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- PDB-4mt7: Crystal structure of collybistin I -

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Basic information

Entry
Database: PDB / ID: 4mt7
TitleCrystal structure of collybistin I
ComponentsRho guanine nucleotide exchange factor 9
KeywordsPROTEIN BINDING / extended conformation
Function / homology
Function and homology information


GABA receptor activation / regulation of postsynaptic specialization assembly / NRAGE signals death through JNK / G alpha (12/13) signalling events / RHOQ GTPase cycle / CDC42 GTPase cycle / postsynaptic specialization / glycinergic synapse / GABA-ergic synapse / receptor clustering ...GABA receptor activation / regulation of postsynaptic specialization assembly / NRAGE signals death through JNK / G alpha (12/13) signalling events / RHOQ GTPase cycle / CDC42 GTPase cycle / postsynaptic specialization / glycinergic synapse / GABA-ergic synapse / receptor clustering / guanyl-nucleotide exchange factor activity / cell cortex / postsynaptic density / anchoring junction / plasma membrane / cytosol
Similarity search - Function
Rho guanine nucleotide exchange factor 9, SH3 domain / Dbl Homology Domain; Chain A / Dbl homology (DH) domain / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain superfamily / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like ...Rho guanine nucleotide exchange factor 9, SH3 domain / Dbl Homology Domain; Chain A / Dbl homology (DH) domain / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain superfamily / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / SH3 domain / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / PH-like domain superfamily / Roll / Up-down Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Rho guanine nucleotide exchange factor 9
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.5 Å
AuthorsSchneeberger, D. / Schindelin, H.
CitationJournal: Embo J. / Year: 2014
Title: A conformational switch in collybistin determines the differentiation of inhibitory postsynapses.
Authors: Soykan, T. / Schneeberger, D. / Tria, G. / Buechner, C. / Bader, N. / Svergun, D. / Tessmer, I. / Poulopoulos, A. / Papadopoulos, T. / Varoqueaux, F. / Schindelin, H. / Brose, N.
History
DepositionSep 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 13, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rho guanine nucleotide exchange factor 9


Theoretical massNumber of molelcules
Total (without water)57,3681
Polymers57,3681
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.930, 165.430, 129.120
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Rho guanine nucleotide exchange factor 9 / Collybistin / Rac/Cdc42 guanine nucleotide exchange factor 9


Mass: 57368.105 Da / Num. of mol.: 1 / Fragment: unp residues 10-493
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Arhgef9 / Plasmid: pTXB1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9QX73

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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: 3.86 Å3/Da / Density % sol: 68.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100mM MES, 15% PEG 20000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 18, 2011
RadiationMonochromator: horizontally diffracting Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 3.5→129.12 Å / Num. all: 11560 / Num. obs: 11560 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Biso Wilson estimate: 131.69 Å2 / Rsym value: 0.08 / Net I/σ(I): 9.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
3.5-3.694.60.7141.10.7141100
3.69-3.914.50.4461.70.4461100
3.91-4.184.50.262.90.261100
4.18-4.524.50.1285.50.1281100
4.52-4.954.50.0818.30.0811100
4.95-5.534.50.07180.0711100
5.53-6.394.50.1045.50.1041100
6.39-7.834.40.0698.60.0691100
7.83-11.074.30.04112.40.0411100
11.07-64.563.90.02522.80.025198.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHASERphasing
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
DNAdata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→50.893 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.44 / σ(F): 1.35 / Phase error: 32.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2487 865 7.54 %
Rwork0.2207 --
obs0.2228 11474 99.33 %
all-11474 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 120.8885 Å2
Refinement stepCycle: LAST / Resolution: 3.5→50.893 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2859 0 0 0 2859
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052917
X-RAY DIFFRACTIONf_angle_d0.9233915
X-RAY DIFFRACTIONf_dihedral_angle_d17.0561128
X-RAY DIFFRACTIONf_chiral_restr0.072401
X-RAY DIFFRACTIONf_plane_restr0.003512
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5002-3.71940.39771530.35061725X-RAY DIFFRACTION99
3.7194-4.00650.33511590.29461712X-RAY DIFFRACTION99
4.0065-4.40950.27631310.24251767X-RAY DIFFRACTION99
4.4095-5.04710.21831460.18671742X-RAY DIFFRACTION99
5.0471-6.35680.24841410.24571792X-RAY DIFFRACTION100
6.3568-50.89840.21251350.1881871X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
16.04020.0146-0.70095.6561-2.51885.07920.02330.9860.9047-0.5207-0.731-0.6567-0.29570.60110.33120.70140.16680.03810.73010.42810.5593-22.5157-18.659712.824
23.6816-0.83350.07871.9441-0.04732.9471-0.5578-0.2777-0.50940.5608-0.1518-0.04090.5182-0.6220.63090.84350.18220.21170.6035-0.16980.6365-12.0627-51.6849-9.7989
35.4005-2.28160.38814.9392-2.18645.41250.009-0.8511-1.83621.071-0.02880.96592.4461-0.56880.53332.1452-0.40280.28841.37730.32841.0322-10.9718-63.4248-1.596
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 45 through 233 )
2X-RAY DIFFRACTION2chain 'A' and (resid 234 through 306 )
3X-RAY DIFFRACTION3chain 'A' and (resid 307 through 381 )

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