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- PDB-1qdn: AMINO TERMINAL DOMAIN OF THE N-ETHYLMALEIMIDE SENSITIVE FUSION PR... -

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Basic information

Entry
Database: PDB / ID: 1qdn
TitleAMINO TERMINAL DOMAIN OF THE N-ETHYLMALEIMIDE SENSITIVE FUSION PROTEIN (NSF)
ComponentsPROTEIN (N-ETHYLMALEIMIDE SENSITIVE FUSION PROTEIN (NSF))
KeywordsFUSION PROTEIN / DOUBLE-PSI BETA BARREL ALPHA/BETA BARREL / VESICULAR-FUSION PROTEIN
Function / homology
Function and homology information


SNARE complex disassembly / ATP-dependent protein disaggregase activity / vesicle-fusing ATPase / syntaxin-1 binding / positive regulation of receptor recycling / ionotropic glutamate receptor binding / SNARE binding / PDZ domain binding / intracellular protein transport / potassium ion transport ...SNARE complex disassembly / ATP-dependent protein disaggregase activity / vesicle-fusing ATPase / syntaxin-1 binding / positive regulation of receptor recycling / ionotropic glutamate receptor binding / SNARE binding / PDZ domain binding / intracellular protein transport / potassium ion transport / positive regulation of protein catabolic process / midbody / protein-containing complex binding / protein kinase binding / Golgi apparatus / ATP hydrolysis activity / ATP binding / identical protein binding / metal ion binding / plasma membrane / cytosol
Similarity search - Function
Vesicle-fusing ATPase / Vcp-like ATPase; Chain A, domain 2 - #10 / Vcp-like ATPase; Chain A, domain 2 / Barwin-like endoglucanases - #20 / Barwin-like endoglucanases / Cell division protein 48 (CDC48), N-terminal domain / CDC48, N-terminal subdomain / Cell division protein 48 (CDC48) N-terminal domain / CDC48, domain 2 / Cell division protein 48 (CDC48), domain 2 ...Vesicle-fusing ATPase / Vcp-like ATPase; Chain A, domain 2 - #10 / Vcp-like ATPase; Chain A, domain 2 / Barwin-like endoglucanases - #20 / Barwin-like endoglucanases / Cell division protein 48 (CDC48), N-terminal domain / CDC48, N-terminal subdomain / Cell division protein 48 (CDC48) N-terminal domain / CDC48, domain 2 / Cell division protein 48 (CDC48), domain 2 / Cell division protein 48 (CDC48) domain 2 / CDC48 domain 2-like superfamily / Aspartate decarboxylase-like domain superfamily / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Roll / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / Vesicle-fusing ATPase
Similarity search - Component
Biological speciesCricetulus griseus (Chinese hamster)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsMay, A.P. / Misura, K.M.S. / Whiteheart, S.W. / Weis, W.I.
CitationJournal: Nat.Cell Biol. / Year: 1999
Title: Crystal structure of the amino-terminal domain of N-ethylmaleimide-sensitive fusion protein.
Authors: May, A.P. / Misura, K.M. / Whiteheart, S.W. / Weis, W.I.
History
DepositionMay 21, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (N-ETHYLMALEIMIDE SENSITIVE FUSION PROTEIN (NSF))
B: PROTEIN (N-ETHYLMALEIMIDE SENSITIVE FUSION PROTEIN (NSF))
C: PROTEIN (N-ETHYLMALEIMIDE SENSITIVE FUSION PROTEIN (NSF))
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,75417
Polymers67,5173
Non-polymers1,23714
Water4,360242
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6010 Å2
ΔGint-117 kcal/mol
Surface area27120 Å2
MethodPISA
2
A: PROTEIN (N-ETHYLMALEIMIDE SENSITIVE FUSION PROTEIN (NSF))
B: PROTEIN (N-ETHYLMALEIMIDE SENSITIVE FUSION PROTEIN (NSF))
C: PROTEIN (N-ETHYLMALEIMIDE SENSITIVE FUSION PROTEIN (NSF))
hetero molecules

A: PROTEIN (N-ETHYLMALEIMIDE SENSITIVE FUSION PROTEIN (NSF))
B: PROTEIN (N-ETHYLMALEIMIDE SENSITIVE FUSION PROTEIN (NSF))
C: PROTEIN (N-ETHYLMALEIMIDE SENSITIVE FUSION PROTEIN (NSF))
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,50834
Polymers135,0346
Non-polymers2,47528
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area20000 Å2
ΔGint-282 kcal/mol
Surface area46260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.900, 101.900, 126.940
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein PROTEIN (N-ETHYLMALEIMIDE SENSITIVE FUSION PROTEIN (NSF))


Mass: 22505.625 Da / Num. of mol.: 3 / Fragment: AMINO TERMINAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cricetulus griseus (Chinese hamster) / Organ: OVARY / Plasmid: PQE9 / Production host: Escherichia coli (E. coli) / References: UniProt: P18708
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6OS
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 242 / 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: 2.44 Å3/Da / Density % sol: 49.58 %
Crystal growpH: 8.2
Details: TRIS, AMMONIUM SULPHATE, 2- MERCAPTOETHANOL, pH 8.2
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
128 mg/mlprotein1drop
225 mMTris-HCl1drop
3150 mM1dropKCl
410 mM2-mercaptoethanol1drop
5100 mMTris-HCl1reservoir
61.85-2.05 Mammonium sulfate1reservoir
710 mM2-mercaptoethanol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 11, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 28518 / % possible obs: 98.9 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 20.2 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 19.6
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.312 / % possible all: 98.7
Reflection shell
*PLUS
% possible obs: 98.7 %

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Processing

Software
NameVersionClassification
CNS0.5refinement
DENZOdata reduction
SCALEPACKdata scaling
CNS0.5phasing
RefinementResolution: 2.3→30 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 3541190.6 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.26 1675 5.9 %RANDOM
Rwork0.22 ---
obs0.22 28518 94 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.87 Å2 / ksol: 0.358 e/Å3
Displacement parametersBiso mean: 34.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.99 Å20 Å20 Å2
2--0.99 Å20 Å2
3----1.98 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.35 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4436 0 64 242 4742
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.68
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.261.5
X-RAY DIFFRACTIONc_mcangle_it2.152
X-RAY DIFFRACTIONc_scbond_it1.842
X-RAY DIFFRACTIONc_scangle_it2.822.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.341 263 6 %
Rwork0.273 4102 -
obs--88.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAWATER.TOP
X-RAY DIFFRACTION3BME.PARBME.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.68

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