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- PDB-1doi: 2FE-2S FERREDOXIN FROM HALOARCULA MARISMORTUI -

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Basic information

Entry
Database: PDB / ID: 1doi
Title2FE-2S FERREDOXIN FROM HALOARCULA MARISMORTUI
Components2FE-2S FERREDOXIN
KeywordsELECTRON TRANSPORT / HALOPHILIC PROTEIN / REDOX PROTEIN / IRON-SULFUR
Function / homology2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin, iron-sulphur binding site / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-like superfamily / 2Fe-2S iron-sulfur cluster binding domain / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2 iron, 2 sulfur cluster binding / electron transfer activity / metal ion binding / Ferredoxin-1
Function and homology information
Specimen sourceHaloarcula marismortui (Halophile)
MethodX-RAY DIFFRACTION / SIR, NATIVE ANOMALOUS SCATTERING SOFTWARE USED : NULL STARTING MODEL FOR MOLECULAR REPLACEMENT: NULL / 1.9 Å resolution
AuthorsFrolow, F. / Harel, M. / Sussman, J.L. / Shoham, M.
Citation
Journal: Nat.Struct.Biol. / Year: 1996
Title: Insights into protein adaptation to a saturated salt environment from the crystal structure of a halophilic 2Fe-2S ferredoxin.
Authors: Frolow, F. / Harel, M. / Sussman, J.L. / Mevarech, M. / Shoham, M.
#1: Journal: Iron-Sulfur Protein Research / Year: 1986
Title: X-Ray Structural Studies of a Salt-Loving 2Fe-2S Ferredoxin from Halobacterium of the Dead Sea
Authors: Sussman, J.L. / Brown, J.H. / Shoham, M.
#2: Journal: J.Mol.Biol. / Year: 1979
Title: Preliminary X-Ray Diffraction Studies on 2 Fe-Ferredoxin from Halobacterium of the Dead Sea
Authors: Sussman, J.L. / Zipori, P. / Harel, M. / Yonath, A. / Werber, M.M.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Apr 8, 1996 / Release: Aug 1, 1996
RevisionDateData content typeGroupProviderType
1.0Aug 1, 1996Structure modelrepositoryInitial release
1.1Mar 24, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2FE-2S FERREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8248
Polyers14,4141
Non-polymers4107
Water4,270237
1
A: 2FE-2S FERREDOXIN
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)88,94448
Polyers86,4816
Non-polymers2,46242
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation11_555-x+y,y,-z+1/21
crystal symmetry operation10_555-y,-x,-z+1/21
crystal symmetry operation12_555x,x-y,-z+1/21
Unit cell
γ
α
β
Length a, b, c (Å)59.180, 59.180, 124.230
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP 63 2 2

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Components

#1: Protein/peptide 2FE-2S FERREDOXIN


Mass: 14413.550 Da / Num. of mol.: 1 / Source: (natural) Haloarcula marismortui (Halophile) / Genus: Haloarcula / References: UniProt: P00217
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 6 / Formula: K / Potassium
#3: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Formula: Fe2S2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / Formula: H2O / Water
Nonpolymer detailsTHE CRITERION TO ASSIGN A SOLVENT PEAK AS A POTASSIUM ION WAS THE ISOTROPIC TEMPERATURE FACTOR UPON ...THE CRITERION TO ASSIGN A SOLVENT PEAK AS A POTASSIUM ION WAS THE ISOTROPIC TEMPERATURE FACTOR UPON REFINEMENT IN X-PLOR. IF B REFINED TO 2.0, THE MINIMUM POSSIBLE IN X-PLOR, THEN THE SOLVENT PEAK WAS ASSIGNED AS POTASSIUM ION (PRESENT IN THE MOTHER LIQUOR) INSTEAD OF A WATER MOLECULE. FOR SIX SOLVENT PEAKS THE REFINEMENT PROCEEDED SMOOTHLY WHEN ASSIGNED TO BE POTASSIUM IONS.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.24 / Density percent sol: 55 %
Crystal growpH: 7 / Details: pH 7.0
Crystal grow
*PLUS
pH: 7 / Method: microdialysis / Details: Sussman, J.L., (1979) J.Mol.Biol., 134, 375.
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol IDChemical formula
110 mg/mlprotein11
24 M11NaCl
34 Mphosphate12

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Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionD resolution high: 1.9 Å / D resolution low: 3 Å / Number obs: 9760 / Observed criterion sigma I: 0 / Percent possible obs: 99
Reflection
*PLUS
Rmerge I obs: 0.04

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
XENGENdata reduction
XENGENdata scaling
X-PLOR3.1phasing
RefineMethod to determine structure: SIR, NATIVE ANOMALOUS SCATTERING SOFTWARE USED : NULL STARTING MODEL FOR MOLECULAR REPLACEMENT: NULL
Sigma F: 0
Least-squares processR factor R work: 0.195 / R factor obs: 0.195 / Highest resolution: 1.9 Å / Lowest resolution: 3 Å / Number reflection obs: 9760 / Percent reflection obs: 99
Refine hist #LASTHighest resolution: 1.9 Å / Lowest resolution: 3 Å
Number of atoms included #LASTProtein: 1008 / Nucleic acid: 0 / Ligand: 4 / Solvent: 243 / Total: 1255
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.018
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.29
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.27
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Xplor file
Refine IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2PARAM.HFD FOR FE2S2 CLUSTTOPH11.K FOR POTASSIUM IONS
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.9
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.27

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