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- PDB-8rxn: REFINEMENT OF RUBREDOXIN FROM DESULFOVIBRIO VULGARIS AT 1.0 ANGST... -

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Basic information

Entry
Database: PDB / ID: 8rxn
TitleREFINEMENT OF RUBREDOXIN FROM DESULFOVIBRIO VULGARIS AT 1.0 ANGSTROMS WITH AND WITHOUT RESTRAINTS
ComponentsRUBREDOXIN
KeywordsELECTRON TRANSPORT(IRON)
Function / homology
Function and homology information


alkane catabolic process / electron transfer activity / iron ion binding / cytoplasm
Similarity search - Function
Rubredoxin / : / Rubredoxin, iron-binding site / Rubredoxin signature. / Rubrerythrin, domain 2 - #10 / Rubredoxin domain / Rubredoxin / Rubredoxin-like domain / Rubredoxin-like domain profile. / Rubrerythrin, domain 2 ...Rubredoxin / : / Rubredoxin, iron-binding site / Rubredoxin signature. / 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 speciesDesulfovibrio vulgaris (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1 Å
AuthorsDauter, Z. / Sieker, L. / Wilson, K.
CitationJournal: Acta Crystallogr.,Sect.B / Year: 1992
Title: Refinement of rubredoxin from Desulfovibrio vulgaris at 1.0 A with and without restraints.
Authors: Dauter, Z. / Sieker, L.C. / Wilson, K.S.
History
DepositionAug 26, 1991Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 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 / 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 / _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

Downloads & links

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Assembly

Deposited unit
A: RUBREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,7303
Polymers5,5781
Non-polymers1522
Water1,838102
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)19.970, 41.450, 24.410
Angle α, β, γ (deg.)90.00, 108.30, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein RUBREDOXIN


Mass: 5578.174 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio vulgaris (bacteria) / References: UniProt: P00269
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.72 Å3/Da / Density % sol: 28.47 %
Crystal grow
*PLUS
pH: 4 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
11 %protein11
20.1 Macetate11or citrate
32 M11(NH4)2SO4

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Data collection

Reflection
*PLUS
Highest resolution: 1 Å / Lowest resolution: 2.5 Å / Num. obs: 18545 / Num. measured all: 59492 / Rmerge(I) obs: 0.058 / Biso Wilson estimate: 5.9 Å2

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementRfactor obs: 0.147 / Highest resolution: 1 Å
Refinement stepCycle: LAST / Highest resolution: 1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms397 0 6 102 505
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.035
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Highest resolution: 1 Å / Lowest resolution: 10 Å / Num. reflection obs: 18532 / Rfactor obs: 0.147
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONp_bond_d0.06
X-RAY DIFFRACTIONp_angle_d0.0650.04
X-RAY DIFFRACTIONp_plane_restr0.030.017
X-RAY DIFFRACTIONp_chiral_restr0.30.21

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