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- PDB-7rxn: STRUCTURE OF RUBREDOXIN FROM DESULFOVIBRIO VULGARIS AT 1.5 A RESO... -

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Basic information

Entry
Database: PDB / ID: 7rxn
TitleSTRUCTURE OF RUBREDOXIN FROM DESULFOVIBRIO VULGARIS AT 1.5 A RESOLUTION
ComponentsRUBREDOXIN
KeywordsELECTRON TRANSFER(IRON-SULFUR PROTEIN)
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: 1.5 Å
AuthorsAdman, E.T. / Sieker, L.C. / Jensen, L.H.
Citation
Journal: J.Mol.Biol. / Year: 1991
Title: Structure of rubredoxin from Desulfovibrio vulgaris at 1.5 A resolution.
Authors: Adman, E.T. / Sieker, L.C. / Jensen, L.H.
#1: Journal: Am.Cryst.Assoc.,Abstr.Papers (Winter Meeting) / Year: 1979
Title: Progress on Refinement of Rubredoxin (D.Vulgaris) at 1.5 Angstroms
Authors: Adman, E.T. / Jensen, L.H.
#2: Journal: J.Mol.Biol. / Year: 1977
Title: A Structural Model of Rubredoxin from Desulfovibrio Vulgaris at 2 Angstroms Resolution
Authors: Adman, E.T. / Sieker, L.C. / Jensen, L.H. / Bruschi, M. / Legall, J.
History
DepositionMay 11, 1990Processing site: BNL
SupersessionJul 15, 1991ID: 3RXN
Revision 1.0Jul 15, 1991Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 6, 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_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.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: RUBREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,7303
Polymers5,5781
Non-polymers1522
Water3,243180
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)19.993, 41.505, 24.404
Angle α, β, γ (deg.)90.00, 107.60, 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.: 180 / 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: 1.73 Å3/Da / Density % sol: 28.91 %
Crystal grow
*PLUS
pH: 4 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
11 %protein11
20.1 Macetate11or citrate
32 Mammonium sulphate11

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Data collection

Reflection
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 5 Å / Observed criterion σ(F): 2

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementRfactor obs: 0.098 / Highest resolution: 1.5 Å
Refinement stepCycle: LAST / Highest resolution: 1.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms389 0 6 180 575
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0260.02
X-RAY DIFFRACTIONp_angle_d0.0450.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0640.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.22
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it32
X-RAY DIFFRACTIONp_scangle_it6.43
X-RAY DIFFRACTIONp_plane_restr0.0360.05
X-RAY DIFFRACTIONp_chiral_restr0.1420.1
X-RAY DIFFRACTIONp_singtor_nbd0.1610.2
X-RAY DIFFRACTIONp_multtor_nbd0.1670.2
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2340.2
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor4.33
X-RAY DIFFRACTIONp_staggered_tor12.915
X-RAY DIFFRACTIONp_orthonormal_tor14.420
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: 'PROLSQ, PROTIN' / Classification: refinement
Refinement
*PLUS
Lowest resolution: 9999 Å / Num. reflection obs: 5707 / Rfactor obs: 0.098
Solvent computation
*PLUS
Displacement parameters
*PLUS

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