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- PDB-2nty: Rop4-GDP-PRONE8 -

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Basic information

Entry
Database: PDB / ID: 2nty
TitleRop4-GDP-PRONE8
Components
  • Emb|CAB41934.1
  • Rac-like GTP-binding protein ARAC5
KeywordsSIGNALING PROTEIN / complex of PRONE-GEF with Rop substrate
Function / homology
Function and homology information


root hair initiation / pollen tube growth / phragmoplast / root hair elongation / cortical cytoskeleton organization / small GTPase-mediated signal transduction / guanyl-nucleotide exchange factor activity / cell projection / regulation of actin cytoskeleton organization / actin filament organization ...root hair initiation / pollen tube growth / phragmoplast / root hair elongation / cortical cytoskeleton organization / small GTPase-mediated signal transduction / guanyl-nucleotide exchange factor activity / cell projection / regulation of actin cytoskeleton organization / actin filament organization / cell cortex / regulation of cell shape / cytoplasmic vesicle / actin cytoskeleton organization / cytoskeleton / intracellular membrane-bounded organelle / GTPase activity / nucleolus / GTP binding / protein kinase binding / mitochondrion / identical protein binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
PRONE domain, subdomain 2 / PRONE domain, subdomain 1 / PRONE domain / Rop guanine nucleotide exchange factor / PRONE (Plant-specific Rop nucleotide exchanger) / PRONE domain profile. / Small GTPase Rho / small GTPase Rho family profile. / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Small GTPase ...PRONE domain, subdomain 2 / PRONE domain, subdomain 1 / PRONE domain / Rop guanine nucleotide exchange factor / PRONE (Plant-specific Rop nucleotide exchanger) / PRONE domain profile. / Small GTPase Rho / small GTPase Rho family profile. / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Small GTPase / Ras family / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / Up-down Bundle / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Rac-like GTP-binding protein ARAC5 / Rho guanine nucleotide exchange factor 8
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsThomas, C. / Fricke, I. / Scrima, A. / Berken, A. / Wittinghofer, A.
Citation
Journal: Mol.Cell / Year: 2007
Title: Structural Evidence for a Common Intermediate in Small G Protein-GEF Reactions
Authors: Thomas, C. / Fricke, I. / Scrima, A. / Berken, A. / Wittinghofer, A.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2006
Title: Purification and crystallization of the catalytic PRONE domain of RopGEF8 and its complex with Rop4 from Arabidopsis thaliana
Authors: Thomas, C. / Weyand, M. / Wittinghofer, A. / Berken, A.
History
DepositionNov 8, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 23, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 25, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Emb|CAB41934.1
B: Emb|CAB41934.1
C: Rac-like GTP-binding protein ARAC5
D: Rac-like GTP-binding protein ARAC5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,5746
Polymers122,6884
Non-polymers8862
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12120 Å2
ΔGint-66 kcal/mol
Surface area43780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)211.170, 211.170, 81.110
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Emb|CAB41934.1 / PRONE8


Mass: 41516.367 Da / Num. of mol.: 2 / Fragment: residues 76-440 based on the database numbering
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Strain: Columbia / Gene: At3g24620 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q9LV40
#2: Protein Rac-like GTP-binding protein ARAC5 / GTPase protein ROP4


Mass: 19827.680 Da / Num. of mol.: 2 / Fragment: residues 1-180
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Strain: Columbia / Gene: ATU52350 / Plasmid: pGEX-4T-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q38937
#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

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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: 4.25 Å3/Da / Density % sol: 71.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 18%(v/v) Tacsimate(Hampton Research), 4%(w/v) PEG 3350, 0.1M Tris-HCl, pH 7.3, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9788 Å
DetectorType: MAR CCD 225 mm / Detector: CCD / Date: Mar 3, 2006 / Details: MAR CCD 225 mm
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 37649 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 56.835 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 16.81
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique all% possible all
3.1-3.20.4394.217144337499.8
3.2-3.30.3685.115153298199.8
3.3-3.40.3225.713590266999.9
3.4-3.60.3588.232816447199.9
3.6-3.80.32811.735339357799.5
3.8-40.27114.528550288899.6
4-4.50.20119.751605522199.8
4.5-50.14726.232849334399.8
5-60.14623.6374043795100
6-80.10327.829366305599.9
8-120.06345.614750159199.9
12-160.06246.9359339899.7
16-200.063461267145100
200.06745.265675100

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2NTX

2ntx


Resolution: 3.1→24.87 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.905 / SU B: 33.327 / SU ML: 0.272 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.753 / ESU R Free: 0.344 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.236 1879 5 %RANDOM
Rwork0.199 ---
obs0.201 37579 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: 57.315 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20.09 Å20 Å2
2--0.17 Å20 Å2
3----0.26 Å2
Refinement stepCycle: LAST / Resolution: 3.1→24.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7564 0 56 0 7620
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0227744
X-RAY DIFFRACTIONr_angle_refined_deg1.9261.96610556
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.96251001
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.99724.597298
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.701151208
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.8781535
X-RAY DIFFRACTIONr_chiral_restr0.1210.21246
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025764
X-RAY DIFFRACTIONr_nbd_refined0.2620.23490
X-RAY DIFFRACTIONr_nbtor_refined0.330.25427
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.2225
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1790.230
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1510.23
X-RAY DIFFRACTIONr_mcbond_it0.8731.55102
X-RAY DIFFRACTIONr_mcangle_it1.14728017
X-RAY DIFFRACTIONr_scbond_it2.13832996
X-RAY DIFFRACTIONr_scangle_it3.0174.52539
LS refinement shellResolution: 3.1→3.179 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 134 -
Rwork0.276 2552 -
obs-2686 100 %
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)
11.6208-0.476-0.46860.74860.24882.5388-0.00640.1409-0.1218-0.16640.0321-0.1340.04130.3605-0.0258-0.24980.0388-0.0305-0.08310.0484-0.052659.647156.6362-4.1489
21.5831-0.7243-0.65740.74210.2652.6697-0.0069-0.08730.08530.08910.02320.138-0.2926-0.2943-0.0163-0.13980.1035-0.0573-0.1616-0.0159-0.087718.823679.83774.1493
33.4204-1.3594-0.27862.5668-1.21455.51560.14420.1379-0.2775-0.035-0.2042-0.0963-0.02450.2170.06-0.28980.0591-0.0652-0.2369-0.0682-0.234648.447960.1385-26.9556
43.4604-1.1790.94932.13060.96685.3567-0.0797-0.213-0.0956-0.08470.08390.2759-0.2495-0.1066-0.0042-0.31390.0580.0476-0.21530.1004-0.230227.6671.937127.4025
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA10 - 36310 - 363
22BB9 - 3649 - 364
33CC4 - 1794 - 179
44DD5 - 1795 - 179

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