[English] 日本語
Yorodumi
- PDB-4qxt: Crystal Structure of anti-MSP2 Fv fragment (mAb6D8)in complex wit... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4qxt
TitleCrystal Structure of anti-MSP2 Fv fragment (mAb6D8)in complex with FC27-MSP2 14-30
Components
  • Fv fragment(mAb6D8) heavy chain
  • Fv fragment(mAb6D8) light chain
  • Merozoite surface antigen 2
KeywordsIMMUNE SYSTEM / Immunoglobulin fold / N-TERMINAL MSP2 / unstructured antigen
Function / homology
Function and homology information


side of membrane / cell adhesion / plasma membrane
Similarity search - Function
Merozoite surface antigen 2 (MSA-2) / Merozoite Surface Antigen 2 (MSA-2) family / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Merozoite surface protein 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
Plasmodium falciparum K1 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsMorales, R.A.V. / MacRaild, C.A. / Seow, J. / Bankala, K. / Drinkwater, N. / McGowan, S. / Rouet, R. / Christ, D. / Anders, R.F. / Norton, R.S.
CitationJournal: Sci Rep / Year: 2015
Title: Structural basis for epitope masking and strain specificity of a conserved epitope in an intrinsically disordered malaria vaccine candidate.
Authors: Morales, R.A. / MacRaild, C.A. / Seow, J. / Krishnarjuna, B. / Drinkwater, N. / Rouet, R. / Anders, R.F. / Christ, D. / McGowan, S. / Norton, R.S.
History
DepositionJul 22, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 3, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Fv fragment(mAb6D8) heavy chain
B: Fv fragment(mAb6D8) light chain
Q: Merozoite surface antigen 2


Theoretical massNumber of molelcules
Total (without water)26,3903
Polymers26,3903
Non-polymers00
Water5,873326
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2770 Å2
ΔGint-15 kcal/mol
Surface area10330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.097, 60.213, 43.437
Angle α, β, γ (deg.)90.00, 107.12, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Antibody Fv fragment(mAb6D8) heavy chain


Mass: 12489.899 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#2: Antibody Fv fragment(mAb6D8) light chain


Mass: 11959.071 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#3: Protein/peptide Merozoite surface antigen 2 / MEROZOITE SURFACE PROTEIN 2 / MSA-2


Mass: 1941.137 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 33-49 / Source method: obtained synthetically / Source: (synth.) Plasmodium falciparum K1 (eukaryote) / References: UniProt: Q03643
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 326 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 1.99 Å3/Da / Density % sol: 38.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.4
Details: 30% PEG 8000, 0.2M NaCl, 0.1M NaOAc, pH 4.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Apr 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.58→34.4 Å / Num. all: 28478 / Num. obs: 28505 / % possible obs: 99.9 %
Reflection shellResolution: 1.58→1.67 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.157 / Mean I/σ(I) obs: 6.8 / % possible all: 99.7

-
Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QYO

4qyo


Resolution: 1.58→34.388 Å / SU ML: 0.15 / σ(F): 1.35 / Phase error: 18.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1775 1509 5.3 %
Rwork0.1561 --
obs0.1573 28475 99.86 %
all-28478 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.58→34.388 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1789 0 0 326 2115
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081856
X-RAY DIFFRACTIONf_angle_d1.182528
X-RAY DIFFRACTIONf_dihedral_angle_d11.83663
X-RAY DIFFRACTIONf_chiral_restr0.048278
X-RAY DIFFRACTIONf_plane_restr0.005331
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5795-1.63050.27031230.17462448X-RAY DIFFRACTION99
1.6305-1.68880.20431240.17142441X-RAY DIFFRACTION100
1.6888-1.75640.20071360.15852467X-RAY DIFFRACTION100
1.7564-1.83630.18141380.15742414X-RAY DIFFRACTION100
1.8363-1.93310.20261300.1932432X-RAY DIFFRACTION100
1.9331-2.05420.18621330.1512445X-RAY DIFFRACTION100
2.0542-2.21280.17181460.15082473X-RAY DIFFRACTION100
2.2128-2.43550.18731520.17212421X-RAY DIFFRACTION100
2.4355-2.78770.21071420.16332448X-RAY DIFFRACTION100
2.7877-3.51170.14721380.14512476X-RAY DIFFRACTION100
3.5117-34.39620.1551470.14092501X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -5.1739 Å / Origin y: -12.609 Å / Origin z: -12.2338 Å
111213212223313233
T0.0905 Å2-0.0211 Å20.006 Å2-0.1043 Å2-0.026 Å2--0.0887 Å2
L0.9206 °2-0.4097 °20.3265 °2-1.5414 °2-0.5899 °2--0.8266 °2
S-0.0597 Å °-0.0626 Å °0.0449 Å °0.0668 Å °0.059 Å °-0.1331 Å °-0.0118 Å °-0.0655 Å °-0.003 Å °
Refinement TLS groupSelection details: ALL

+
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