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- PDB-4ts6: Crystal structure of the RIM C2A domain from Drosophila. -

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Basic information

Entry
Database: PDB / ID: 4ts6
TitleCrystal structure of the RIM C2A domain from Drosophila.
ComponentsRab3 interacting molecule variant 2
KeywordsTRANSPORT PROTEIN / C2A domain
Function / homology
Function and homology information


small GTPase binding => GO:0031267 / exocytosis / intracellular protein transport / synapse / membrane / metal ion binding
Similarity search - Function
Rim-like / 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. / C2 domain / C2 domain / Protein kinase C conserved region 2 (CalB) ...Rim-like / 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. / C2 domain / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain profile. / C2 domain superfamily / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Rab3 interacting molecule variant 2
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.92 Å
AuthorsHatzopoulos, G.N. / Shiroma, J. / Vakonakis, I.
CitationJournal: To Be Published
Title: Crystal structure of the RIM C2A domain from Drosophila.
Authors: Paul, M. / Heckmann, M. / Gehring, J. / Kittel, R.J. / Ulzhoefer, S. / Neuser, K. / DiAntonio, A. / Hatzopoulos, G.N. / Shiroma, J. / Vakonakis, I. / Langenhan, T.
History
DepositionJun 18, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Rab3 interacting molecule variant 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0442
Polymers14,9521
Non-polymers921
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint-0 kcal/mol
Surface area6870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.080, 38.700, 131.370
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Rab3 interacting molecule variant 2


Mass: 14952.046 Da / Num. of mol.: 1 / Fragment: Residues 836-962
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Rim / Production host: Escherichia coli (E. coli) / References: UniProt: V5M2P5
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 2.73 Å3/Da / Density % sol: 54.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.2 M tri-lithium citrate, 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.999 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 15, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 1.92→65.68 Å / Num. obs: 13188 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 36.806 Å2 / Rmerge F obs: 0.998 / Rmerge(I) obs: 0.057 / Rrim(I) all: 0.066 / Net I/σ(I): 12.39 / Num. measured all: 90891
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.92-1.970.6940.6431.976649176317560.75199.6
1.97-2.020.8710.3973.096723176917690.462100
2.02-2.080.8770.3373.796314166416620.39499.9
2.08-2.150.9140.2924.326499171117090.3499.9
2.15-2.220.9650.2135.75791152015190.24899.9
2.22-2.290.960.1886.766072159315920.21999.9
2.29-2.380.9730.1567.885510144614440.18299.9
2.38-2.480.9780.1398.945513145514540.16299.9
2.48-2.590.9850.11510.445177136913650.13599.7
2.59-2.720.9910.08813.164900129912990.102100
2.72-2.860.9920.07814.994720125412490.09199.6
2.86-3.040.9950.06217.954399117711700.07299.4
3.04-3.250.9970.04921.854226114411360.05799.3
3.25-3.510.9970.04324.533763102810200.0599.2
3.51-3.840.9970.03927.1634459409280.04598.7
3.84-4.290.9980.03727.9931118538450.04499.1
4.29-4.960.9970.03329.1327457707600.03998.7
4.96-6.070.9990.02728.3624376366320.03199.4
6.07-8.590.9990.02628.7719265015000.0399.8
8.590.9990.02528.689712812690.02995.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless3.11data scaling
Cootmodel building
PHENIX(phenix.refine: 1.8.2_1309)refinement
MrBUMPphasing
XSCALEdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BWQ

2bwq


Resolution: 1.92→65.68 Å / Occupancy max: 1 / Occupancy min: 0.42 / FOM work R set: 0.8336 / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2182 648 4.93 %
Rwork0.1843 12492 -
obs0.186 13140 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 91.22 Å2 / Biso mean: 37.6901 Å2 / Biso min: 15.1 Å2
Refinement stepCycle: LAST / Resolution: 1.92→65.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1017 0 6 94 1117
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071058
X-RAY DIFFRACTIONf_angle_d1.191436
X-RAY DIFFRACTIONf_chiral_restr0.086159
X-RAY DIFFRACTIONf_plane_restr0.004184
X-RAY DIFFRACTIONf_dihedral_angle_d13.69392
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / % reflection obs: 100 %

Resolution (Å)Highest resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.9201-2.06830.2951370.22672418
2.0683-2.27650.24711200.19622486
2.2765-2.60590.20931320.19542442
2.6059-3.28320.2551200.19092517
3.28320.1881390.17042629
Refinement TLS params.Method: refined / Origin x: 14.3144 Å / Origin y: 4.2403 Å / Origin z: -17.8546 Å
111213212223313233
T0.1424 Å2-0.0329 Å20.0283 Å2-0.2094 Å2-0.0483 Å2--0.2187 Å2
L2.5579 °2-0.7521 °2-0.7027 °2-2.9456 °21.0375 °2--3.2253 °2
S-0.0471 Å °-0.3888 Å °0.2443 Å °-0.0716 Å °0.176 Å °-0.3199 Å °-0.0017 Å °0.1437 Å °-0.1061 Å °
Refinement TLS groupSelection details: chain 'A' and (resid -1 through 962)

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