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- PDB-2g0n: The Crystal Structure of the Human RAC3 in complex with GDP and C... -

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Basic information

Entry
Database: PDB / ID: 2g0n
TitleThe Crystal Structure of the Human RAC3 in complex with GDP and Chloride
ComponentsRas-related C3 botulinum toxin substrate 3
KeywordsSIGNALING PROTEIN / GTPase RAC3A / small GTP binding protein / p21 rac / ras-related C3 botulinum toxin substrate 3 / signalling protein / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


cerebral cortex GABAergic interneuron development / regulation of neuron maturation / regulation of neutrophil migration / postsynaptic actin cytoskeleton organization / NADPH oxidase complex / engulfment of apoptotic cell / cortical cytoskeleton organization / respiratory burst / cell projection assembly / PCP/CE pathway ...cerebral cortex GABAergic interneuron development / regulation of neuron maturation / regulation of neutrophil migration / postsynaptic actin cytoskeleton organization / NADPH oxidase complex / engulfment of apoptotic cell / cortical cytoskeleton organization / respiratory burst / cell projection assembly / PCP/CE pathway / synaptic transmission, GABAergic / motor neuron axon guidance / positive regulation of cell adhesion mediated by integrin / establishment or maintenance of cell polarity / Rac protein signal transduction / filamentous actin / neuromuscular process controlling balance / RAC3 GTPase cycle / endomembrane system / positive regulation of substrate adhesion-dependent cell spreading / homeostasis of number of cells within a tissue / cell chemotaxis / small monomeric GTPase / G protein activity / actin filament organization / cell periphery / regulation of actin cytoskeleton organization / Wnt signaling pathway / calcium-dependent protein binding / lamellipodium / regulation of cell shape / growth cone / cytoplasmic vesicle / actin cytoskeleton organization / cytoskeleton / neuron projection / intracellular signal transduction / GTPase activity / neuronal cell body / glutamatergic synapse / GTP binding / endoplasmic reticulum membrane / protein kinase binding / perinuclear region of cytoplasm / extracellular exosome / plasma membrane / cytosol
Similarity search - Function
Small GTPase Rho / small GTPase Rho family profile. / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase ...Small GTPase Rho / small GTPase Rho family profile. / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Ras-related C3 botulinum toxin substrate 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsUgochukwu, E. / Yang, X. / Zao, Y. / Elkins, J. / Gileadi, C. / Burgess, N. / Colebrook, S. / Gileadi, O. / Fedorov, O. / Bunkoczi, G. ...Ugochukwu, E. / Yang, X. / Zao, Y. / Elkins, J. / Gileadi, C. / Burgess, N. / Colebrook, S. / Gileadi, O. / Fedorov, O. / Bunkoczi, G. / Sundstrom, M. / Arrowsmith, C. / Weigelt, J. / Edwards, A. / von Delft, F. / Doyle, D. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: The Crystal Structure of the Human RAC3 in complex with GDP and Chloride
Authors: Ugochukwu, E. / Yang, X. / Zao, Y. / Elkins, J. / Gileadi, C. / Burgess, N. / Colebrook, S. / Gileadi, O. / Fedorov, O. / Bunkoczi, G. / Sundstrom, M. / Arrowsmith, C. / Weigelt, J. / ...Authors: Ugochukwu, E. / Yang, X. / Zao, Y. / Elkins, J. / Gileadi, C. / Burgess, N. / Colebrook, S. / Gileadi, O. / Fedorov, O. / Bunkoczi, G. / Sundstrom, M. / Arrowsmith, C. / Weigelt, J. / Edwards, A. / von Delft, F. / Doyle, D.
History
DepositionFeb 13, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ras-related C3 botulinum toxin substrate 3
B: Ras-related C3 botulinum toxin substrate 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9119
Polymers39,8702
Non-polymers1,0417
Water4,972276
1
A: Ras-related C3 botulinum toxin substrate 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4735
Polymers19,9351
Non-polymers5384
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ras-related C3 botulinum toxin substrate 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4384
Polymers19,9351
Non-polymers5033
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.932, 80.841, 84.563
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B
71A
81B

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNPHEPHE2AA2 - 283 - 29
21GLNGLNPHEPHE2BB2 - 283 - 29
32PROPROTYRTYR6AA29 - 3230 - 33
42PROPROTYRTYR6BB29 - 3230 - 33
53ILEILEASNASN2AA33 - 3934 - 40
63ILEILEASNASN2BB33 - 3934 - 40
74TYRTYRVALVAL6AA40 - 5141 - 52
84TYRTYRVALVAL6BB40 - 5141 - 52

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Components

#1: Protein Ras-related C3 botulinum toxin substrate 3 / p21-Rac3


Mass: 19934.928 Da / Num. of mol.: 2 / Fragment: RAC3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAC3 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)-R3 / References: UniProt: P60763
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 276 / 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: 2.31 Å3/Da / Density % sol: 46.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M Bis-Tris, 25% PEG 3350, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Oct 28, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→22.43 Å / Num. obs: 29868 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.9→2 Å / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MH1

1mh1


Resolution: 1.9→22.43 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.938 / SU B: 6.526 / SU ML: 0.104 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.141 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22098 1515 5.1 %RANDOM
Rwork0.16528 ---
all0.16809 28345 --
obs0.16809 28345 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 30.426 Å2
Baniso -1Baniso -2Baniso -3
1--0.44 Å20 Å20 Å2
2--1.38 Å20 Å2
3----0.94 Å2
Refinement stepCycle: LAST / Resolution: 1.9→22.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2739 0 61 276 3076
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222888
X-RAY DIFFRACTIONr_bond_other_d0.0020.021907
X-RAY DIFFRACTIONr_angle_refined_deg1.3532.0013959
X-RAY DIFFRACTIONr_angle_other_deg0.9334667
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6825365
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.82723.565115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.81315456
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1971519
X-RAY DIFFRACTIONr_chiral_restr0.0790.2459
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023185
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02574
X-RAY DIFFRACTIONr_nbd_refined0.2040.2561
X-RAY DIFFRACTIONr_nbd_other0.20.22022
X-RAY DIFFRACTIONr_nbtor_refined0.1770.21413
X-RAY DIFFRACTIONr_nbtor_other0.0850.21409
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2216
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1390.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1950.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1680.221
X-RAY DIFFRACTIONr_mcbond_it3.14131944
X-RAY DIFFRACTIONr_mcbond_other0.883719
X-RAY DIFFRACTIONr_mcangle_it4.03352923
X-RAY DIFFRACTIONr_scbond_it6.53471218
X-RAY DIFFRACTIONr_scangle_it8.468111031
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
200tight positional0.050.05
197medium positional0.390.5
160loose positional0.755
200tight thermal0.170.5
197medium thermal1.092
160loose thermal3.1210
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 115 -
Rwork0.238 2064 -
obs--100 %
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.1450.147-0.03091.3485-0.00071.5857-0.00660.04850.0505-0.02760.01850.05710.05260.0541-0.0119-0.15690.00550.0116-0.1512-0.0013-0.1109-16.04514.7602-7.3973
21.76590.0327-0.01571.48890.84172.09020.0367-0.1306-0.00110.19230.01910.0290.34470.1576-0.0558-0.06260.0328-0.0086-0.13590.0054-0.1309-10.2087-13.8694-12.6975
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 1773 - 178
2X-RAY DIFFRACTION2BB2 - 1773 - 178

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