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- PDB-4klz: Inhibition of Small GTPases by Stabilization of the GDP Complex, ... -

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Basic information

Entry
Database: PDB / ID: 4klz
TitleInhibition of Small GTPases by Stabilization of the GDP Complex, a Novel Approach applied to Rit1, a Target for Rheumatoid Arthritis
ComponentsGTP-binding protein Rit1
KeywordsPROTEIN BINDING / small GTPase / molecular switch (GTPase) / GDP/GTP binding / GUANINE NUCLEOTIDE BINDING
Function / homology
Function and homology information


Signalling to p38 via RIT and RIN / small monomeric GTPase / GDP binding / Ras protein signal transduction / calmodulin binding / GTPase activity / GTP binding / signal transduction / plasma membrane
Similarity search - Function
Small GTPase, Ras-type / small GTPase Ras family profile. / Small GTPase / Ras family / 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 / GTP-binding protein Rit1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsShah, D.M. / Kobayashi, M. / Keizers, P.H. / Tuin, A.W. / Ab, E. / Manning, L. / Rzepiela, A.A. / Andrews, M. / Hoedemaeker, F.J. / Siegal, G.
CitationJournal: To be Published
Title: Inhibition of Small GTPases by Stabilization of the GDP Complex, a Novel Approach applied to Rit1, a Target for Rheumatoid Arthritis
Authors: Shah, D.M. / Kobayashi, M. / Keizers, P.H. / Tuin, A.W. / Ab, E. / Manning, L. / Rzepiela, A.A. / Andrews, M. / Hoedemaeker, F.J. / Siegal, G.
History
DepositionMay 7, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 17, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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_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_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

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Assembly

Deposited unit
A: GTP-binding protein Rit1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5533
Polymers20,0861
Non-polymers4682
Water32418
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.278, 37.048, 40.736
Angle α, β, γ (deg.)90.00, 95.90, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein GTP-binding protein Rit1 / Ras-like protein expressed in many tissues / Ras-like without CAAX protein 1


Mass: 20085.787 Da / Num. of mol.: 1 / Fragment: GTP binding domain, unp residues 19-189
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RIT1, RIBB, RIT, ROC1 / Plasmid: pQTEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3+ RP / References: UniProt: Q92963
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 18 / 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

Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 11-14% w/v PEG4000, 5-8% v/v Jeffamine M600, imidazole , VAPOR DIFFUSION, SITTING DROP, temperature 291K
PH range: 7.0-7.2

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Data collection

DiffractionMean temperature: 99 K
Diffraction sourceSource: ROTATING ANODE / Type: OTHER / Wavelength: 1.54146 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Feb 27, 2007
RadiationMonochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54146 Å / Relative weight: 1
ReflectionResolution: 2.3→40.5 Å / Num. all: 5464 / Num. obs: 5464 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.0547 / Net I/σ(I): 36.45

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Processing

Software
NameVersionClassification
PROTEUM PLUSPLUSdata collection
Cootmodel building
REFMAC5.2.0019refinement
PROTEUM PLUSPLUSdata reduction
PROTEUM PLUSPLUSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2ery

2ery


Resolution: 2.3→40.5 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.833 / SU B: 11.23 / SU ML: 0.285 / Cross valid method: THROUGHOUT / ESU R Free: 0.39 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31099 520 9.7 %RANDOM
Rwork0.18538 ---
obs0.19786 4860 98.57 %-
all-82115 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.06 Å2
Baniso -1Baniso -2Baniso -3
1-2.07 Å20 Å2-0.12 Å2
2---1.11 Å20 Å2
3----0.99 Å2
Refinement stepCycle: LAST / Resolution: 2.3→40.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1278 0 29 18 1325
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0420.0221345
X-RAY DIFFRACTIONr_bond_other_d0.0020.02951
X-RAY DIFFRACTIONr_angle_refined_deg3.1771.9881817
X-RAY DIFFRACTIONr_angle_other_deg1.56732283
X-RAY DIFFRACTIONr_dihedral_angle_1_deg12.1935158
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.12322.42970
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.60815240
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7041516
X-RAY DIFFRACTIONr_chiral_restr0.1810.2194
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.021474
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02306
X-RAY DIFFRACTIONr_nbd_refined0.3070.2368
X-RAY DIFFRACTIONr_nbd_other0.270.21041
X-RAY DIFFRACTIONr_nbtor_refined0.2210.2595
X-RAY DIFFRACTIONr_nbtor_other0.1080.2750
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.270.250
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0120.21
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2510.232
X-RAY DIFFRACTIONr_symmetry_vdw_other0.360.296
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4460.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6781.5975
X-RAY DIFFRACTIONr_mcbond_other0.3681.5317
X-RAY DIFFRACTIONr_mcangle_it2.06321261
X-RAY DIFFRACTIONr_scbond_it3.3373661
X-RAY DIFFRACTIONr_scangle_it4.4034.5554
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.298→2.358 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.417 47 -
Rwork0.174 335 -
obs--93.4 %

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