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- PDB-6a68: the crystal structure of rat calcium-dependent activator protein ... -

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Basic information

Entry
Database: PDB / ID: 6a68
Titlethe crystal structure of rat calcium-dependent activator protein for secretion (CAPS) DAMH domain
ComponentsCalcium-dependent secretion activator 1
KeywordsEXOCYTOSIS / exocytosis DCV transition
Function / homology
Function and homology information


extrinsic component of neuronal dense core vesicle membrane / catecholamine secretion / dense core granule / regulated exocytosis / presynaptic dense core vesicle exocytosis / vesicle organization / positive regulation of calcium ion-dependent exocytosis / synaptic vesicle priming / exocytosis / positive regulation of exocytosis ...extrinsic component of neuronal dense core vesicle membrane / catecholamine secretion / dense core granule / regulated exocytosis / presynaptic dense core vesicle exocytosis / vesicle organization / positive regulation of calcium ion-dependent exocytosis / synaptic vesicle priming / exocytosis / positive regulation of exocytosis / phosphatidylinositol-4,5-bisphosphate binding / establishment of localization in cell / protein transport / presynapse / cytoplasmic vesicle / glutamatergic synapse / calcium ion binding / protein kinase binding
Similarity search - Function
Calcium-dependent secretion activator / MUN domain / Munc13 homology 1 / MUN domain / Munc13-homology domain 1 (MHD1) profile. / Domain of Unknown Function (DUF1041) / C2 domain / C2 domain profile. / PH domain / PH domain profile. ...Calcium-dependent secretion activator / MUN domain / Munc13 homology 1 / MUN domain / Munc13-homology domain 1 (MHD1) profile. / Domain of Unknown Function (DUF1041) / C2 domain / C2 domain profile. / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily
Similarity search - Domain/homology
: / Calcium-dependent secretion activator 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.901 Å
AuthorsZhou, H. / Wei, Z.Q. / Yao, D.Q. / Zhang, R.G. / Ma, C.
CitationJournal: Cell Rep / Year: 2019
Title: Structural and Functional Analysis of the CAPS SNARE-Binding Domain Required for SNARE Complex Formation and Exocytosis.
Authors: Zhou, H. / Wei, Z. / Wang, S. / Yao, D. / Zhang, R. / Ma, C.
History
DepositionJun 26, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI
Revision 1.2Nov 20, 2019Group: Database references / Category: citation / citation_author
Item: _citation.page_last / _citation.pdbx_database_id_PubMed ..._citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Calcium-dependent secretion activator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6022
Polymers21,5631
Non-polymers391
Water19811
1
A: Calcium-dependent secretion activator 1
hetero molecules

A: Calcium-dependent secretion activator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2044
Polymers43,1252
Non-polymers782
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
Buried area4120 Å2
ΔGint-45 kcal/mol
Surface area20730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.305, 149.305, 81.414
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number177
Space group name H-MP622
Components on special symmetry positions
IDModelComponents
11A-1101-

K

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Components

#1: Protein Calcium-dependent secretion activator 1 / Calcium-dependent activator protein for secretion 1 / rCAPS


Mass: 21562.670 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Cadps, Caps, Caps1 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q62717
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 6.13 Å3/Da / Density % sol: 79.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 18-25% (v/v) PEG 3350, 0.1M Succinic acid (pH 7.0-7.5)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.9→25 Å / Num. obs: 12274 / % possible obs: 99.7 % / Redundancy: 9.6 % / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.041 / Net I/σ(I): 16.8
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.828 / Mean I/σ(I) obs: 2.4 / Rpim(I) all: 0.276 / % possible all: 99.8

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-3000data reduction
HKL-3000data scaling
SHELXphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.901→24.884 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 29.19 / Stereochemistry target values: ML
Details: Anomalous signal for residue 0 MET was very weak, and could not be identified as MSE.
RfactorNum. reflection% reflection
Rfree0.2862 559 4.87 %
Rwork0.2559 10926 -
obs0.2574 11485 93.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 153.88 Å2 / Biso mean: 49.1338 Å2 / Biso min: 6.4 Å2
Refinement stepCycle: final / Resolution: 2.901→24.884 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1282 0 1 11 1294
Biso mean--40.53 23.43 -
Num. residues----162
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051317
X-RAY DIFFRACTIONf_angle_d0.741795
X-RAY DIFFRACTIONf_chiral_restr0.044198
X-RAY DIFFRACTIONf_plane_restr0.006233
X-RAY DIFFRACTIONf_dihedral_angle_d2.957766
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9009-3.19220.3941170.35112155227276
3.1922-3.65290.33921230.28942842296598
3.6529-4.59750.27441500.22929103060100
4.5975-24.88510.2421690.2313019318899

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