[English] 日本語
Yorodumi
- PDB-7zvh: Penicillium expansum antifungal protein B -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7zvh
TitlePenicillium expansum antifungal protein B
ComponentsAntifungal protein
KeywordsANTIFUNGAL PROTEIN / Penicillium expansum / antifungal protein B
Function / homologyAntifungal protein / Antifungal protein domain superfamily / Antifungal protein / defense response to fungus / killing of cells of another organism / Antifungal protein
Function and homology information
Biological speciesPenicillium expansum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsGallego del Sol, F. / Marina, A. / Manzanares, P. / Marcos, J.F. / Giner Llorca, M.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and Universities Spain
CitationJournal: Int.J.Biol.Macromol. / Year: 2023
Title: Rationally designed antifungal protein chimeras reveal new insights into structure-activity relationship.
Authors: Giner-Llorca, M. / Del Sol, F.G. / Marcos, J.F. / Marina, A. / Manzanares, P.
History
DepositionMay 16, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 22, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Antifungal protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,7463
Polymers6,6751
Non-polymers712
Water1,29772
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint-11 kcal/mol
Surface area4160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.712, 46.712, 42.176
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-247-

HOH

-
Components

#1: Protein Antifungal protein


Mass: 6675.479 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Penicillium expansum (fungus) / References: UniProt: A0A0A2K0J0
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.99 Å3/Da / Density % sol: 38.19 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Magnesium chloride, 0.1 M HEPES pH 7.5, 30% PEG 400

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87313 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87313 Å / Relative weight: 1
ReflectionResolution: 1.2→40.454 Å / Num. all: 17032 / Num. obs: 17032 / % possible obs: 100 % / Redundancy: 8.9 % / Rpim(I) all: 0.026 / Rrim(I) all: 0.078 / Rsym value: 0.074 / Net I/av σ(I): 4.8 / Net I/σ(I): 13.1 / Num. measured all: 151614
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.2-1.266.50.5351.41593324400.2230.5820.5352.799.8
1.26-1.348.90.4771.62069823130.1680.5060.4773.8100
1.34-1.439.40.3252.32036021710.1110.3440.3255.799.9
1.43-1.559.50.2233.21952920590.0760.2360.2238.1100
1.55-1.79.60.1624.31805118790.0550.1710.16211.2100
1.7-1.99.60.1155.91641017130.0390.1220.11515.5100
1.9-2.199.50.0768.51442815160.0260.080.07623100
2.19-2.689.30.063101212513080.0220.0670.06328.3100
2.68-3.798.60.05210.3875810230.0180.0550.05234.6100
3.79-42.1768.70.04510.753226100.0160.0480.04537.799.9

-
Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
REFMAC5.8.0158refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7ZTF

7ztf


Resolution: 1.2→40.45 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.979 / SU B: 1.167 / SU ML: 0.023 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.038 / ESU R Free: 0.036 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.155 1204 7.1 %RANDOM
Rwork0.1351 ---
obs0.1366 15799 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 60.51 Å2 / Biso mean: 17.378 Å2 / Biso min: 8.91 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20.03 Å20 Å2
2--0.06 Å2-0 Å2
3----0.19 Å2
Refinement stepCycle: final / Resolution: 1.2→40.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms454 0 2 72 528
Biso mean--13.89 27.13 -
Num. residues----57
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.019500
X-RAY DIFFRACTIONr_bond_other_d0.0020.02450
X-RAY DIFFRACTIONr_angle_refined_deg1.5391.953675
X-RAY DIFFRACTIONr_angle_other_deg0.93131077
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.122564
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.80626.2524
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.71815106
X-RAY DIFFRACTIONr_dihedral_angle_4_deg0.06151
X-RAY DIFFRACTIONr_chiral_restr0.0940.268
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02554
X-RAY DIFFRACTIONr_gen_planes_other0.0020.0283
X-RAY DIFFRACTIONr_rigid_bond_restr1.5843950
X-RAY DIFFRACTIONr_sphericity_free22.175542
X-RAY DIFFRACTIONr_sphericity_bonded7.4085966
LS refinement shellResolution: 1.2→1.231 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.233 90 -
Rwork0.205 1159 -
all-1249 -
obs--99.52 %

+
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