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- PDB-1qcs: N-TERMINAL DOMAIN OF N-ETHYLMALEIMIDE SENSITIVE FACTOR (NSF) -

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Basic information

Entry
Database: PDB / ID: 1qcs
TitleN-TERMINAL DOMAIN OF N-ETHYLMALEIMIDE SENSITIVE FACTOR (NSF)
ComponentsN-ETHYLMALEIMIDE SENSITIVE FACTOR (NSF-N)
KeywordsFUSION PROTEIN / DOUBLE-PSI BETA BARREL ALPHA BETA ROLL
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
Vesicle-fusing ATPase
Similarity search - Component
Biological speciesCricetulus griseus (Chinese hamster)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å
AuthorsYu, R.C. / Jahn, R. / Brunger, A.T.
CitationJournal: Mol.Cell / Year: 1999
Title: NSF N-terminal domain crystal structure: models of NSF function.
Authors: Yu, R.C. / Jahn, R. / Brunger, A.T.
History
DepositionMay 14, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 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

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Assembly

Deposited unit
A: N-ETHYLMALEIMIDE SENSITIVE FACTOR (NSF-N)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8374
Polymers23,5491
Non-polymers2883
Water2,342130
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.042, 175.362, 79.663
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsIs one domain of three in the NSF protomer. Biologically NSF is a hexamer. SYMMETRY OPERATORS AND RELEVANT TRANSLATIONS FOR HEXAMERIZATION ARE UNKNOWN. NSF CONTAINS 3 DOMAINS: N, D1, AND D2. D2 IS THE HEXAMERIZATION DOMAIN. BOTH THE SPATIAL ORIENTATION OF N RELATIVE TO D2, AND THE STRUCTURE OF IN THE INTERMEDIATE D1 DOMAIN ARE NOT KNOWN.

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Components

#1: Protein N-ETHYLMALEIMIDE SENSITIVE FACTOR (NSF-N)


Mass: 23548.947 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN OF NSF
Source method: isolated from a genetically manipulated source
Details: THIS PROTEIN IS ONE DOMAIN OF THREE IN THE NSF PROTOMER. BIOLOGICALLY NSF IS A HEXAMER.
Source: (gene. exp.) Cricetulus griseus (Chinese hamster) / Tissue: OVARY / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
Keywords: THIS PROTEIN IS ONE DOMAIN OF THREE IN THE NSF PROTOMER. BIOLOGICALLY NSF IS A HEXAMER.
References: UniProt: P18708
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 2.38 Å3/Da / Density % sol: 48.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.7
Details: Vapor diffusion, hanging drop, 100 mM Tris pH 8.7, 2.0 M ammonium sulfate, 10 mM dithiothreitol (DTT), VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
2100 mMTris-HCl1drop
32.0 Mammonium sulfate1drop
410 mMdithiothreitol1drop
5100 mMTris-HCl1reservoir
62.0 Mammonium sulfate1reservoir
710 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9799, 0.9801, 0.9998, 0.9537
DetectorType: ADSC / Detector: CCD / Date: Feb 13, 1998
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97991
20.98011
30.99981
40.95371
ReflectionResolution: 1.9→50 Å / Num. all: 37996 / Num. obs: 32752 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Biso Wilson estimate: 12.1 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 20.4
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.051 / Num. unique all: 3100 / % possible all: 92.7
Reflection
*PLUS
Num. obs: 33216
Reflection shell
*PLUS
% possible obs: 92.7 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 5.1

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Processing

Software
NameClassification
CNSrefinement
ADSCdata collection
SCALEPACKdata scaling
CNSphasing
RefinementResolution: 1.9→50 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2145257.79 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh and Huber
Details: MLHL target function and density modified, combined phases used in refinements. Wavelength 3 (low energy remote, 0.9998 Angstrom) data used for refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.242 3195 9.8 %random 10%
Rwork0.21 ---
all0.213 34181 --
obs0.213 32739 95.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.28 Å2 / ksol: 0.403 e/Å3
Displacement parametersBiso mean: 25.5 Å2
Baniso -1Baniso -2Baniso -3
1--5.53 Å20 Å20 Å2
2---3.62 Å20 Å2
3---9.16 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1517 0 15 130 1662
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d25.3
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_mcbond_it1.111.5
X-RAY DIFFRACTIONc_mcangle_it1.822
X-RAY DIFFRACTIONc_scbond_it2.72
X-RAY DIFFRACTIONc_scangle_it3.732.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.259 478 9.9 %
Rwork0.227 4359 -
obs--85.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 25.53 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.42
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.79
LS refinement shell
*PLUS
Lowest resolution: 1.97 Å / Rfactor Rfree: 0.281 / Rfactor Rwork: 0.24 / Total num. of bins used: 10

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