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- PDB-1nzn: Cytosolic domain of the human mitchondrial fission protein Fis1 a... -

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Basic information

Entry
Database: PDB / ID: 1nzn
TitleCytosolic domain of the human mitchondrial fission protein Fis1 adopts a TPR fold
ComponentsFission protein Fis1p
KeywordsUNKNOWN FUNCTION / TPR
Function / homology
Function and homology information


negative regulation of fatty acid transport / negative regulation of ATP metabolic process / Class I peroxisomal membrane protein import / positive regulation of mitochondrial calcium ion concentration / peroxisome fission / mitochondrial fragmentation involved in apoptotic process / negative regulation of endoplasmic reticulum calcium ion concentration / autophagy of mitochondrion / protein targeting to mitochondrion / mitochondrial fission ...negative regulation of fatty acid transport / negative regulation of ATP metabolic process / Class I peroxisomal membrane protein import / positive regulation of mitochondrial calcium ion concentration / peroxisome fission / mitochondrial fragmentation involved in apoptotic process / negative regulation of endoplasmic reticulum calcium ion concentration / autophagy of mitochondrion / protein targeting to mitochondrion / mitochondrial fission / regulation of mitochondrion organization / peroxisomal membrane / mitochondrial fusion / positive regulation of mitochondrial fission / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / : / positive regulation of protein targeting to membrane / positive regulation of intrinsic apoptotic signaling pathway / mitochondrion organization / release of cytochrome c from mitochondria / peroxisome / positive regulation of cytosolic calcium ion concentration / mitochondrial outer membrane / molecular adaptor activity / lipid binding / endoplasmic reticulum / protein-containing complex / mitochondrion / membrane / identical protein binding / cytosol
Similarity search - Function
Mitochondria fission 1 protein / Fis1, N-terminal tetratricopeptide repeat / Fis1, C-terminal tetratricopeptide repeat / Mitochondria fission protein Fis1, cytosolic domain / Fis1 N-terminal tetratricopeptide repeat / Fis1 C-terminal tetratricopeptide repeat / Tetratricopeptide repeat domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha
Similarity search - Domain/homology
Mitochondrial fission 1 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsGittis, A.G. / Dohm, J.A. / Hill, R.B.
CitationJournal: Proteins / Year: 2004
Title: Cytosolic domain of the human mitchondrial fission protein Fis1 adopts a TPR fold
Authors: Dohm, J.A. / Lee, S.J. / Hardwick, J.M. / Hill, R.B. / Gittis, A.G.
History
DepositionFeb 18, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fission protein Fis1p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9563
Polymers14,7681
Non-polymers1882
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: Fission protein Fis1p
hetero molecules

A: Fission protein Fis1p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9116
Polymers29,5352
Non-polymers3764
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_555-x,-x+y,-z+1/31
Buried area3980 Å2
ΔGint-60 kcal/mol
Surface area13470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.985, 48.985, 169.199
Angle α, β, γ (deg.)90.0, 90.0, 120.0
Int Tables number179
Cell settinghexagonal
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-245-

HOH

21A-257-

HOH

31A-258-

HOH

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Components

#1: Protein Fission protein Fis1p / CGI-135 protein


Mass: 14767.588 Da / Num. of mol.: 1 / Fragment: cytosolic fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Organelle: MitochondriaMitochondrion / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y3D6
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H2O

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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: 1.98 Å3/Da / Density % sol: 38.01 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: Ammonium Sulphate, Sodium Acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
pH: 5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
132 mg/mlprotein1drop
225 mMsodium acetate1drop
32 mMdithiothreitol1droppH5.0
4100 mMsodium acetate1reservoir
52.0 Mammonium sulfate1reservoir
65 %glycerol1reservoirpH4.6

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.96446 Å
DetectorType: SBC-2 / Detector: CCD / Date: Dec 13, 2002
RadiationMonochromator: Si 220 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96446 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. all: 8523 / Num. obs: 8523 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 24.36 Å2 / Rmerge(I) obs: 0.048
Reflection shellResolution: 2→2.05 Å / % possible all: 99.8
Reflection
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 20 Å / Num. obs: 7912 / % possible obs: 99.7 % / Redundancy: 7 % / Rmerge(I) obs: 0.044
Reflection shell
*PLUS
Mean I/σ(I) obs: 26.8

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
RESOLVEmodel building
CNSrefinement
HKL-2000data reduction
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2548 715 9.2 %RANDOM
Rwork0.2304 ---
all-8502 --
obs-7787 --
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1009 0 11 58 1078
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.085
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obs% reflection obs (%)
2-2.050.3533510.2595X-RAY DIFFRACTION52299.8
2.05-2.110.2642470.2364X-RAY DIFFRACTION51299.8
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 20 Å / % reflection Rfree: 8 % / Rfactor Rfree: 0.255 / Rfactor Rwork: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS

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