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- PDB-2cjw: Crystal structure of the small GTPase Gem (GemDNDCaM) in complex ... -

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Basic information

Entry
Database: PDB / ID: 2cjw
TitleCrystal structure of the small GTPase Gem (GemDNDCaM) in complex to Mg.GDP
Components(GTP-BINDING PROTEIN GEM) x 2
KeywordsG-PROTEIN / NUCLEOTIDE-BINDING / GTP-BINDING / SMALL GTPASE / CONFORMATIONAL CHANGE / CYSTEINE-MODIFIED / G-PROTEIN HYDROLASE
Function / homology
Function and homology information


metaphase chromosome alignment / spindle midzone / chromosome organization / NPAS4 regulates expression of target genes / calcium channel regulator activity / cytoplasmic side of plasma membrane / mitotic spindle / GDP binding / mitotic cell cycle / midbody ...metaphase chromosome alignment / spindle midzone / chromosome organization / NPAS4 regulates expression of target genes / calcium channel regulator activity / cytoplasmic side of plasma membrane / mitotic spindle / GDP binding / mitotic cell cycle / midbody / calmodulin binding / cell surface receptor signaling pathway / immune response / GTPase activity / GTP binding / magnesium ion binding / signal transduction / nucleus / plasma membrane
Similarity search - Function
Ras-related small G protein, RGK family / : / Small GTPase Ras domain 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 ...Ras-related small G protein, RGK family / : / Small GTPase Ras domain 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / GTP-binding protein GEM
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSplingard, A. / Menetrey, J. / Perderiset, M. / Cicolari, J. / Hamoudi, F. / Cabanie, L. / El Marjou, A. / Wells, A. / Houdusse, A. / de Gunzburg, J.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Biochemical and Structural Characterization of the Gem Gtpase.
Authors: Splingard, A. / Menetrey, J. / Perderiset, M. / Cicolari, J. / Regazzoni, K. / Hamoudi, F. / Cabanie, L. / El Marjou, A. / Wells, A. / Houdusse, A. / De Gunzburg, J.
History
DepositionApr 9, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 9, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GTP-BINDING PROTEIN GEM
B: GTP-BINDING PROTEIN GEM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7996
Polymers44,8642
Non-polymers9354
Water2,288127
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)116.617, 116.617, 81.409
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein GTP-BINDING PROTEIN GEM / GEM / GTP-BINDING MITOGEN-INDUCED T-CELL PROTEIN / RAS-LIKE PROTEIN KIR


Mass: 22431.904 Da / Num. of mol.: 1 / Fragment: G DOMAIN, RESIDUES 74-261
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P55040
#2: Protein GTP-BINDING PROTEIN GEM / GEM / GTP-BINDING MITOGEN-INDUCED T-CELL PROTEIN / RAS-LIKE PROTEIN KIR


Mass: 22431.904 Da / Num. of mol.: 1 / Fragment: G DOMAIN, RESIDUES 74-261
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P55040
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsRESIDUES 70-72 (EFG) IN MOLECULE B BELONG TO THE REMAINING PART OF THE TAG.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.65 Å3/Da / Density % sol: 66.3 %
Crystal growDetails: 0.1M NACACODYLATE PH6.5, 0.9M NAACETATE, 5MM MGCL2 AND 2MM DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.96115
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 8, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96115 Å / Relative weight: 1
ReflectionResolution: 2.1→60 Å / Num. obs: 36826 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 7.7 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 19
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.342 / Mean I/σ(I) obs: 5.3 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KAO

1kao


Resolution: 2.1→60 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.918 / SU B: 3.452 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.168 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 102-105 AND 136-139 IN MOLECULE A AND RESIDUES 99-110 AND 136-142 IN MOLECULE B WERE DISORDERED AND NOT MODELED. SOME SIDE-CHAINS ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 102-105 AND 136-139 IN MOLECULE A AND RESIDUES 99-110 AND 136-142 IN MOLECULE B WERE DISORDERED AND NOT MODELED. SOME SIDE-CHAINS WERE MODELED WITH 0.0 OR PARTIAL OCCUPANCY RATE.
RfactorNum. reflection% reflectionSelection details
Rfree0.241 3669 10 %RANDOM
Rwork0.209 ---
obs0.212 33159 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.22 Å2
Baniso -1Baniso -2Baniso -3
1-1.2 Å20.6 Å20 Å2
2--1.2 Å20 Å2
3----1.79 Å2
Refinement stepCycle: LAST / Resolution: 2.1→60 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2834 0 58 127 3019
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222841
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2711.9913827
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5895345
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.15322.932133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.84315494
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9121531
X-RAY DIFFRACTIONr_chiral_restr0.0890.2428
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022086
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2040.21219
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2990.21925
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2137
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.210.252
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2260.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1991.51786
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.42322741
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.88631230
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.8944.51086
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.244 260
Rwork0.225 2480

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