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- PDB-1nsf: D2 HEXAMERIZATION DOMAIN OF N-ETHYLMALEIMIDE SENSITIVE FACTOR (NSF) -

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Basic information

Entry
Database: PDB / ID: 1nsf
TitleD2 HEXAMERIZATION DOMAIN OF N-ETHYLMALEIMIDE SENSITIVE FACTOR (NSF)
ComponentsN-ETHYLMALEIMIDE SENSITIVE FACTOR
KeywordsPROTEIN TRANSPORT / ENDOPLASMIC RETICULUM / GOLGI STACK / ATP-BINDING
Function / homologyAspartate decarboxylase-like domain superfamily / CDC48, domain 2 / AAA-protein family signature. / Cell division protein 48 (CDC48), domain 2 / Cell division protein 48 (CDC48), N-terminal domain / ATPase, AAA-type, conserved site / ATPase, AAA-type, core / AAA+ ATPase domain / CDC48, N-terminal subdomain / ATPase family associated with various cellular activities (AAA) ...Aspartate decarboxylase-like domain superfamily / CDC48, domain 2 / AAA-protein family signature. / Cell division protein 48 (CDC48), domain 2 / Cell division protein 48 (CDC48), N-terminal domain / ATPase, AAA-type, conserved site / ATPase, AAA-type, core / AAA+ ATPase domain / CDC48, N-terminal subdomain / ATPase family associated with various cellular activities (AAA) / CDC48 domain 2-like superfamily / Vesicle-fusing ATPase / P-loop containing nucleoside triphosphate hydrolase / SNARE complex disassembly / vesicle-fusing ATPase / positive regulation of receptor recycling / syntaxin-1 binding / ionotropic glutamate receptor binding / SNARE binding / potassium ion transport / ATPase activity, coupled / PDZ domain binding / positive regulation of protein catabolic process / intracellular protein transport / midbody / ATPase activity / protein-containing complex binding / myelin sheath / protein kinase binding / ATP binding / identical protein binding / plasma membrane / metal ion binding / cytosol / Vesicle-fusing ATPase
Function and homology information
Specimen sourceCricetulus griseus (Chinese hamster)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / 1.9 Å resolution
AuthorsYu, R.C. / Hanson, P.I. / Jahn, R. / Brunger, A.T.
Citation
Journal: Nat.Struct.Biol. / Year: 1998
Title: Structure of the ATP-dependent oligomerization domain of N-ethylmaleimide sensitive factor complexed with ATP.
Authors: Yu, R.C. / Hanson, P.I. / Jahn, R. / Brunger, A.T.
#1: Journal: J.Biol.Chem. / Year: 1993
Title: Domain Structure of an N-Ethylmaleimide-Sensitive Fusion Protein Involved in Vesicular Transport
Authors: Tagaya, M. / Wilson, D.W. / Brunner, M. / Arango, N. / Rothman, J.E.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jun 26, 1998 / Release: Nov 25, 1998
RevisionDateData content typeGroupProviderType
1.0Nov 25, 1998Structure modelrepositoryInitial release
1.1Mar 24, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelDerived calculations / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N-ETHYLMALEIMIDE SENSITIVE FACTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0183
Polyers30,4861
Non-polymers5312
Water2,198122
1
A: N-ETHYLMALEIMIDE SENSITIVE FACTOR
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)186,10818
Polyers182,9196
Non-polymers3,18912
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555-x,-y,z1
crystal symmetry operation5_555y,-x+y,z1
crystal symmetry operation6_555x-y,x,z1
Buried area (Å2)22840
ΔGint (kcal/M)-157
Surface area (Å2)60170
MethodPISA,PQS
Unit cell
γ
α
β
Length a, b, c (Å)115.996, 115.996, 44.130
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP 6

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Components

#1: Protein/peptide N-ETHYLMALEIMIDE SENSITIVE FACTOR / VESICULAR-FUSION PROTEIN NSF


Mass: 30486.451 Da / Num. of mol.: 1 / Fragment: D2 HEXAMERIZATION DOMAIN / Source: (gene. exp.) Cricetulus griseus (Chinese hamster) / Genus: Cricetulus / Cell line: CHO / Plasmid name: PET28B / Genus (production host): Escherichia / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P18708
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Formula: Mg / Magnesium
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Formula: C10H16N5O13P3 / Adenosine triphosphate / Comment: ATP (energy-carrying molecule) *YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / Formula: H2O / Water

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 2.81 / Density percent sol: 56.23 %
Crystal growpH: 6.05 / Details: pH 6.05
Crystal grow
*PLUS
Temp: 4 ℃ / pH: 7 / Method: vapor diffusion, hanging drop
Details: drop contains equal volume of protein and reservoir solutions
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol IDChemical formula
115 mg/mlprotein1drop
220 mMHEPES1drop
3100 mM1dropNaCl
420 mMADP1drop
55 mM1dropMgCl2
62 %glycerol1drop
720 mMdithiothreitol1drop
8100 mMMES1reservoir
90.5 %PEG60001reservoir

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Data collection

DiffractionMean temperature: 80
SourceSource: SYNCHROTRON / Type: SSRL BEAMLINE BL1-5 / Synchrotron site: SSRL / Beamline: BL1-5 / Wavelength: 1
DetectorType: ADSC QUANTUM / Details: BENT MIRROR / Detector: CCD / Collection date: Mar 1, 1998
RadiationMonochromator: SI(111) / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 / Relative weight: 1
ReflectionB iso Wilson estimate: 20.7 / D resolution high: 1.9 / D resolution low: 5 / Number obs: 50548 / Observed criterion sigma I: 3 / Rmerge I obs: 0.053 / Rsym value: 0.053 / NetI over sigmaI: 33.3 / Redundancy: 6.7 % / Percent possible obs: 96.5
Reflection shellRmerge I obs: 0.334 / Highest resolution: 1.9 / Lowest resolution: 1.97 / MeanI over sigI obs: 4.8 / Rsym value: 0.334 / Redundancy: 5 % / Percent possible all: 97.5

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Processing

Software
NameVersionClassification
CNS0.4refinement
DENZOdata reduction
SCALEPACKdata scaling
CNS0.4phasing
RefineMethod to determine structure: MAD / R Free selection details: RANDOM / Data cutoff high absF: 1105949.83 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Sigma F: 0 / Stereochemistry target values: MLHL
Solvent computationSolvent model details: FLAT MODEL / Solvent model param bsol: 70.69 / Solvent model param ksol: 0.374
Displacement parametersB iso mean: 35.5 / Aniso B11: -8.49 / Aniso B12: -3.54 / Aniso B13: 0 / Aniso B22: -8.49 / Aniso B23: 0 / Aniso B33: 16.99
Least-squares processR factor R free: 0.244 / R factor R free error: 0.003 / R factor R work: 0.224 / R factor obs: 0.224 / Highest resolution: 1.9 / Lowest resolution: 5 / Number reflection R free: 4947 / Number reflection obs: 50548 / Percent reflection R free: 9.8 / Percent reflection obs: 96.4
Refine analyzeLuzzati coordinate error free: 0.27 / Luzzati coordinate error obs: 0.24 / Luzzati d res low obs: 5 / Luzzati sigma a free: 0.26 / Luzzati sigma a obs: 0.21
Refine hist #LASTHighest resolution: 1.9 / Lowest resolution: 5
Number of atoms included #LASTProtein: 1942 / Nucleic acid: 0 / Ligand: 32 / Solvent: 122 / Total: 2096
Refine LS restraints
Refine IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.681.50
X-RAY DIFFRACTIONc_mcangle_it2.392.00
X-RAY DIFFRACTIONc_scbond_it2.972.00
X-RAY DIFFRACTIONc_scangle_it4.192.50
Refine LS shellHighest resolution: 1.9 / R factor R free: 0.335 / R factor R free error: 0.016 / R factor R work: 0.287 / Lowest resolution: 1.97 / Number reflection R free: 451 / Number reflection R work: 4169 / Total number of bins used: 10 / Percent reflection R free: 9.8 / Percent reflection obs: 88.1
Xplor file
Refine IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ATP.PARATP.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMTOPMG.PRO
X-RAY DIFFRACTION4PAR_MG.PRO
Software
*PLUS
Name: CNS / Version: 0.4 / Classification: refinement
Refine LS restraints
*PLUS
Refine IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.26
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.77
Refine LS shell
*PLUS
R factor obs: 0.288 / R factor R free: 0.333

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