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- PDB-3iez: Crystal structure of the RasGAP C-terminal (RGC) domain of IQGAP2 -

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Basic information

Entry
Database: PDB / ID: 3iez
TitleCrystal structure of the RasGAP C-terminal (RGC) domain of IQGAP2
ComponentsRas GTPase-activating-like protein IQGAP2
KeywordsSIGNALING PROTEIN / gap / structural genomics consortium / sgc / Calmodulin-binding / Phosphoprotein
Function / homology
Function and homology information


mitotic actomyosin contractile ring assembly actin filament organization / thrombin-activated receptor signaling pathway / Arp2/3 complex-mediated actin nucleation / Arp2/3 complex binding / GTPase inhibitor activity / phosphatidylinositol-3,4,5-trisphosphate binding / microvillus / CDC42 GTPase cycle / RHOG GTPase cycle / RHO GTPases activate IQGAPs ...mitotic actomyosin contractile ring assembly actin filament organization / thrombin-activated receptor signaling pathway / Arp2/3 complex-mediated actin nucleation / Arp2/3 complex binding / GTPase inhibitor activity / phosphatidylinositol-3,4,5-trisphosphate binding / microvillus / CDC42 GTPase cycle / RHOG GTPase cycle / RHO GTPases activate IQGAPs / RAC1 GTPase cycle / GTPase activator activity / secretory granule membrane / filopodium / regulation of actin cytoskeleton organization / small GTPase binding / actin filament binding / actin cytoskeleton / lamellipodium / actin binding / cell cortex / microtubule / calmodulin binding / Neutrophil degranulation / cell surface / signal transduction / extracellular exosome / plasma membrane / cytosol / cytoplasm
Similarity search - Function
RasGAP protein, C-terminal / RasGAP C-terminus / Ras GTPase-activating protein, conserved site / Ras GTPase-activating proteins domain signature. / GTPase-activator protein for Ras-like GTPase / Ras GTPase-activating proteins profile. / GTPase-activator protein for Ras-like GTPases / Ras GTPase-activating domain / IQ calmodulin-binding motif / Calponin homology domain ...RasGAP protein, C-terminal / RasGAP C-terminus / Ras GTPase-activating protein, conserved site / Ras GTPase-activating proteins domain signature. / GTPase-activator protein for Ras-like GTPase / Ras GTPase-activating proteins profile. / GTPase-activator protein for Ras-like GTPases / Ras GTPase-activating domain / IQ calmodulin-binding motif / Calponin homology domain / Calponin homology (CH) domain / Rho GTPase activation protein / Short calmodulin-binding motif containing conserved Ile and Gln residues. / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / IQ motif, EF-hand binding site / IQ motif profile. / WW/rsp5/WWP domain signature. / WW/rsp5/WWP domain profile. / WW domain
Similarity search - Domain/homology
Ras GTPase-activating-like protein IQGAP2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / sad / Resolution: 1.5 Å
AuthorsNedyalkova, L. / Tempel, W. / Tong, Y. / Zhong, N. / Crombet, L. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. ...Nedyalkova, L. / Tempel, W. / Tong, Y. / Zhong, N. / Crombet, L. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. / Park, H. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of the RasGAP C-terminal (RGC) domain of IQGAP2
Authors: Nedyalkova, L. / Tempel, W. / Tong, Y. / Zhong, N. / Crombet, L. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. / Park, H.
History
DepositionJul 23, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Ras GTPase-activating-like protein IQGAP2
B: Ras GTPase-activating-like protein IQGAP2


Theoretical massNumber of molelcules
Total (without water)26,46510
Polymers26,4652
Non-polymers08
Water2,342130
1
A: Ras GTPase-activating-like protein IQGAP2


Theoretical massNumber of molelcules
Total (without water)13,2325
Polymers13,2321
Non-polymers04
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ras GTPase-activating-like protein IQGAP2


Theoretical massNumber of molelcules
Total (without water)13,2325
Polymers13,2321
Non-polymers04
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.083, 47.256, 46.661
Angle α, β, γ (deg.)90.000, 95.510, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ras GTPase-activating-like protein IQGAP2


Mass: 13232.346 Da / Num. of mol.: 2 / Fragment: UNP residues 1476-1571
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IQGAP2 / Plasmid: pET28-mhl / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-V2R-pRARE2 / References: UniProt: Q13576
#2: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 8 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 1.87 Å3/Da / Density % sol: 34.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 30% PEG-MME, 0.2M ammonium sulfate, 0.1M MES, 1:100 (w/w) chymotrypsin, pH 6.5, vapor diffusion, sitting drop, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 23-ID-B10.97946
SYNCHROTRONAPS 23-ID-B21.07205
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 20, 2009
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979461
21.072051
ReflectionRedundancy: 4.3 % / Av σ(I) over netI: 16.9 / Number: 58756 / Rmerge(I) obs: 0.093 / Χ2: 5.66 / D res high: 2 Å / D res low: 50 Å / Num. obs: 13539 / % possible obs: 98.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.435099.410.08522.6054.4
4.315.4310010.07215.6614.6
3.764.3110010.079.4774.7
3.423.7699.910.077.5944.6
3.173.4210010.0766.3564.7
2.993.1710010.0865.7554.7
2.842.9910010.14.8874.7
2.712.8410010.1114.1634.7
2.612.7110010.1153.7734.7
2.522.6110010.1273.374.7
2.442.5210010.1412.9364.6
2.372.4499.910.1452.5394.5
2.312.3799.910.1692.144.4
2.252.3199.410.1932.3024.3
2.22.2599.410.2042.7784.2
2.152.298.810.1981.9064
2.112.1598.210.2091.7283.8
2.072.1196.410.2451.8883.7
2.032.0794.310.2432.2733.3
22.0391.610.2611.5333.2
ReflectionResolution: 1.5→50 Å / Num. obs: 31015 / % possible obs: 98.8 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.042 / Χ2: 1.371 / Net I/σ(I): 17.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.5-1.532.50.23913561.4051,287.5
1.53-1.552.70.22114811.1171,293.4
1.55-1.583.10.21314831.1991,296.7
1.58-1.623.30.19915541.2581,298.6
1.62-1.653.60.19615411.261,299.8
1.65-1.693.90.18615481.4321,299.7
1.69-1.734.10.18615751.2461,2100
1.73-1.784.70.17615401.2471,2100
1.78-1.835.40.17215631.191,2100
1.83-1.896.30.15515761.2061,2100
1.89-1.9670.12415731.2241,2100
1.96-2.047.30.115541.2881,2100
2.04-2.137.50.08615831.3861,2100
2.13-2.247.50.07415691.51,2100
2.24-2.387.50.06115601.4661,2100
2.38-2.567.60.05515701.4841,2100
2.56-2.827.60.04715781.5341,2100
2.82-3.237.60.03515871.4951,2100
3.23-4.077.50.02815891.4461,2100
4.07-507.20.02516351.4221,299.9

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Phasing

PhasingMethod: sad

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
REFMACrefmac_5.5.0102refinement
PDB_EXTRACT3.005data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.5→30 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.931 / WRfactor Rfree: 0.266 / WRfactor Rwork: 0.211 / SU B: 1.548 / SU ML: 0.059 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.086 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: A POTASSIUM HEXAIODOPLATIN-(IV)-ATE DERIVATIVE WAS USED FOR PHASING. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY. ARP/WARP, COOT, MOLPROBITY WERE ALSO USED DURING REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.257 1038 3.4 %THIN SHELLS (SFTOOLS)
Rwork0.207 ---
obs0.209 30969 98.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.078 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20 Å2-0.49 Å2
2---0.45 Å20 Å2
3---0.12 Å2
Refinement stepCycle: LAST / Resolution: 1.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1486 0 8 130 1624
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221609
X-RAY DIFFRACTIONr_bond_other_d0.0010.021046
X-RAY DIFFRACTIONr_angle_refined_deg1.591.9762198
X-RAY DIFFRACTIONr_angle_other_deg0.87432621
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4575219
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.5926.98673
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.89415318
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.092152
X-RAY DIFFRACTIONr_chiral_restr0.0860.2269
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021789
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02289
X-RAY DIFFRACTIONr_mcbond_it1.1921.5991
X-RAY DIFFRACTIONr_mcbond_other0.3091.5400
X-RAY DIFFRACTIONr_mcangle_it2.13421623
X-RAY DIFFRACTIONr_scbond_it3.1283618
X-RAY DIFFRACTIONr_scangle_it5.0524.5561
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.5400.3052047230188.961
1.54-1.5820.2941020.2722044223995.846
1.582-1.6280.313890.2462064217898.852
1.628-1.6780.253970.242024212899.671
1.678-1.7320.284870.2191968205899.854
1.732-1.7930.257610.2151914197999.798
1.793-1.8610.256640.2021855192199.896
1.861-1.9360.23200.2051836185999.839
1.936-2.0220.253830.1931682176899.83
2.022-2.120.234690.19316411710100
2.12-2.2340.271480.19515571605100
2.234-2.3690.19440.18615051549100
2.369-2.5310.214360.19713801416100
2.531-2.7320.218420.19413101352100
2.732-2.9910.316520.22212011253100
2.991-3.340.245360.21510871123100
3.34-3.8480.265180.1969851003100
3.848-4.6940.224550.165797852100
4.694-6.5590.31140.233660674100
6.559-300.331210.252374395100

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