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- PDB-4rxn: CRYSTALLOGRAPHIC REFINEMENT OF RUBREDOXIN AT 1.2 ANGSTROMS RESOLUTION -

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Basic information

Entry
Database: PDB / ID: 4rxn
TitleCRYSTALLOGRAPHIC REFINEMENT OF RUBREDOXIN AT 1.2 ANGSTROMS RESOLUTION
ComponentsRUBREDOXIN
KeywordsELECTRON TRANSFER(IRON-SULFUR PROTEIN)
Function / homology
Function and homology information


alkane catabolic process / electron transfer activity / iron ion binding
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 speciesClostridium pasteurianum (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.2 Å
AuthorsWatenpaugh, K.D. / Sieker, L.C. / Jensen, L.H.
Citation
Journal: J.Mol.Biol. / Year: 1980
Title: Crystallographic refinement of rubredoxin at 1 x 2 A degrees resolution.
Authors: Watenpaugh, K.D. / Sieker, L.C. / Jensen, L.H.
#1: Journal: J.Mol.Biol. / Year: 1979
Title: The Structure of Rubredoxin at 1.2 Angstroms Resolution
Authors: Watenpaugh, K.D. / Sieker, L.C. / Jensen, L.H.
#2: Journal: J.Mol.Biol. / Year: 1978
Title: Water Structure in a Protein Crystal. Rubredoxin at 1.2 Angstroms Resolution.
Authors: Watenpaugh, K.D. / Margulis, T.N. / Sieker, L.C. / Jensen, L.H.
#3: Journal: Acta Crystallogr.,Sect.B / Year: 1973
Title: Refinement of the Model of a Protein. Rubredoxin at 1.5 Angstroms Resolution
Authors: Watenpaugh, K.D. / Sieker, L.C. / Herriott, J.R. / Jensen, L.H.
#4: Journal: J.Mol.Biol. / Year: 1973
Title: Sequence of Rubredoxin by X-Ray Diffraction
Authors: Herriott, J.R. / Watenpaugh, K.D. / Sieker, L.C. / Jensen, L.H.
#5: Journal: Cold Spring Harbor Symp.Quant.Biol. / Year: 1972
Title: The Structure of a Non-Heme Iron Protein, Rubredoxin at 1.5 Angstroms Resolution
Authors: Watenpaugh, K.D. / Sieker, L.C. / Herriott, J.R. / Jensen, L.H.
#6: Journal: Thesis / Year: 1972
Title: The Primary Structure of Clostridium Pasteurianum Rubredoxin
Authors: Mccarthy, K.F.
#7: Journal: J.Mol.Biol. / Year: 1970
Title: Structure of Rubredoxin. An X-Ray Study to 2.5 Angstroms Resolution
Authors: Herriott, J.R. / Sieker, L.C. / Jensen, L.H. / Lovenberg, W.
History
DepositionOct 15, 1984Processing site: BNL
SupersessionApr 1, 1985ID: 2RXN
Revision 1.0Apr 1, 1985Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 28, 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_ref_seq_dif / 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_ref_seq_dif.details / _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)6,1102
Polymers6,0551
Non-polymers561
Water2,288127
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.290, 64.290, 32.490
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein RUBREDOXIN


Mass: 6054.566 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium pasteurianum (bacteria) / References: UniProt: P00268
#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.: 127 / 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: 2.13 Å3/Da / Density % sol: 42.32 %
Crystal grow
*PLUS
Temperature: 23 ℃ / pH: 4 / Method: unknown / Details: salting out
Components of the solutions
*PLUS
Conc.: 80 %sat / Chemical formula: (NH4)2SO4

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Data collection

Reflection
*PLUS
Observed criterion σ(I): 4 / Num. measured all: 17000 / Rmerge(I) obs: 0.038

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Processing

RefinementResolution: 1.2→10 Å
Details: EACH HYDROGEN ATOM POSITION HAS BEEN CALCULATED FROM THE COORDINATES OF THE ATOM IT IS BONDED TO. THE B-VALUE OF THE HEAVIER ATOM WAS ASSIGNED TO THE HYDROGEN ATOM. THE CELL DIMENSIONS ...Details: EACH HYDROGEN ATOM POSITION HAS BEEN CALCULATED FROM THE COORDINATES OF THE ATOM IT IS BONDED TO. THE B-VALUE OF THE HEAVIER ATOM WAS ASSIGNED TO THE HYDROGEN ATOM. THE CELL DIMENSIONS VARIED FROM START TO FINISH OF DATA COLLECTION. THE VALUES GIVEN ARE THOSE AT THE MID-POINT OF DATA COLLECTION.
RfactorNum. reflection
Rwork0.128 -
obs-10936
Refinement stepCycle: LAST / Resolution: 1.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms756 0 1 127 884
Refinement
*PLUS
Highest resolution: 1.2 Å / Lowest resolution: 10 Å / Num. reflection obs: 10936 / σ(I): 2 / Rfactor obs: 0.128
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 12 Å2

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