[English] 日本語
Yorodumi
- PDB-7bae: Crystal structure of PAFB -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7bae
TitleCrystal structure of PAFB
ComponentsAntifungal proteinAntifungal protein family
KeywordsANTIFUNGAL PROTEIN / Penicillium chrysogenum antifungal protein B / calix[n]arene / porous framework / zinc
Function / homologyAntifungal protein / Antifungal protein domain superfamily / Antifungal protein / defense response to fungus / killing of cells of another organism / host cell cytoplasm / extracellular region / Antifungal protein B
Function and homology information
Biological speciesPenicillium rubens
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsGuagnini, F. / Huber, A. / Alex, J.M. / Marx, F. / Crowley, P.B.
Funding support Ireland, 2items
OrganizationGrant numberCountry
Science Foundation Ireland13/CDA/2168 Ireland
Irish Research CouncilGOIPD/2019/513 Ireland
CitationJournal: J.Struct.Biol. / Year: 2021
Title: Porous assembly of an antifungal protein mediated by zinc and sulfonato-calix[8]arene.
Authors: Guagnini, F. / Huber, A. / Alex, J.M. / Marx, F. / Crowley, P.B.
History
DepositionDec 15, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.2Jan 31, 2024Group: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Antifungal protein


Theoretical massNumber of molelcules
Total (without water)6,5161
Polymers6,5161
Non-polymers00
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR relaxation study
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area3830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.124, 36.953, 24.878
Angle α, β, γ (deg.)90, 103.84, 90
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Antifungal protein / Antifungal protein family


Mass: 6516.394 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Penicillium rubens (strain ATCC 28089 / DSM 1075 / NRRL 1951 / Wisconsin 54-1255) (fungus)
Strain: ATCC 28089 / DSM 1075 / NRRL 1951 / Wisconsin 54-1255
Gene: afp, Pc12g08290
Production host: Penicillium rubens Wisconsin 54-1255 (fungus)
References: UniProt: B6GXZ8
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 2.13 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 0.7 mM Palmitic acid, 0.1 M Potassium phosphate citrate pH 4.2, 40 % PEG 300

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98013 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Sep 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98013 Å / Relative weight: 1
ReflectionResolution: 1.2→31.51 Å / Num. obs: 16905 / % possible obs: 98.3 % / Redundancy: 6.7 % / CC1/2: 0.997 / Net I/σ(I): 13.9
Reflection shellResolution: 1.2→1.2 Å / Num. unique obs: 799 / CC1/2: 0.712

-
Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
Aimlessdata reduction
pointlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6HAJ

6haj


Resolution: 1.2→31.5 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.913 / SU R Cruickshank DPI: 0.046 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.049 / SU Rfree Blow DPI: 0.049 / SU Rfree Cruickshank DPI: 0.047
RfactorNum. reflection% reflectionSelection details
Rfree0.23 809 -RANDOM
Rwork0.2114 ---
obs0.2123 16905 98.2 %-
Solvent computationVDW probe radii: 11 Å
Displacement parametersBiso mean: 19.74 Å2
Baniso -1Baniso -2Baniso -3
1-0.9793 Å20 Å2-0.7275 Å2
2---1.7117 Å20 Å2
3---0.7323 Å2
Refine analyzeLuzzati coordinate error obs: 0.16 Å
Refinement stepCycle: LAST / Resolution: 1.2→31.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms444 0 0 54 498
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.01456HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.04610HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d164SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes78HARMONIC5
X-RAY DIFFRACTIONt_it456HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion55SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact433SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion4.09
X-RAY DIFFRACTIONt_other_torsion11.3
LS refinement shellResolution: 1.2→1.21 Å
RfactorNum. reflection% reflection
Rfree0.2136 26 -
Rwork0.1918 --
obs0.1931 423 94.04 %
Refinement TLS params.Method: refined / Origin x: 12.0151 Å / Origin y: 8.0073 Å / Origin z: 16.3364 Å
111213212223313233
T0.0011 Å2-0.0059 Å20.0033 Å2--0.0057 Å2-0.0005 Å2---0.0022 Å2
L0.3308 °2-0.5501 °20.1765 °2-0.8338 °20.0943 °2--0.2845 °2
S0.012 Å °-0.045 Å °-0.0249 Å °-0.045 Å °0.0032 Å °-0.0017 Å °-0.0249 Å °-0.0017 Å °-0.0152 Å °
Refinement TLS groupSelection details: { A|-2 - A|55 }

+
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