+Open data
-Basic information
Entry | Database: PDB / ID: 2vkr | ||||||
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Title | 3Fe-4S, 4Fe-4S plus Zn Acidianus ambivalens ferredoxin | ||||||
Components | ZINC-CONTAINING FERREDOXIN | ||||||
Keywords | ELECTRON TRANSPORT / ZINC / IRON / 3FE-4S / 4FE-4S / TRANSPORT / ZN CENTER / HEMIHEDRIC TWINNIG / IRON-SULFUR PROTEIN / FERREDOXIN / METHYLATION / THERMOPHILE / IRON-SULFUR / THERMOSTABLE PROTEIN / METAL-BINDING / PROTEIN FOLDING | ||||||
Function / homology | Function and homology information 3 iron, 4 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / zinc ion binding Similarity search - Function | ||||||
Biological species | ACIDIANUS AMBIVALENS (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å | ||||||
Authors | Frazao, C. / Aragao, D. / Coelho, R. / Leal, S.S. / Gomes, C.M. / Teixeira, M. / Carrondo, M.A. | ||||||
Citation | Journal: FEBS Lett. / Year: 2008 Title: Crystallographic analysis of the intact metal centres [3Fe-4S](1+/0) and [4Fe-4S](2+/1+) in a Zn(2+) -containing ferredoxin. Authors: Frazao, C. / Aragao, D. / Coelho, R. / Leal, S.S. / Gomes, C.M. / Teixeira, M. / Carrondo, M.A. #1: Journal: Biochemistry / Year: 2007 Title: A Spectroscopic Study of the Temperature Induced Modifications on Ferredoxin Folding and Iron-Sulfur Moieties Authors: Todorovic, S. / Leal, S.S. / Salgueiro, C.A. / Zebger, I. / Hildebrandt, P. / Murgida, D.H. / Gomes, C.M. #2: Journal: Proteins: Struct.,Funct., Genet. / Year: 2007 Title: Studies of the Molten Globule State of Ferredoxin: Structural Characterisation and Implications on Protein Folding and Iron-Sulfur Centre Assembly Authors: Leal, S.S. / Gomes, C.M. #3: Journal: Biochemistry / Year: 2006 Title: Natural Domain Design: Enhanced Thermal Stability of a Zinc Lacking Ferredoxin Isoform Shows that a Hydrophobic Core Efficiently Replaces the Structural Metal Site Authors: Rocha, R. / Leal, S. / Teixeira, M. / Regalla, M. / Huber, H. / Baptista, A. / Soares, C.M. / Gomes, C.M. #4: Journal: J.Biol.Inorg.Chem. / Year: 1998 Title: ,Di-Cluster, Seven-Iron Ferredoxins from Hyperthermophilic Sulfolobales Authors: Gomes, C.M. / Faria, A. / Carita, J.C. / Mendes, J. / Regalla, M. / Chicau, P. / Huber, H. / Stetter, K.O. / Teixeira, M. #5: Journal: Eur.J.Biochem. / Year: 1995 Title: A Seven Iron Ferredoxin from the Thermoacidophilic Archaeon Desulfurolobus Ambivalens Authors: Teixeira, M. / Batista, R. / Campos, A. / Gomes, C. / Mendes, J. / Pacheco, I. / Anemuller, S. / Hagen, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vkr.cif.gz | 152.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vkr.ent.gz | 121.6 KB | Display | PDB format |
PDBx/mmJSON format | 2vkr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vk/2vkr ftp://data.pdbj.org/pub/pdb/validation_reports/vk/2vkr | HTTPS FTP |
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-Related structure data
Related structure data | 1xerS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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3 |
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4 |
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7 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 11014.585 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) ACIDIANUS AMBIVALENS (archaea) / References: UniProt: P49949 #2: Chemical | ChemComp-F3S / #3: Chemical | ChemComp-SF4 / #4: Chemical | ChemComp-ZN / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.85 Å3/Da / Density % sol: 33.6 % / Description: HEMIHEDRIC TWINNED CRYSTAL |
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Crystal grow | Method: vapor diffusion Details: VAPOR DIFFUSION METHOD USING 2 MICROL DROPS OF FRESHLY PURIFIED PROTEIN AT 4.7 MG/ML IN 40 MM POTASSIUM PHOSPHATE PH 6.5 AND 150 NACL, PLUS 2 MICROL OF WELL SOLUTION, 2.4-3.0 M AMMONIUM ...Details: VAPOR DIFFUSION METHOD USING 2 MICROL DROPS OF FRESHLY PURIFIED PROTEIN AT 4.7 MG/ML IN 40 MM POTASSIUM PHOSPHATE PH 6.5 AND 150 NACL, PLUS 2 MICROL OF WELL SOLUTION, 2.4-3.0 M AMMONIUM SULPHATE BUFFERED WITH TRIS-HCL 0.1 M PH 8 AND 0.5 MICROL LAURYLDIMETHYLAMINE-OXIDE (LDAO) 7% (W/V). |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Sep 23, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.01→19.48 Å / Num. obs: 52106 / % possible obs: 99.2 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 2.01→2.07 Å / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.5 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1XER Resolution: 2.01→19.48 Å / Num. parameters: 22469 / Num. restraintsaints: 52080 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: HEMIHEDRIC TWIN LAW 1 0 0, -1 -1 0, 0 0 -1, TWIN RATIO 0.39/0.61. NO INTER-MOLECULES TRANSFORMATION MATRICES WERE EVER USED FOR NCS RESTRAINTS. INSTEAD, NCS SIMILARITIES RESTRAINTS WERE ...Details: HEMIHEDRIC TWIN LAW 1 0 0, -1 -1 0, 0 0 -1, TWIN RATIO 0.39/0.61. NO INTER-MOLECULES TRANSFORMATION MATRICES WERE EVER USED FOR NCS RESTRAINTS. INSTEAD, NCS SIMILARITIES RESTRAINTS WERE APPLIED: 1. ATOMIC 1 TO 4 DISTANCES (DIHEDRALS) AND 2. ATOMIC DISPLACEMENT DISPLACEMENT PARAMETERS BETWEEN HOMOLOGOUS ATOMS, AMONG THE SEVEN MOLECULES IN THE ASYMMETRIC UNIT, WERE RESTRAINED TO THEIR COMMON VALUES. 3. THE STEREOCHEMISTRY OF THE METAL CENTERS AND THEIR LIGANDS WERE RESTRAINED TO THEIR COMMON GEOMETRY WITHOUT TARGET VALUES.
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Refine analyze | Num. disordered residues: 1 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 5395 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.01→19.48 Å
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Refine LS restraints |
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