, H.
History
DepositionJan 16, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 29, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 14, 2017Group: Structure summary / Category: pdbx_nmr_representative / Item: _pdbx_nmr_representative.conformer_id
Revision 1.4Jan 17, 2018Group: Database references / Source and taxonomy / Structure summary
Category: citation / citation_author ...citation / citation_author / entity_src_gen / struct
Item: _citation.page_last / _citation.pdbx_database_id_DOI ..._citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.name / _entity_src_gen.gene_src_strain / _struct.title
Revision 1.5May 15, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_conn_angle / 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.status_code_mr / _pdbx_nmr_software.name / _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
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RUBREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,7832
Polymers6,7181
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)29 / 120LEAST RESTRAINT VIOLATION, LOWEST ENERGY
RepresentativeModel #1

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Components

#1: Protein RUBREDOXIN


Mass: 6717.714 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) GUILLARDIA THETA (eukaryote)
Description: THE RBX-GENE IS ENCODED ON THE G.THETA NUCLEOMORPH (CHROMOSOME II)
Organelle: NUCLEOMORPH / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9XG40
#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
1111H-1H NOESY
1211H-1H TOCSY 1H-15N HSQC
1311H-13C CT-HS 15N-EDITED NOESY(3D)
14113C-EDITED NOESY(3D) HNCO HNCA
151HN(CA)CB
161CBCA(CO)NH HBHA (CO)NH
171HNHA
181(H)CCH-CO
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON 13C, 15N-LABELED, ZINC-SUBSTITUTED RUBREDOXIN

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Sample preparation

Sample conditionspH: 6.4 / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DRXBrukerDRX6002

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Processing

NMR software
NameDeveloperClassification
X-PLORBRUNGERrefinement
NMRViewstructure solution
NDEEstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE. THE IRON-ATOM PRESENT IN THE NATIVE RUBREDOXIN WAS REPLACE BY ZINC IN ORDER TO AVOID PARAMAGNETIC EFFECTS.
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION, LOWEST ENERGY
Conformers calculated total number: 120 / Conformers submitted total number: 29

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