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- PDB-2cm5: crystal structure of the C2B domain of rabphilin -

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Basic information

Entry
Database: PDB / ID: 2cm5
Titlecrystal structure of the C2B domain of rabphilin
ComponentsRABPHILIN-3A
KeywordsPROTEIN TRANSPORT / ZINC-FINGER / RABPHILIN3A / CA2+ BINDING / METAL-BINDING / SYNAPTIC EXOCYTOSIS / C2A-C2B LINKER FRAGMENT / C2B / ZINC / SYNAPSE / C2 DOMAIN / TRANSPORT
Function / homology
Function and homology information


selenium binding / spontaneous neurotransmitter secretion / extrinsic component of synaptic vesicle membrane / regulation of calcium ion-dependent exocytosis / cholinergic synapse / inositol 1,4,5 trisphosphate binding / calcium-dependent phospholipid binding / dendritic spine organization / synaptic vesicle priming / extrinsic component of membrane ...selenium binding / spontaneous neurotransmitter secretion / extrinsic component of synaptic vesicle membrane / regulation of calcium ion-dependent exocytosis / cholinergic synapse / inositol 1,4,5 trisphosphate binding / calcium-dependent phospholipid binding / dendritic spine organization / synaptic vesicle priming / extrinsic component of membrane / phosphate ion binding / exocytosis / regulation of NMDA receptor activity / phosphatidylinositol-4,5-bisphosphate binding / secretory granule / phospholipid binding / intracellular protein transport / neuromuscular junction / synaptic vesicle membrane / small GTPase binding / synaptic vesicle / postsynaptic membrane / dendritic spine / neuron projection / synapse / calcium ion binding / protein-containing complex binding / protein-containing complex / zinc ion binding
Similarity search - Function
Rabphilin-3A / : / Rabphilin/DOC2/Noc2 / Rab-binding domain / FYVE-type zinc finger / FYVE-type zinc finger / Rab-binding domain profile. / Zinc finger, FYVE-related / Zinc finger FYVE/FYVE-related type profile. / Synaptotagmin ...Rabphilin-3A / : / Rabphilin/DOC2/Noc2 / Rab-binding domain / FYVE-type zinc finger / FYVE-type zinc finger / Rab-binding domain profile. / Zinc finger, FYVE-related / Zinc finger FYVE/FYVE-related type profile. / Synaptotagmin / C2 domain / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain profile. / C2 domain superfamily / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.28 Å
AuthorsSchlicker, C. / Montaville, P. / Sheldrick, G.M. / Becker, S.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: The C2A-C2B Linker Defines the High Affinity Ca2+ Binding Mode of Rabphilin-3A.
Authors: Montaville, P. / Schlicker, C. / Leonov, A. / Zweckstetter, M. / Sheldrick, G.M. / Becker, S.
History
DepositionMay 4, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 4, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: 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: RABPHILIN-3A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3763
Polymers19,2951
Non-polymers802
Water1,22568
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)53.898, 60.043, 41.928
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-2036-

HOH

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Components

#1: Protein RABPHILIN-3A / C2B DOMAIN / EXOPHILIN-1


Mass: 19295.396 Da / Num. of mol.: 1 / Fragment: C2B DOMAIN AND LINKER, RESIDUES 519-684
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Plasmid: PGEX-2T-RABPHILIN3A-519-684 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B843 / References: UniProt: P47709
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 38 %
Crystal growDetails: 0.1M HEPES PH 8.5,20 % PEG MME 2000 OR 20 % PEG 8000

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Data collection

DiffractionMean temperature: 89.7 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.95,0.9796
DetectorDate: Nov 21, 2005
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.951
20.97961
ReflectionResolution: 1.28→40.11 Å / Num. obs: 33387 / % possible obs: 94.2 % / Observed criterion σ(I): 2.75 / Redundancy: 1.72 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 14.38
Reflection shellResolution: 1.28→1.38 Å / Redundancy: 1.16 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 2.84 / % possible all: 72.7

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Processing

Software
NameClassification
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXCDphasing
SHELXDphasing
SHELXEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.28→40.11 Å / Num. restraintsaints: 13375 / Cross valid method: THROUGHOUT / σ(F): 2.75
RfactorNum. reflection% reflectionSelection details
Rfree0.1937 3060 5 %RANDOM
all0.1453 61145 --
obs0.144 -94.2 %-
Refinement stepCycle: LAST / Resolution: 1.28→40.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1123 0 2 68 1193
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.011
X-RAY DIFFRACTIONs_angle_d0.03
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.0342
X-RAY DIFFRACTIONs_zero_chiral_vol0.061
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.067
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.024
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.004
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.061
X-RAY DIFFRACTIONs_approx_iso_adps0.088

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