[English] 日本語
Yorodumi
- PDB-4z0f: Crystal structure of FVO strain Plasmodium falciparum AMA1 in com... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4z0f
TitleCrystal structure of FVO strain Plasmodium falciparum AMA1 in complex with the RON2hp [Phe2038(6CW)] peptide
Components
  • Apical membrane antigen 1
  • Rhoptry neck protein 2
KeywordsCELL INVASION / inhibitor / AMA1 / malaria
Function / homology
Function and homology information


rhoptry neck / membrane
Similarity search - Function
Apical membrane antigen 1 domain superfamily / Apical membrane antigen 1 / Apical membrane antigen 1 / Apical membrane antigen 1 / Hepatocyte Growth Factor / Hepatocyte Growth Factor / 3-Layer(bba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Apical membrane antigen 1 / Rhoptry neck protein 2
Similarity search - Component
Biological speciesPlasmodium falciparum Vietnam Oak-Knoll (eukaryote)
Plasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsWang, G. / McGowan, S. / Norton, R.S. / Scanlon, M.J.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1025150 Australia
CitationJournal: J.Mol.Biol. / Year: 2016
Title: Structure-Activity Studies of beta-Hairpin Peptide Inhibitors of the Plasmodium falciparum AMA1-RON2 Interaction.
Authors: Wang, G. / Drinkwater, N. / Drew, D.R. / MacRaild, C.A. / Chalmers, D.K. / Mohanty, B. / Lim, S.S. / Anders, R.F. / Beeson, J.G. / Thompson, P.E. / McGowan, S. / Simpson, J.S. / Norton, R.S. / Scanlon, M.J.
History
DepositionMar 26, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2016Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations
Category: citation / diffrn_source ...citation / diffrn_source / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Apical membrane antigen 1
C: Rhoptry neck protein 2


Theoretical massNumber of molelcules
Total (without water)39,9202
Polymers39,9202
Non-polymers00
Water2,954164
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint-12 kcal/mol
Surface area12950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.100, 72.181, 115.740
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Apical membrane antigen 1


Mass: 38333.805 Da / Num. of mol.: 1 / Fragment: UNP residues 104-438
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum Vietnam Oak-Knoll (FVO) (eukaryote)
Strain: FVO / Gene: PFFVO_05649 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A024UZE1
#2: Protein/peptide Rhoptry neck protein 2


Mass: 1586.276 Da / Num. of mol.: 1 / Fragment: UNP residues 1217-1229 / Mutation: Phe2038(6CW) / Source method: obtained synthetically
Source: (synth.) Plasmodium falciparum (malaria parasite P. falciparum)
References: UniProt: Q8IKV6*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.02 Å3/Da / Density % sol: 39.04 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 15-20% PEG400, 0.1 M Tris-HCl, pH 8.6, 0.1 M sodium acetate and 20% isopropanol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 2, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.3→36.19 Å / Num. obs: 14350 / % possible obs: 96.6 % / Redundancy: 6.7 % / Biso Wilson estimate: 15.91 Å2 / CC1/2: 0.985 / Rmerge(I) obs: 0.162 / Rpim(I) all: 0.065 / Net I/σ(I): 8.8 / Num. measured all: 96681 / Scaling rejects: 233
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.3-2.386.10.4744.6836413680.9190.20395.5
8.9-36.195.90.0871217362920.9760.03996.5

-
Processing

Software
NameVersionClassification
SCALAdata scaling
PHASERphasing
Cootmodel building
PHENIX1.9_1692refinement
PDB_EXTRACT3.15data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4R1A

4r1a


Resolution: 2.3→36.09 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2397 692 4.85 %
Rwork0.1939 13586 -
obs0.1962 14278 96.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 78.37 Å2 / Biso mean: 19.6465 Å2 / Biso min: 5.09 Å2
Refinement stepCycle: final / Resolution: 2.3→36.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2256 0 0 164 2420
Biso mean---21.98 -
Num. residues----291
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022327
X-RAY DIFFRACTIONf_angle_d0.6213159
X-RAY DIFFRACTIONf_chiral_restr0.025335
X-RAY DIFFRACTIONf_plane_restr0.003417
X-RAY DIFFRACTIONf_dihedral_angle_d10.577826
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3002-2.47780.25851440.20622709285398
2.4778-2.72710.28111310.20472624275594
2.7271-3.12150.25971340.209427752909100
3.1215-3.9320.26671300.1942571270191
3.932-36.09490.18071530.17442907306098
Refinement TLS params.Method: refined / Origin x: -8.6196 Å / Origin y: 2.7964 Å / Origin z: -7.4512 Å
111213212223313233
T0.0527 Å2-0.0083 Å20.0147 Å2-0.0338 Å2-0.016 Å2--0.1356 Å2
L0.7442 °2-0.3463 °20.3113 °2-2.5486 °2-0.4425 °2--0.7043 °2
S0.0375 Å °0.0868 Å °0.0333 Å °-0.1926 Å °-0.0312 Å °-0.0322 Å °-0.0286 Å °0.0163 Å °-0.0041 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA107 - 438
2X-RAY DIFFRACTION1allB1 - 246
3X-RAY DIFFRACTION1allC1 - 13

+
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