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- PDB-3ref: Crystal structure of EhRho1 bound to GDP and Magnesium -

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Basic information

Entry
Database: PDB / ID: 3ref
TitleCrystal structure of EhRho1 bound to GDP and Magnesium
ComponentsRho-like small GTPase
KeywordsSIGNALING PROTEIN / cytoskeleton / nucleotide-binding / GTP-binding / lipoprotein / prenylation
Function / homology
Function and homology information


protein localization to phagocytic vesicle / adhesion of symbiont to host cell / phagocytic cup / small GTPase-mediated signal transduction / positive regulation of phagocytosis / phagocytic vesicle / phagocytosis / small monomeric GTPase / cell projection / cytoskeleton ...protein localization to phagocytic vesicle / adhesion of symbiont to host cell / phagocytic cup / small GTPase-mediated signal transduction / positive regulation of phagocytosis / phagocytic vesicle / phagocytosis / small monomeric GTPase / cell projection / cytoskeleton / GTPase activity / GTP binding / magnesium ion binding / plasma membrane
Similarity search - Function
small GTPase Rab1 family profile. / Small GTPase Rho / small GTPase Rho family profile. / 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 ...small GTPase Rab1 family profile. / Small GTPase Rho / small GTPase Rho family profile. / 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Ras-like GTP-binding protein RHO1 / Rho-like small GTPase
Similarity search - Component
Biological speciesEntamoeba histolytica (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsBosch, D.E. / Qiu, C. / Siderovski, D.P.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Unique structural and nucleotide exchange features of the Rho1 GTPase of Entamoeba histolytica.
Authors: Bosch, D.E. / Wittchen, E.S. / Qiu, C. / Burridge, K. / Siderovski, D.P.
History
DepositionApr 4, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 14, 2012Group: Database references
Revision 1.2Sep 13, 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_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_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
B: Rho-like small GTPase
A: Rho-like small GTPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0889
Polymers42,8652
Non-polymers1,2237
Water3,837213
1
A: Rho-like small GTPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0925
Polymers21,4321
Non-polymers6604
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Rho-like small GTPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9964
Polymers21,4321
Non-polymers5643
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.300, 54.476, 132.285
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Rho-like small GTPase


Mass: 21432.455 Da / Num. of mol.: 2 / Fragment: UNP residues 1-191
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Strain: HM1:IMSS / Gene: EhRho1 / Plasmid: pLIC-His / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q95TD4, UniProt: C4M4W4*PLUS
#2: 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
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 213 / 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: 2.11 Å3/Da / Density % sol: 41.82 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: EhRho1 at 15 mg/mL in crystallization buffer (50 mM Tris pH 8.0, 250 mM NaCl, 2.5% (v/v) glycerol, 5 mM DTT, 50 microM GDP, 1 mM magnesium chloride) was mixed 1:1 with and equilibrated ...Details: EhRho1 at 15 mg/mL in crystallization buffer (50 mM Tris pH 8.0, 250 mM NaCl, 2.5% (v/v) glycerol, 5 mM DTT, 50 microM GDP, 1 mM magnesium chloride) was mixed 1:1 with and equilibrated against crystallization solution (1.5 M ammonium sulfate, 100 mM Tris pH 8.0), VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Nov 5, 2010 / Details: custom
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→28.324 Å / Num. all: 27432 / Num. obs: 27267 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 21.9
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.187 / Mean I/σ(I) obs: 2.5 / % possible all: 99.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.6_289)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DPF

1dpf


Resolution: 1.95→28.324 Å / SU ML: 0.22 / σ(F): 0.12 / Phase error: 19.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1974 1366 5.03 %
Rwork0.1565 --
obs0.1586 27158 99.58 %
all-27432 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.838 Å2 / ksol: 0.381 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.0786 Å20 Å20 Å2
2--0.1266 Å2-0 Å2
3----0.048 Å2
Refinement stepCycle: LAST / Resolution: 1.95→28.324 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2759 0 73 213 3045
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092881
X-RAY DIFFRACTIONf_angle_d1.263909
X-RAY DIFFRACTIONf_dihedral_angle_d161041
X-RAY DIFFRACTIONf_chiral_restr0.088444
X-RAY DIFFRACTIONf_plane_restr0.006484
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.01940.25851230.18972537X-RAY DIFFRACTION99
2.0194-2.10020.22571240.1642545X-RAY DIFFRACTION100
2.1002-2.19580.23031230.15542539X-RAY DIFFRACTION100
2.1958-2.31150.20481320.15142542X-RAY DIFFRACTION99
2.3115-2.45620.24241280.15332551X-RAY DIFFRACTION100
2.4562-2.64580.20751460.16322569X-RAY DIFFRACTION100
2.6458-2.91180.22051320.17232562X-RAY DIFFRACTION100
2.9118-3.33250.24671460.17332586X-RAY DIFFRACTION100
3.3325-4.19650.16631420.14112635X-RAY DIFFRACTION100
4.1965-28.32670.15361700.14122726X-RAY DIFFRACTION100
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)
12.33480.495-0.70470.5017-1.13643.03460.2125-0.10190.4130.40020.0967-0.1752-0.73790.2076-0.2980.3049-0.03790.07150.1492-0.05940.19537.38634.22473.5314
22.8053-1.28790.88534.9021-0.59327.07210.546-0.20030.52580.1535-0.2198-0.6221-0.39941.3435-0.28980.3302-0.13740.02390.4164-0.12160.3714.26651.93177.705
31.22110.1401-1.14330.75310.95482.93990.2531-0.21910.17530.1481-0.02190.1149-0.63090.2525-0.2090.3127-0.0220.04120.1985-0.0580.21374.47932.38958.0432
40.38960.2906-0.42530.8079-0.4861.81440.01350.0798-0.0795-0.01920.04790.1571-0.0512-0.2439-0.0430.13070.0128-0.00940.1854-0.01530.1530.0619-8.1515-0.3294
51.254-0.3243-1.30611.42210.01391.62440.15780.38820.0269-0.3174-0.03240.0766-0.305-0.3094-0.09570.20460.0787-0.02290.23480.0180.16931.5097-2.5077-7.8591
60.32690.3703-0.30882.983-0.52592.6664-0.09390.1096-0.1605-0.15950.12660.4540.1453-0.5068-0.04610.1068-0.0189-0.02730.2297-0.00080.20868.7044-5.9967-33.3799
72.37080.7022-0.39620.83920.05440.1832-0.0240.3481-0.0607-0.3293-0.0062-0.0880.15060.05330.04960.23710.00190.00180.21470.00490.208424.1189-2.1933-41.151
80.5894-0.0274-0.47930.21460.09551.18560.0269-0.0410.18920.0951-0.0907-0.0396-0.38860.1040.06160.1799-0.0259-0.02720.13570.00140.189320.81973.4654-28.4191
91.54780.9159-0.80311.59450.18822.72320.1174-0.23320.26770.3189-0.04980.0663-0.3170.0824-0.06990.2187-0.0118-0.00510.2028-0.04250.184616.132.9919-19.1068
100.265-0.0706-0.04030.88610.05580.3521-0.3163-0.07640.07290.04290.2907-0.3014-0.0601-0.02020.0650.16740.1371-0.02160.18450.07190.2235-2.44558.8453-29.5332
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 15:48)
2X-RAY DIFFRACTION2(chain A and resid 49:64)
3X-RAY DIFFRACTION3(chain A and resid 65:92)
4X-RAY DIFFRACTION4(chain A and resid 93:144)
5X-RAY DIFFRACTION5(chain A and resid 145:187)
6X-RAY DIFFRACTION6(chain B and resid 15:80)
7X-RAY DIFFRACTION7(chain B and resid 81:94)
8X-RAY DIFFRACTION8(chain B and resid 95:140)
9X-RAY DIFFRACTION9(chain B and resid 141:179)
10X-RAY DIFFRACTION10(chain B and resid 180:194)

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