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

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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 / 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 / 1.9 Å resolution
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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: May 14, 1999 / Release: May 18, 1999
RevisionDateData content typeGroupProviderType
1.0May 18, 1999Structure modelrepositoryInitial release
1.1Apr 27, 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: N-ETHYLMALEIMIDE SENSITIVE FACTOR (NSF-N)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8374
Polyers23,5491
Non-polymers2883
Water2,342130
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
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-MC 2 2 21
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/peptide N-ETHYLMALEIMIDE SENSITIVE FACTOR (NSF-N)


Mass: 23548.947 Da / Num. of mol.: 1
Details: THIS PROTEIN IS ONE DOMAIN OF THREE IN THE NSF PROTOMER. BIOLOGICALLY NSF IS A HEXAMER.
Fragment: N-TERMINAL DOMAIN OF NSF / Source: (gene. exp.) Cricetulus griseus (Chinese hamster) / Genus: Cricetulus / Tissue: OVARY / Genus (production host): Escherichia / 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


Mass: 96.063 Da / Num. of mol.: 3 / Formula: SO4 / Sulfate
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / Formula: H2O / Water

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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 / Density percent sol: 48.21 %
Crystal growTemp: 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
Temp: 20 ℃ / Method: vapor diffusion, sitting drop
components of the solutions
*PLUS
IDConcCommon 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
SourceSource: SYNCHROTRON / Type: ALS BEAMLINE 5.0.2 / Synchrotron site: ALS / Beamline: 5.0.2 / Wavelength: 0.9799, 0.9801, 0.9998, 0.9537
DetectorType: ADSC / Detector: CCD / Collection date: Feb 13, 1998
RadiationDiffraction protocol: MAD / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelength
IDWavelengthRelative weight
10.97991.0
20.98011.0
30.99981.0
40.95371.0
ReflectionB iso Wilson estimate: 12.1 / D resolution high: 1.9 / D resolution low: 50 / Number all: 37996 / Number obs: 32752 / Observed criterion sigma F: 0 / Observed criterion sigma I: -3 / Rmerge I obs: 0.057 / NetI over sigmaI: 20.4 / Redundancy: 3.2 % / Percent possible obs: 98
Reflection shellRmerge I obs: 0.051 / Highest resolution: 1.9 / Lowest resolution: 1.97 / Number unique all: 3100 / Redundancy: 2.7 % / Percent possible all: 92.7
Reflection
*PLUS
Number obs: 33216
Reflection shell
*PLUS
Percent possible obs: 92.7 / Rmerge I obs: 0.27 / MeanI over sigI obs: 5.1

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Processing

Software
NameClassification
CNSrefinement
ADSCdata collection
SCALEPACKdata scaling
CNSphasing
RefineDetails: MLHL target function and density modified, combined phases used in refinements. Wavelength 3 (low energy remote, 0.9998 Angstrom) data used for refinement.
R Free selection details: random 10% / Data cutoff high absF: 2145257.79 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Sigma F: 0 / Sigma I: 0 / Stereochemistry target values: Engh and Huber
Solvent computationSolvent model details: FLAT MODEL / Solvent model param bsol: 46.28 / Solvent model param ksol: 0.403
Displacement parametersB iso mean: 25.5 / Aniso B11: -5.53 / Aniso B12: 0 / Aniso B13: 0 / Aniso B22: -3.62 / Aniso B23: 0 / Aniso B33: 9.16
Least-squares processR factor R free: 0.242 / R factor R free error: 0.004 / R factor R work: 0.21 / R factor all: 0.213 / R factor obs: 0.213 / Highest resolution: 1.9 / Lowest resolution: 5 / Number reflection R free: 3195 / Number reflection all: 34181 / Number reflection obs: 32739 / Percent reflection R free: 9.8 / Percent reflection obs: 95.8
Refine analyzeLuzzati coordinate error free: 0.26 / Luzzati coordinate error obs: 0.21 / Luzzati d res low obs: 5 / Luzzati sigma a free: 0.14 / Luzzati sigma a obs: 0.15
Refine hist #LASTHighest resolution: 1.9 / Lowest resolution: 5
Number of atoms included #LASTProtein: 1517 / Nucleic acid: 0 / Ligand: 15 / Solvent: 130 / Total: 1662
Refine LS restraints
Refine IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.010
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d25.3
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_mcbond_it1.111.50
X-RAY DIFFRACTIONc_mcangle_it1.822.00
X-RAY DIFFRACTIONc_scbond_it2.702.00
X-RAY DIFFRACTIONc_scangle_it3.732.50
Refine LS shellHighest resolution: 1.9 / R factor R free: 0.259 / R factor R free error: 0.012 / R factor R work: 0.227 / Lowest resolution: 2.02 / Number reflection R free: 478 / Number reflection R work: 4359 / Total number of bins used: 6 / Percent reflection R free: 9.9 / Percent reflection 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
Displacement parameters
*PLUS
B iso mean: 25.53
Least-squares process
*PLUS
R factor obs: 0.21
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
Refine LS shell
*PLUS
Total number of bins used: 10 / Lowest resolution: 1.97 / R factor R free: 0.281 / R factor R work: 0.24

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