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- PDB-6m4c: C. albicans actin interacting protein Aip5 -

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Basic information

Entry
Database: PDB / ID: 6m4c
TitleC. albicans actin interacting protein Aip5
ComponentsC. albicans actin interacting protein Aip5
KeywordsCYTOSOLIC PROTEIN / Actin / Polarisome / Nucleation promoting factor
Function / homologyhyphal growth / SH3-binding, glutamic acid-rich protein / SH3-binding, glutamic acid-rich protein / positive regulation of actin filament bundle assembly / Glutaredoxin / Glutaredoxin domain profile. / protein-disulfide reductase activity / Thioredoxin-like superfamily / Glutaredoxin domain-containing protein
Function and homology information
Biological speciesCandida albicans SC5314 (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsLoh, Z.Y. / Gao, Y.G. / Xie, Y. / Miao, Y.
Funding support Singapore, 1items
OrganizationGrant numberCountry
Ministry of Education (MoE, Singapore) Singapore
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Orchestrated actin nucleation by the Candida albicans polarisome complex enables filamentous growth.
Authors: Xie, Y. / Loh, Z.Y. / Xue, J. / Zhou, F. / Sun, J. / Qiao, Z. / Jin, S. / Deng, Y. / Li, H. / Wang, Y. / Lu, L. / Gao, Y. / Miao, Y.
History
DepositionMar 6, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Sep 16, 2020Group: Database references / Category: citation / Item: _citation.title
Revision 1.3Nov 18, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.4Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: C. albicans actin interacting protein Aip5


Theoretical massNumber of molelcules
Total (without water)11,3131
Polymers11,3131
Non-polymers00
Water25214
1
A: C. albicans actin interacting protein Aip5

A: C. albicans actin interacting protein Aip5


Theoretical massNumber of molelcules
Total (without water)22,6252
Polymers22,6252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+4/31
Unit cell
Length a, b, c (Å)95.116, 95.116, 74.119
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6
Components on special symmetry positions
IDModelComponents
11A-106-

HOH

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Components

#1: Protein C. albicans actin interacting protein Aip5


Mass: 11312.712 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans SC5314 (yeast) / Strain: SC5314 / ATCC MYA-2876 / Gene: orf19.92, CAALFM_C600910CA / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A1D8PPH3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 4.27 Å3/Da / Density % sol: 71.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.1M Tris pH 7.4, 0.2M calcium acetate, 12.5% PEG 3000

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. obs: 5823 / % possible obs: 91.9 % / Redundancy: 30.94 % / Biso Wilson estimate: 83.02 Å2 / CC1/2: 1 / Net I/σ(I): 30.51
Reflection shellResolution: 2.65→2.75 Å / Num. unique obs: 602 / CC1/2: 0.84

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ABR

6abr


Resolution: 2.65→47.6 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.921 / SU B: 14.57 / SU ML: 0.278 / Cross valid method: THROUGHOUT / ESU R: 0.414 / ESU R Free: 0.322 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.30573 882 14.4 %RANDOM
Rwork0.25852 ---
obs0.26538 5241 99.95 %-
Solvent computationIon probe radii: 1 Å / Shrinkage radii: 1 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 90.87 Å2
Baniso -1Baniso -2Baniso -3
1-2.91 Å21.46 Å2-0 Å2
2--2.91 Å20 Å2
3----9.45 Å2
Refinement stepCycle: 1 / Resolution: 2.65→47.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms729 0 0 15 744
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.011742
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6041.6291011
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.779597
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.78723.540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.7415105
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.381154
X-RAY DIFFRACTIONr_chiral_restr0.120.2100
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02588
X-RAY DIFFRACTIONr_gen_planes_other
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_it10.1889.809391
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it13.95914.697487
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it10.729.83350
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined18.6183042
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.65→2.719 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.426 62 -
Rwork0.493 367 -
obs--99.77 %

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