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- PDB-5zvp: Aspergillus fumigatus Rho1 F25N -

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Basic information

Entry
Database: PDB / ID: 5zvp
TitleAspergillus fumigatus Rho1 F25N
ComponentsRho GTPase Rho1
KeywordsANTIBIOTIC / Aspergillus fumigatus / Rho1 GTPase / cell wall target
Function / homology
Function and homology information


asexual sporulation resulting in formation of a cellular spore / 1,3-beta-D-glucan synthase complex / hyphal tip / small GTPase-mediated signal transduction / GTPase activity / GTP binding / metal ion binding / plasma membrane
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 ...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 nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Rho GTPase Rho1
Similarity search - Component
Biological speciesAspergillus fumigatus Af293 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.42 Å
AuthorsWei, W.F. / Van Aalten, D.M.F.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom) United Kingdom
CitationJournal: To Be Published
Title: Aspergillus fumigateurs Rho1 F25N
Authors: Wei, W.F. / Van Aalten, D.M.F.
History
DepositionMay 12, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rho GTPase Rho1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8924
Polymers20,3281
Non-polymers5643
Water3,369187
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-13 kcal/mol
Surface area9550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.815, 53.815, 62.789
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Rho GTPase Rho1


Mass: 20328.240 Da / Num. of mol.: 1 / Mutation: F25N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus Af293 (mold) / Strain: Af293 / Gene: rho1, AFUA_6G06900 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A068C8U8
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 2.24 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 37.1% w/v PEG 5000 MME, 150 mM Tris pH 8.0, 40 mM magnesium sulphate.

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Data collection

DiffractionMean temperature: 253 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.988 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Mar 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.988 Å / Relative weight: 1
ReflectionResolution: 1.4→100 Å / Num. obs: 31770 / % possible obs: 99 % / Redundancy: 4.14 % / Net I/σ(I): 18.79
Reflection shellResolution: 1.42→1.47 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementResolution: 1.42→53.82 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.138 / SU ML: 0.043 / Cross valid method: THROUGHOUT / ESU R: 0.058 / ESU R Free: 0.061 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18482 1701 5.1 %RANDOM
Rwork0.15536 ---
obs0.15683 31770 98.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 23.694 Å2
Baniso -1Baniso -2Baniso -3
1-0.56 Å20 Å20 Å2
2--0.56 Å20 Å2
3----1.12 Å2
Refinement stepCycle: 1 / Resolution: 1.42→53.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1426 0 34 187 1647
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0191488
X-RAY DIFFRACTIONr_bond_other_d0.0020.021416
X-RAY DIFFRACTIONr_angle_refined_deg2.29722025
X-RAY DIFFRACTIONr_angle_other_deg1.14233274
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7375180
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.7424.46265
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.62915258
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.652159
X-RAY DIFFRACTIONr_chiral_restr0.1610.2231
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211631
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02312
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_it2.2282.006723
X-RAY DIFFRACTIONr_mcbond_other2.2172.004722
X-RAY DIFFRACTIONr_mcangle_it3.3862.999902
X-RAY DIFFRACTIONr_mcangle_other3.3863.001903
X-RAY DIFFRACTIONr_scbond_it3.8152.482765
X-RAY DIFFRACTIONr_scbond_other3.8372.49753
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.7983.5421105
X-RAY DIFFRACTIONr_long_range_B_refined6.87817.8171815
X-RAY DIFFRACTIONr_long_range_B_other6.85217.081700
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.42→1.457 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 146 -
Rwork0.309 2250 -
obs--96.3 %

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