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- PDB-6rxn: THE STRUCTURE OF RUBREDOXIN FROM DESULFOVIBRIO DESULFURICANS -

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Basic information

Entry
Database: PDB / ID: 6rxn
TitleTHE STRUCTURE OF RUBREDOXIN FROM DESULFOVIBRIO DESULFURICANS
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, 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 desulfuricans (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.5 Å
AuthorsStenkamp, R.E. / Sieker, L.C. / Jensen, L.H.
Citation
Journal: Proteins / Year: 1990
Title: The structure of rubredoxin from Desulfovibrio desulfuricans strain 27774 at 1.5 A resolution.
Authors: Stenkamp, R.E. / Sieker, L.C. / Jensen, L.H.
#1: Journal: FEBS Lett. / Year: 1986
Title: Structure of Rubredoxin from the Bacterium Desulfovibrio Desulfuricans
Authors: Sieker, L.C. / Stenkamp, R.E. / Jensen, L.H. / Prickril, B. / Legall, J.
#2: Journal: J.Mol.Biol. / Year: 1983
Title: Crystallographic Study of Rubredoxin from the Bacterium Desulfovibrio Desulfuricans Strain 27774
Authors: Sieker, L.C. / Jensen, L.H. / Pickril, B.C. / Legall, J.
History
DepositionJan 16, 1990Processing site: BNL
Revision 1.0Jan 15, 1991Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_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.pdbx_leaving_atom_flag / _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 700SHEET RESIDUES 4 - 7, 11 - 13, AND 48 - 52 DISPLAY A SHEET-LIKE HYDROGEN BONDING PATTERN, BUT THE ...SHEET RESIDUES 4 - 7, 11 - 13, AND 48 - 52 DISPLAY A SHEET-LIKE HYDROGEN BONDING PATTERN, BUT THE TORSION ANGLES FOR THE POLYPEPTIDE CHAIN ARE NOT IDEAL FOR BETA SHEETS.

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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)5,1862
Polymers5,1301
Non-polymers561
Water2,180121
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)24.920, 17.790, 19.720
Angle α, β, γ (deg.)101.00, 83.40, 104.50
Int Tables number1
Space group name H-MP1
Atom site foot note1: THIS ENTRY CONTAINS ALTERNATE SIDE CHAIN CONFORMATIONS FOR RESIDUES GLU 12, GLN 32, CYS 38, AND LYS 46.
2: RESIDUES 4 - 7, 11 - 13, AND 48 - 52 DISPLAY A SHEET-LIKE HYDROGEN BONDING PATTERN, BUT THE TORSION ANGLES FOR THE POLYPEPTIDE CHAIN ARE NOT IDEAL FOR BETA SHEETS.

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Components

#1: Protein/peptide RUBREDOXIN


Mass: 5129.667 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio desulfuricans (bacteria) / References: UniProt: P04170
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.62 Å3/Da / Density % sol: 23.87 %
Crystal grow
*PLUS
Temperature: 23 ℃ / pH: 4 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11 %(w/v)protein1drop
20.1 Mcitrate1reservoir
325 %satammonium sulfate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.5 Å / Num. measured all: 11616

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.5→5 Å
Details: THE FE ATOM HAS BEEN REFINED WITH AN ANISOTROPIC TEMPERATURE FACTOR. THE VALUE GIVEN IN THE B-VALUE FIELD IS THE EQUIVALENT B-VALUE. (B(EQ) = 8*PI**2*(U11+U22+U33)/3). THE ANISOTROPIC ...Details: THE FE ATOM HAS BEEN REFINED WITH AN ANISOTROPIC TEMPERATURE FACTOR. THE VALUE GIVEN IN THE B-VALUE FIELD IS THE EQUIVALENT B-VALUE. (B(EQ) = 8*PI**2*(U11+U22+U33)/3). THE ANISOTROPIC TEMPERATURE FACTORS FOR THE FE IN U(IJ) ARE U(1,1) = 0.0923 U(2,2) = 0.0932 U(3,3) = 0.0762 U(1,2) = 0.0132 U(1,3) = -0.0013 U(2,3) = -0.0030
RfactorNum. reflection
obs0.093 4867
Refinement stepCycle: LAST / Resolution: 1.5→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms369 0 1 121 491
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0190.02
X-RAY DIFFRACTIONp_angle_d0.0370.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0530.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.412
X-RAY DIFFRACTIONp_mcangle_it1.832
X-RAY DIFFRACTIONp_scbond_it2.973
X-RAY DIFFRACTIONp_scangle_it3.783
X-RAY DIFFRACTIONp_plane_restr0.0290.05
X-RAY DIFFRACTIONp_chiral_restr0.1410.1
X-RAY DIFFRACTIONp_singtor_nbd0.350.35
X-RAY DIFFRACTIONp_multtor_nbd0.2250.225
X-RAY DIFFRACTIONp_xhyhbond_nbd0.650.65
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor4.23
X-RAY DIFFRACTIONp_staggered_tor11.915
X-RAY DIFFRACTIONp_orthonormal_tor1620
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 5 Å / Num. reflection obs: 4867 / Rfactor obs: 0.093
Solvent computation
*PLUS
Displacement parameters
*PLUS

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