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- PDB-9t3d: RACB with GPPNHP bound -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 9t3d
TitleRACB with GPPNHP bound
ComponentsRACB protein
KeywordsPLANT PROTEIN / RACB / Hordeum vulgare / GPPNHP
Function / homology
Function and homology information


small GTPase-mediated signal transduction / GTPase activity / GTP binding / plasma membrane / cytoplasm
Similarity search - Function
Small GTPase Rho / Small GTPase Rab domain profile. / Small GTPase Rho domain profile. / 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 nucleoside triphosphate hydrolase
Similarity search - Domain/homology
FLUORIDE ION / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / RACB protein
Similarity search - Component
Biological speciesHordeum vulgare (barley)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.33 Å
AuthorsJanowski, R. / Mohamadi, M. / Hagn, F. / Niessing, D.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Commun Biol / Year: 2026
Title: Nucleotide-dependent switching and RIPb effector recognition of the barley susceptibility factor RACB.
Authors: Mohamadi, M. / Bradai, M. / Janowski, R. / Gunsel, U. / Tran, M. / Kahl, S.M. / McCollum, C. / Niessing, D. / Huckelhoven, R. / Hagn, F.
History
DepositionOct 27, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2026Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2026Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RACB protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6849
Polymers21,8091
Non-polymers8758
Water3,855214
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1870 Å2
ΔGint-2 kcal/mol
Surface area10090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.710, 66.700, 37.100
Angle α, β, γ (deg.)90.00, 93.59, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein RACB protein


Mass: 21809.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hordeum vulgare (barley) / Gene: pRacB / Production host: Escherichia coli (E. coli) / References: UniProt: Q8RW50

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Non-polymers , 5 types, 222 molecules

#2: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3 / Feature type: SUBJECT OF INVESTIGATION
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-F / FLUORIDE ION


Mass: 18.998 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: F
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.43 Å3/Da / Density % sol: 49.31 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 300 mM Sodium Fluoride and 18% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.03319 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Apr 6, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03319 Å / Relative weight: 1
ReflectionResolution: 1.33→50 Å / Num. obs: 47328 / % possible obs: 99 % / Redundancy: 6.8 % / CC1/2: 1 / Net I/σ(I): 21.5
Reflection shellResolution: 1.33→1.36 Å / Mean I/σ(I) obs: 3.2 / Num. unique obs: 3247 / CC1/2: 0.881 / % possible all: 97.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
PDB_EXTRACTdata extraction
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.33→42.81 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.976 / SU B: 1.173 / SU ML: 0.022 / Cross valid method: THROUGHOUT / ESU R: 0.043 / ESU R Free: 0.04 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.13948 2430 5.1 %RANDOM
Rwork0.11643 ---
obs0.11768 44898 98.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.564 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å2-0 Å2-0.27 Å2
2--0.03 Å20 Å2
3----0.32 Å2
Refinement stepCycle: 1 / Resolution: 1.33→42.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1417 0 54 214 1685
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0121805
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161729
X-RAY DIFFRACTIONr_angle_refined_deg1.8481.8322473
X-RAY DIFFRACTIONr_angle_other_deg0.6661.7614013
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8295234
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.8257
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.17710301
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1170.2277
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022112
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02394
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.9471.681891
X-RAY DIFFRACTIONr_mcbond_other5.861.68891
X-RAY DIFFRACTIONr_mcangle_it8.3983.0111140
X-RAY DIFFRACTIONr_mcangle_other8.43.0141141
X-RAY DIFFRACTIONr_scbond_it7.652.014914
X-RAY DIFFRACTIONr_scbond_other7.6472.016915
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other10.8893.5451334
X-RAY DIFFRACTIONr_long_range_B_refined16.75618.932037
X-RAY DIFFRACTIONr_long_range_B_other15.63517.881968
X-RAY DIFFRACTIONr_rigid_bond_restr4.39433534
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.33→1.365 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.236 187 -
Rwork0.22 3247 -
obs--97.53 %
Refinement TLS params.Method: refined / Origin x: 18.3013 Å / Origin y: 0.461 Å / Origin z: 1.276 Å
111213212223313233
T0.0001 Å2-0.0002 Å20.0002 Å2-0.0136 Å2-0.0003 Å2--0.0145 Å2
L0.0004 °2-0.0002 °20.0001 °2-0.0001 °2-0 °2--0 °2
S0.0001 Å °0.0006 Å °0.0003 Å °-0.0001 Å °-0.0002 Å °-0.0005 Å °0 Å °-0 Å °0.0001 Å °

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