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- PDB-1irn: RUBREDOXIN (ZN-SUBSTITUTED) AT 1.2 ANGSTROMS RESOLUTION -

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Basic information

Entry
Database: PDB / ID: 1irn
TitleRUBREDOXIN (ZN-SUBSTITUTED) AT 1.2 ANGSTROMS RESOLUTION
ComponentsRUBREDOXIN
KeywordsELECTRON TRANSPORT
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 / Single Sheet / Mainly Beta
Similarity search - Domain/homology
Biological speciesClostridium pasteurianum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.2 Å
AuthorsDauter, Z. / Wilson, K.S. / Sieker, L.C. / Moulis, J.M. / Meyer, J.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1996
Title: Zinc- and iron-rubredoxins from Clostridium pasteurianum at atomic resolution: a high-precision model of a ZnS4 coordination unit in a protein.
Authors: Dauter, Z. / Wilson, K.S. / Sieker, L.C. / Moulis, J.M. / Meyer, J.
#1: Journal: J.Mol.Biol. / Year: 1980
Title: Crystallographic Refinement of Rubredoxin at 1.2 Angstroms Resolution
Authors: Watenpaugh, K.D. / Sieker, L.C. / Jensen, L.H.
#2: 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.
#3: 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
DepositionDec 13, 1995Processing site: BNL
Revision 1.0Apr 3, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_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)6,1172
Polymers6,0521
Non-polymers651
Water1,56787
1
A: RUBREDOXIN
hetero molecules

A: RUBREDOXIN
hetero molecules

A: RUBREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3516
Polymers18,1553
Non-polymers1963
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Unit cell
Length a, b, c (Å)64.100, 64.100, 33.050
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: 6051.611 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ZN-SUBSTITUTED / Source: (natural) Clostridium pasteurianum (bacteria) / References: UniProt: P00268
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 2.16 Å3/Da / Density % sol: 42.99 %
Crystal growpH: 4 / Details: pH 4.0
Crystal grow
*PLUS
Temperature: 23 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.8-1.6 mMprotein1drop
20.82 Mammonium sulfate1drop20%saturated
330 mMcitrate1drop
42.46 Mammonium sulfate1reservoir60%saturated
5100 mMcitrate1reservoir

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Data collection

DiffractionMean temperature: 298 K / Ambient temp details: ROOM
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.93 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 1, 1993 / Details: FOCUSING MIRRORS
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionRedundancy: 5.5 % / Rmerge(I) obs: 0.059
Reflection
*PLUS
Highest resolution: 1.2 Å / Lowest resolution: 25 Å / Num. obs: 15659 / % possible obs: 99 % / Rmerge(I) obs: 0.059
Reflection shell
*PLUS
Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 3.6

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Processing

Software
NameClassification
SHELXL-93model building
SHELXL-93refinement
ARPmodel building
DENZOdata reduction
SCALEPACKdata scaling
SHELXL-93phasing
RefinementResolution: 1.2→10 Å / Num. parameters: 4604 / Num. restraintsaints: 5447 / σ(F): -3 / Stereochemistry target values: ENGH AND HUBER /
RfactorNum. reflection% reflection
obs0.1068 28046 99 %
Refine analyzeNum. disordered residues: 3 / Occupancy sum non hydrogen: 498
Refinement stepCycle: LAST / Resolution: 1.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms763 0 1 87 851

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