[English] 日本語
Yorodumi
- PDB-6ha4: Crystal structure of PAF - p-sulfonatocalix[4]arene complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ha4
TitleCrystal structure of PAF - p-sulfonatocalix[4]arene complex
ComponentsPc24g00380 protein
KeywordsANTIFUNGAL PROTEIN / Penicillium chrysogenum / calixarene / molecular glues / nucleating agent
Function / homology
Function and homology information


defense response to fungus / killing of cells of another organism
Similarity search - Function
Antifungal protein domain / Antifungal protein / Antifungal protein domain superfamily / Antifungal protein / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-T3Y / Pc24g00380 protein
Similarity search - Component
Biological speciesPenicillium rubens
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.33 Å
AuthorsAlex, J.M. / Rennie, M. / Engilberge, S. / Batta, G. / Crowley, P.B.
Funding support Ireland, 2items
OrganizationGrant numberCountry
Science Foundation Ireland13/CDA/2168 Ireland
Science Foundation Ireland13/ERC/B2912 Ireland
CitationJournal: Iucrj / Year: 2019
Title: Calixarene-mediated assembly of a small antifungal protein.
Authors: Alex, J.M. / Rennie, M.L. / Engilberge, S. / Lehoczki, G. / Dorottya, H. / Fizil, A. / Batta, G. / Crowley, P.B.
History
DepositionAug 7, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 13, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 17, 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: Pc24g00380 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,1003
Polymers6,2631
Non-polymers8372
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-0 kcal/mol
Surface area4390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)22.719, 37.587, 29.956
Angle α, β, γ (deg.)90.00, 111.75, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Pc24g00380 protein


Mass: 6263.099 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Penicillium rubens (strain ATCC 28089 / DSM 1075 / NRRL 1951 / Wisconsin 54-1255) (fungus)
References: UniProt: B6HWK0
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-T3Y / 25,26,27,28-tetrahydroxypentacyclo[19.3.1.1~3,7~.1~9,13~.1~15,19~]octacosa-1(25),3(28),4,6,9(27),10,12,15(26),16,18,21,23-dodecaene-5,11,17,23-tetrasulfonic acid / 5,11,17,23-tetra-sulphonato-calix[4]arene-25,26,27,28-tetrol


Mass: 744.741 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H24O16S4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 1.9 Å3/Da / Density % sol: 35.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 / Details: 30% PEG 3350 + 0.05 M Sodium acetate pH 5.6

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.3→27.8 Å / Num. obs: 10142 / % possible obs: 92.2 % / Redundancy: 3.4 % / Biso Wilson estimate: 16.37 Å2 / CC1/2: 0.98 / Rpim(I) all: 0.062 / Rrim(I) all: 0.012 / Net I/av σ(I): 6.1 / Net I/σ(I): 6.1
Reflection shellResolution: 1.33→1.37 Å / Mean I/σ(I) obs: 1.3 / CC1/2: 0.34 / Rpim(I) all: 0.34 / Rrim(I) all: 0.61

-
Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2MHV

2mhv


Resolution: 1.33→27.8 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.911 / SU R Cruickshank DPI: 0.076 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.071 / SU Rfree Blow DPI: 0.072 / SU Rfree Cruickshank DPI: 0.069
RfactorNum. reflection% reflectionSelection details
Rfree0.217 526 5.19 %RANDOM
Rwork0.185 ---
obs0.186 10142 92.5 %-
Displacement parametersBiso mean: 20.96 Å2
Baniso -1Baniso -2Baniso -3
1-2.2438 Å20 Å20.718 Å2
2---5.4036 Å20 Å2
3---3.1597 Å2
Refine analyzeLuzzati coordinate error obs: 0.18 Å
Refinement stepCycle: 1 / Resolution: 1.33→27.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms433 0 54 55 542
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.005972HARMONIC6
X-RAY DIFFRACTIONt_angle_deg0.741759HARMONIC6
X-RAY DIFFRACTIONt_dihedral_angle_d230SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes153HARMONIC5
X-RAY DIFFRACTIONt_it972HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion4.9
X-RAY DIFFRACTIONt_other_torsion17.43
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion64SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1154SEMIHARMONIC4
LS refinement shellResolution: 1.33→1.48 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2254 133 4.96 %
Rwork0.208 2546 -
all0.2089 2679 -
obs--86.77 %
Refinement TLS params.Method: refined / Origin x: -3.7966 Å / Origin y: 4.5228 Å / Origin z: 31.3802 Å
111213212223313233
T-0.0129 Å20.007 Å2-0.0213 Å2--0.0297 Å2-0.0182 Å2---0.0202 Å2
L1.1555 °2-0.1822 °20.0215 °2-0.7064 °2-0.2874 °2--1.1753 °2
S0.0249 Å °0.0048 Å °-0.0542 Å °-0.0008 Å °-0.07 Å °0.0213 Å °-0.0123 Å °-0.0299 Å °0.0452 Å °
Refinement TLS groupSelection details: { A|* }

+
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://pdbjlvh1.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