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- PDB-1dx8: Rubredoxin from Guillardia theta -

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Basic information

Entry
Database: PDB / ID: 1dx8
TitleRubredoxin from Guillardia theta
ComponentsRUBREDOXIN
KeywordsELECTRON TRANSPORT / RUBREDOXIN / GUILLARDIA THETA / ZINC-SUBSTITUTION
Function / homology
Function and homology information


alkane catabolic process / DNA-directed RNA polymerase complex / chloroplast / 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
DepositionDec 23, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 4, 2000Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 17, 2018Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title
Revision 1.4May 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RUBREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,8502
Polymers7,7851
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)21 / 60LEAST RESTRAINT VIOLATION, LOWEST ENERGY
Representative

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Components

#1: Protein RUBREDOXIN


Mass: 7784.847 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
Compound detailsTHE IRON-ATOM PRESENT IN THE NATIVE RUBREDOXIN WAS REPLACED BY ZINC IN ORDER TO AVOID PARAMAGNETIC EFFECTS.

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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-HSQC 15N-EDITED NOESY(3D)
14113C-EDITED NOESY(3D) HNCO
151HNCA
161HN(CA)CB
171CBCA(CO)NH HBHA(CO)NH
181HNHA
191(H)CCH-COSY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON 13C, 15N-LABELED, ZINC-SUBSTITUTED RUBREDOXIN

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Sample preparation

DetailsContents: 10% WATER/90% D2O
Sample conditionsIonic strength: 10 mM / pH: 6.4 / Pressure: 1 atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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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.
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION, LOWEST ENERGY
Conformers calculated total number: 60 / Conformers submitted total number: 21

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