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- PDB-3reg: Crystal structure of EhRho1 bound to a GTP analog and Magnesium -

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Basic information

Entry
Database: PDB / ID: 3reg
TitleCrystal structure of EhRho1 bound to a GTP analog 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
5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE / Ras-like GTP-binding protein RHO1 / Rho-like small GTPase
Similarity search - Component
Biological speciesEntamoeba histolytica (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.801 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
A: Rho-like small GTPase
B: Rho-like small GTPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9926
Polymers42,8652
Non-polymers1,1274
Water4,125229
1
A: Rho-like small GTPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9963
Polymers21,4321
Non-polymers5642
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Rho-like small GTPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9963
Polymers21,4321
Non-polymers5642
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.468, 39.497, 63.578
Angle α, β, γ (deg.)81.75, 80.76, 65.44
Int Tables number1
Space group name H-MP1

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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-GSP / 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE


Mass: 539.246 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3S
#3: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 229 / 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: 1.91 Å3/Da / Density % sol: 35.63 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6
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 GTPgammaS, 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 GTPgammaS, 1 mM magnesium chloride) was mixed 1:1 with and equilibrated against crystallization solution (25% PEG 4000, 150 mM ammonium acetate, 100 mM sodium acetate pH 4.6), VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Nov 18, 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: 1.8→40 Å / Num. all: 29325 / Num. obs: 23929 / % possible obs: 81.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 16.1
Reflection shellResolution: 1.8→1.82 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.278 / Mean I/σ(I) obs: 2.8 / % possible all: 45.9

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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 ID 1A2B

1a2b


Resolution: 1.801→32.958 Å / SU ML: 0.22 / σ(F): 1.96 / Phase error: 25.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2221 1214 5.08 %
Rwork0.1718 --
obs0.1744 23882 81.4 %
all-29486 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.113 Å2 / ksol: 0.352 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.3683 Å20.703 Å2-0.5607 Å2
2---1.8001 Å22.6031 Å2
3---1.4318 Å2
Refinement stepCycle: LAST / Resolution: 1.801→32.958 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2658 0 66 229 2953
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092775
X-RAY DIFFRACTIONf_angle_d1.23770
X-RAY DIFFRACTIONf_dihedral_angle_d13.8951004
X-RAY DIFFRACTIONf_chiral_restr0.078431
X-RAY DIFFRACTIONf_plane_restr0.005465
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.801-1.87350.2907860.21541558X-RAY DIFFRACTION50
1.8735-1.95880.29941050.20291931X-RAY DIFFRACTION62
1.9588-2.0620.24541260.19852250X-RAY DIFFRACTION73
2.062-2.19120.25121230.18582480X-RAY DIFFRACTION80
2.1912-2.36030.23391240.18142679X-RAY DIFFRACTION87
2.3603-2.59780.23341460.18212863X-RAY DIFFRACTION92
2.5978-2.97350.24131700.18342914X-RAY DIFFRACTION95
2.9735-3.74540.1981680.15792998X-RAY DIFFRACTION96
3.7454-32.96370.19281660.15272995X-RAY DIFFRACTION97
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)
14.9367-0.59223.53374.4703-1.39924.03110.74370.0655-0.225-0.2245-0.07650.4631-0.0229-0.0377-0.56350.6149-0.01570.26280.0741-0.09860.2797-1.8339-24.394547.4485
20.8707-0.0434-0.91190.86410.32622.8793-0.0902-0.02250.18270.04030.06260.2917-0.4391-0.1785-0.00490.19210.0646-0.00510.17380.00420.16275.4396-2.944345.0753
35.3582-4.5507-2.77415.54694.35695.6838-0.2721-0.5693-0.4568-0.02420.13380.6851-0.3516-0.09110.16170.1294-0.0120.05370.263-0.03260.1555-1.1367-9.592147.7797
41.4918-0.7286-0.89390.86950.37020.91760.0092-0.3694-0.09730.0473-0.14050.2227-0.0367-0.14550.11690.16050.02540.03580.24740.01020.10385.1606-9.780351.8831
50.96440.1017-0.06621.05421.20971.55940.0291-0.4448-0.11790.19980.0642-0.23250.15340.4359-0.07510.12660.0138-0.03050.31170.01880.144617.1894-8.71751.7257
62.84050.0088-1.56080.8724-0.12481.6081-0.0164-0.3755-0.1321-0.16060.1253-0.14980.00670.5186-0.08180.1279-0.01380.00120.2366-0.05010.147223.0692-7.661940.1067
71.55381.7258-1.55953.2383-2.76212.858-0.19790.0184-0.3351-0.47450.0289-0.42370.3956-0.13920.14510.13810.00070.00010.1534-0.02060.19659.3375-13.035138.2427
82.6801-2.11020.61792.55731.50724.5357-0.5433-0.105-2.7511-0.05820.9596-0.5478-0.47210.0109-0.15440.4543-0.06020.14430.2935-0.10390.825710.6807-27.596644.4662
94.5466-0.20563.31687.53081.42622.85010.70420.3766-0.520.8886-0.2659-0.01610.74440.4553-0.66940.57120.2849-0.07310.29660.00450.303631.4624-25.711516.857
101.15710.315-0.56210.3865-0.21121.97510.23720.13230.29070.0209-0.1025-0.1721-0.45820.4039-0.11360.1863-0.06770.02940.1272-0.01340.148625.5405-4.836915.7781
112.6311-1.92413.04022.1834-1.92794.62090.38220.1563-0.68710.1167-0.2927-0.16440.37120.7509-0.05450.20910.0575-0.04580.29960.09080.265631.3931-18.903220.2195
121.21640.56930.14630.25730.12630.19650.13710.58320.19460.03790.1238-0.2469-0.27750.0885-0.20010.26160.12050.05030.38140.03920.105222.6003-7.94533.1973
132.0143-0.4102-0.78121.02040.31843.5010.2490.3324-0.1549-0.0641-0.06980.0026-0.1213-0.31550.0550.13310.0474-0.04020.1376-0.03380.098413.3091-10.672812.5713
140.8318-1.8425-1.27435.20441.77574.94550.14520.1467-0.03320.3256-0.0340.5142-0.2448-1.3056-0.12770.19020.1362-0.0040.35950.04490.21674.1762-5.92423.7208
156.31652.75632.83121.57752.28673.01460.36090.0697-0.7470.19470.0292-0.16330.239-0.0956-0.35160.1303-0.0546-0.01920.0760.00840.182113.2568-12.609121.4555
164.1932-2.75760.22792.19510.90276.34210.0538-0.0495-0.77140.13190.11590.91970.79180.3164-0.12980.1874-0.01-0.04990.09880.04860.296521.815-20.662622.1978
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 2:23)
2X-RAY DIFFRACTION2(chain A and resid 24:56)
3X-RAY DIFFRACTION3(chain A and resid 57:64)
4X-RAY DIFFRACTION4(chain A and resid 65:93)
5X-RAY DIFFRACTION5(chain A and resid 94:135)
6X-RAY DIFFRACTION6(chain A and resid 136:167)
7X-RAY DIFFRACTION7(chain A and resid 168:185)
8X-RAY DIFFRACTION8(chain A and resid 186:191)
9X-RAY DIFFRACTION9(chain B and resid 14:24)
10X-RAY DIFFRACTION10(chain B and resid 25:57)
11X-RAY DIFFRACTION11(chain B and resid 58:75)
12X-RAY DIFFRACTION12(chain B and resid 76:94)
13X-RAY DIFFRACTION13(chain B and resid 95:140)
14X-RAY DIFFRACTION14(chain B and resid 141:154)
15X-RAY DIFFRACTION15(chain B and resid 155:174)
16X-RAY DIFFRACTION16(chain B and resid 175:189)

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