[English] 日本語
Yorodumi
- PDB-5zvp: Aspergillus fumigatus Rho1 F25N -

+
Open data


ID or keywords:

Loading...

-
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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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.

-
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

-
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 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more