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- PDB-2ht6: Crystal structure of Human Gem G-domain bound to GDP -

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Basic information

Entry
Database: PDB / ID: 2ht6
TitleCrystal structure of Human Gem G-domain bound to GDP
ComponentsGTP-binding protein GEM
KeywordsSIGNALING PROTEIN / small G-protein
Function / homology
Function and homology information


metaphase chromosome alignment / calcium channel regulator activity / chromosome organization / spindle midzone / NPAS4 regulates expression of target genes / mitotic spindle / cytoplasmic side of plasma membrane / GDP binding / mitotic cell cycle / midbody ...metaphase chromosome alignment / calcium channel regulator activity / chromosome organization / spindle midzone / NPAS4 regulates expression of target genes / mitotic spindle / cytoplasmic side of plasma membrane / GDP binding / mitotic cell cycle / midbody / cell surface receptor signaling pathway / calmodulin binding / 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 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 ...Ras-related small G protein, RGK family / : / small GTPase Ras 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 / 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 / SAD / Resolution: 2.4 Å
AuthorsOpatowsky, Y. / Hirsch, J.A.
CitationJournal: Febs Lett. / Year: 2006
Title: Structure-function studies of the G-domain from human gem, a novel small G-protein.
Authors: Opatowsky, Y. / Sasson, Y. / Shaked, I. / Ward, Y. / Chomsky-Hecht, O. / Litvak, Y. / Selinger, Z. / Kelly, K. / Hirsch, J.A.
History
DepositionJul 25, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: 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_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

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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)40,1596
Polymers39,2242
Non-polymers9354
Water1,53185
1
A: GTP-binding protein GEM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0803
Polymers19,6121
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GTP-binding protein GEM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0803
Polymers19,6121
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.843, 81.433, 124.095
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

NCS domain segments:

Ens-ID: 1 / Refine code: 2

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11TYRTYRALAALAAA76 - 967 - 27
21TYRTYRALAALABB76 - 967 - 27
32CYSCYSASNASNAA106 - 13537 - 66
42CYSCYSASNASNBB106 - 13537 - 66
53TRPTRPARGARGAA141 - 24072 - 171
63TRPTRPARGARGBB141 - 24072 - 171

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Components

#1: Protein GTP-binding protein GEM / GTP-binding mitogen-induced T-cell protein / RAS-like protein KIR


Mass: 19612.189 Da / Num. of mol.: 2 / Fragment: G-domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GEM, KIR / Plasmid: pET-21 / Production host: Escherichia coli (E. coli) / References: UniProt: P55040
#2: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 85 / 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: 2.57 Å3/Da / Density % sol: 52.07 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG 8000, 0.1 M HEPES, 0.1 M sodium chloride, 0.5 mM magnesium chloride, 1 mM DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9788 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 16, 2004
RadiationMonochromator: Si111 or Si311 crystals / Protocol: SAD - inverse beam / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 16469 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.073 / Net I/σ(I): 21.8
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.282 / Mean I/σ(I) obs: 9.2 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→50 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.897 / SU B: 8.561 / SU ML: 0.202 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.433 / ESU R Free: 0.296 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.287 830 5.1 %RANDOM
Rwork0.226 ---
all0.229 16384 --
obs0.229 16384 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.618 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å20 Å2
2--0.34 Å20 Å2
3----0.24 Å2
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2622 0 58 85 2765
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222710
X-RAY DIFFRACTIONr_angle_refined_deg1.4071.9773663
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4565325
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.78323.485132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.72315480
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4451528
X-RAY DIFFRACTIONr_chiral_restr0.1110.2420
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021994
X-RAY DIFFRACTIONr_nbd_refined0.2120.21223
X-RAY DIFFRACTIONr_nbtor_refined0.3020.21825
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1970.2143
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2950.237
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3970.212
X-RAY DIFFRACTIONr_mcbond_it0.9521.51676
X-RAY DIFFRACTIONr_mcangle_it1.65222623
X-RAY DIFFRACTIONr_scbond_it1.60231184
X-RAY DIFFRACTIONr_scangle_it2.6654.51040
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
604TIGHT POSITIONAL0.060.05
592MEDIUM POSITIONAL0.430.5
604TIGHT THERMAL0.240.5
592MEDIUM THERMAL0.572
LS refinement shellResolution: 2.4→2.463 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 71 -
Rwork0.283 1111 -
obs-1182 98.91 %

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