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- PDB-4mjj: Crystal structure of the C2A domain of DOC2A -

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Basic information

Entry
Database: PDB / ID: 4mjj
TitleCrystal structure of the C2A domain of DOC2A
ComponentsDouble C2-like domain-containing protein alpha
KeywordsMETAL BINDING PROTEIN / C2 domain / DOC2A / calcium binding protein
Function / homology
Function and homology information


spontaneous neurotransmitter secretion / calcium-dependent activation of synaptic vesicle fusion / regulation of calcium ion-dependent exocytosis / positive regulation of calcium ion-dependent exocytosis / extrinsic component of synaptic vesicle membrane / calcium-dependent phospholipid binding / cell junction / nervous system development / chemical synaptic transmission / lysosome ...spontaneous neurotransmitter secretion / calcium-dependent activation of synaptic vesicle fusion / regulation of calcium ion-dependent exocytosis / positive regulation of calcium ion-dependent exocytosis / extrinsic component of synaptic vesicle membrane / calcium-dependent phospholipid binding / cell junction / nervous system development / chemical synaptic transmission / lysosome / neuron projection / synapse / nucleolus / glutamatergic synapse / nucleoplasm / metal ion binding
Similarity search - Function
Double C2 protein, alpha/beta/gamma / Rabphilin/DOC2/Noc2 / : / Synaptotagmin / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain / C2 domain profile. / C2 domain superfamily ...Double C2 protein, alpha/beta/gamma / Rabphilin/DOC2/Noc2 / : / Synaptotagmin / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain / C2 domain profile. / C2 domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Double C2-like domain-containing protein alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHuang, Q.Q.
CitationJournal: To be Published
Title: Crystal structure of the C2A domain of DOC2A
Authors: Huang, Q.Q.
History
DepositionSep 3, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Double C2-like domain-containing protein alpha


Theoretical massNumber of molelcules
Total (without water)15,6521
Polymers15,6521
Non-polymers00
Water1,60389
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Double C2-like domain-containing protein alpha

A: Double C2-like domain-containing protein alpha


Theoretical massNumber of molelcules
Total (without water)31,3042
Polymers31,3042
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Buried area720 Å2
ΔGint-11 kcal/mol
Surface area12820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.977, 33.064, 63.748
Angle α, β, γ (deg.)90.00, 124.55, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-301-

HOH

21A-346-

HOH

31A-350-

HOH

41A-388-

HOH

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Components

#1: Protein Double C2-like domain-containing protein alpha / Doc2 / Doc2-alpha


Mass: 15651.939 Da / Num. of mol.: 1 / Fragment: C2A, unp residues 81-217
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DOC2A / Production host: Escherichia coli (E. coli) / References: UniProt: Q14183
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.33 Å3/Da / Density % sol: 47.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 14% PEG400, 100mM Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.918 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 25, 2013
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.7→35 Å / Num. all: 15800 / Num. obs: 15658 / % possible obs: 99.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.6 % / Rmerge(I) obs: 0.136
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.275 / Num. unique all: 760 / % possible all: 96.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→21.215 Å / SU ML: 0.18 / σ(F): 1 / σ(I): 1 / Phase error: 30.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.267 960 9.95 %random
Rwork0.2184 ---
obs0.2233 9644 96.65 %-
all-9978 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→21.215 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms932 0 0 89 1021
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008948
X-RAY DIFFRACTIONf_angle_d1.1721276
X-RAY DIFFRACTIONf_dihedral_angle_d15.718365
X-RAY DIFFRACTIONf_chiral_restr0.083148
X-RAY DIFFRACTIONf_plane_restr0.004161
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0002-2.10560.28661320.23621164X-RAY DIFFRACTION92
2.1056-2.23740.33061380.23431220X-RAY DIFFRACTION96
2.2374-2.40990.27611310.23411232X-RAY DIFFRACTION96
2.4099-2.6520.26271370.21721244X-RAY DIFFRACTION97
2.652-3.03480.27291360.23191245X-RAY DIFFRACTION98
3.0348-3.81990.24551430.20911292X-RAY DIFFRACTION100
3.8199-21.21650.26221430.21021287X-RAY DIFFRACTION97

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