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- PDB-5o51: AfRom2 CNH domain -

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Basic information

Entry
Database: PDB / ID: 5o51
TitleAfRom2 CNH domain
ComponentsRho guanyl nucleotide exchange factor (Rom2), putative
KeywordsPROTEIN BINDING / WD-40 / Rom2 / CNH domain
Function / homology
Function and homology information


asexual sporulation resulting in formation of a cellular spore / cellular response to xenobiotic stimulus => GO:0071466 / cellular heat acclimation / guanyl-nucleotide exchange factor activity / intracellular signal transduction / plasma membrane
Similarity search - Function
Pleckstrin homology domain 5 / Pleckstrin homology domain / Domain found in NIK1-like kinases, mouse citron and yeast ROM1, ROM2 / Citron homology (CNH) domain / CNH domain / Citron homology (CNH) domain profile. / Domain found in Dishevelled, Egl-10, and Pleckstrin (DEP) / DEP domain profile. / Domain found in Dishevelled, Egl-10, and Pleckstrin / DEP domain ...Pleckstrin homology domain 5 / Pleckstrin homology domain / Domain found in NIK1-like kinases, mouse citron and yeast ROM1, ROM2 / Citron homology (CNH) domain / CNH domain / Citron homology (CNH) domain profile. / Domain found in Dishevelled, Egl-10, and Pleckstrin (DEP) / DEP domain profile. / Domain found in Dishevelled, Egl-10, and Pleckstrin / DEP domain / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / PH-like domain superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Rho guanyl nucleotide exchange factor (Rom2), putative
Similarity search - Component
Biological speciesAspergillus fumigatus Af293 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.01 Å
AuthorsWei, W. / van Aalten, D.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom) United Kingdom
CitationJournal: To Be Published
Title: Rom2 CNH domain from Aspergillus fumigatus is an atypical seven-bladed WD-40 protein
Authors: Wei, W. / van Aalten, D.
History
DepositionMay 31, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Category: reflns_shell

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Rho guanyl nucleotide exchange factor (Rom2), putative


Theoretical massNumber of molelcules
Total (without water)38,3651
Polymers38,3651
Non-polymers00
Water1,29772
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area15710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.980, 93.710, 52.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Rho guanyl nucleotide exchange factor (Rom2), putative


Mass: 38364.582 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus Af293 (mold) / Gene: AFUA_5G08550 / Plasmid: PGEX-6P-1 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q4WUI2
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 2.5 Å3/Da / Density % sol: 50.89 % / Description: cubic
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.02 M L-Na-Glutamate; 0.02 M Alanine (racemic);0.02M Glycine; 0.02M Lysine HCl (racemic); 0.02M Serine (racemic);0.1 M tris Bicine buffer (pH 8.5); 20% v/v Ethylene glycol; 10 % w/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9282 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9282 Å / Relative weight: 1
ReflectionResolution: 2.01→45.87 Å / Num. obs: 26362 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 13.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
xia2data reduction
xia2data scaling
MOLREPphasing
RefinementResolution: 2.01→45.87 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.943 / SU B: 5.838 / SU ML: 0.151 / Cross valid method: THROUGHOUT / ESU R: 0.174 / ESU R Free: 0.162 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24824 1361 5.2 %RANDOM
Rwork0.20463 ---
obs0.20692 24966 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 56.7 Å2
Baniso -1Baniso -2Baniso -3
1--2.81 Å20 Å20 Å2
2---0.66 Å20 Å2
3---3.47 Å2
Refinement stepCycle: 1 / Resolution: 2.01→45.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2467 0 0 72 2539
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0192528
X-RAY DIFFRACTIONr_bond_other_d0.0020.022394
X-RAY DIFFRACTIONr_angle_refined_deg1.9171.9513422
X-RAY DIFFRACTIONr_angle_other_deg1.03935509
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.7535308
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.09723.729118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.90115435
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6471517
X-RAY DIFFRACTIONr_chiral_restr0.1130.2379
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212841
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02598
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_it5.3435.3781238
X-RAY DIFFRACTIONr_mcbond_other5.3215.3751237
X-RAY DIFFRACTIONr_mcangle_it7.6378.041544
X-RAY DIFFRACTIONr_mcangle_other7.648.0451545
X-RAY DIFFRACTIONr_scbond_it5.4035.9491290
X-RAY DIFFRACTIONr_scbond_other5.4015.9531291
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.1178.6961879
X-RAY DIFFRACTIONr_long_range_B_refined11.05743.612613
X-RAY DIFFRACTIONr_long_range_B_other11.06443.622601
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.01→2.062 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 95 -
Rwork0.317 1810 -
obs--100 %

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