[English] 日本語
Yorodumi
- PDB-1w8k: Crystal structure of apical membrane antigen 1 from Plasmodium vivax -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1w8k
TitleCrystal structure of apical membrane antigen 1 from Plasmodium vivax
ComponentsAPICAL MEMBRANE ANTIGEN 1
KeywordsANTIGEN / PLASMODIUM ANTIGEN / MALARIA VACCINE CANDIDATE
Function / homology
Function and homology information


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
IMIDAZOLE / Apical merozoite antigen 1 / Apical membrane antigen 1
Similarity search - Component
Biological speciesPLASMODIUM VIVAX (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsPizarro, J.C. / Vulliez-Le Normand, B. / Chesne-Seck, M.-L. / Kocken, C.H.M. / Thomas, A.W. / Bentley, G.A.
CitationJournal: Science / Year: 2005
Title: Crystal Structure of the Malaria Vaccine Candidate Apical Membrane Antigen 1
Authors: Pizarro, J.C. / Vulliez-Le Normand, B. / Chesne-Seck, M.-L. / Collins, C. / Withers-Martinez, C. / Hackett, F. / Blackman, M. / Faber, B. / Remarque, E. / Kocken, C.H.M. / Thomas, A.W. / Bentley, G.A.
History
DepositionSep 23, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 1, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: APICAL MEMBRANE ANTIGEN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6662
Polymers51,5971
Non-polymers691
Water3,837213
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)150.030, 53.760, 60.290
Angle α, β, γ (deg.)90.00, 113.18, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein APICAL MEMBRANE ANTIGEN 1


Mass: 51597.047 Da / Num. of mol.: 1 / Fragment: ECTOPLASMIC REGION, RESIDUES 1-445 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PLASMODIUM VIVAX (malaria parasite P. vivax)
Strain: SAL I / Production host: PICHIA PASTORIS (fungus) / References: UniProt: Q9TY14, UniProt: O61130*PLUS
#2: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED MUTATION IN CHAIN A, SER 178 TO ASN ENGINEERED MUTATION IN CHAIN A, ASN 226 TO ASP ...ENGINEERED MUTATION IN CHAIN A, SER 178 TO ASN ENGINEERED MUTATION IN CHAIN A, ASN 226 TO ASP ENGINEERED MUTATION IN CHAIN A, ASN 441 TO GLN
Has protein modificationY
Sequence detailsSEQUENCE EXPRESSED COMPRISES RESIDUES 1 TO 445. MUTATIONS S136N, N184D AND N399Q HAVE BEEN ...SEQUENCE EXPRESSED COMPRISES RESIDUES 1 TO 445. MUTATIONS S136N, N184D AND N399Q HAVE BEEN INTRODUCED TO ELIMINATE POTENTIAL N-GLYCOSYLATION SITE.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44 %
Crystal growpH: 7
Details: THE CRYSTALLISATION MIXTURE CONSISTED OF 10-12% (W/V) PEG3350, 100-200MM IMIDAZOLE, PH 7.0, 5-10% (V/V) ISOPROPANOL, AND 1% (V/V) DMF OR 3% (V/V) T-BUTANOL. THE PROTEIN SOLUTION WAS DILUTED ...Details: THE CRYSTALLISATION MIXTURE CONSISTED OF 10-12% (W/V) PEG3350, 100-200MM IMIDAZOLE, PH 7.0, 5-10% (V/V) ISOPROPANOL, AND 1% (V/V) DMF OR 3% (V/V) T-BUTANOL. THE PROTEIN SOLUTION WAS DILUTED BY 40 - 60% REMARK 280 WITH THE CRYSTALLISATION BUFFER, GIVING A FINAL REMARK 280 CONCENTRATION OF 4-6 MG. ML-1 IN SUSPENDED DROPS OF VOLUME REMARK 280 2 - 3 PERCENT.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 14, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 152093 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 10.5
Reflection shellResolution: 1.8→1.9 Å / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 2 / % possible all: 97.3

-
Processing

Software
NameVersionClassification
REFMAC5.2.0003refinement
XDSdata reduction
XSCALEdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→19.34 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.933 / SU B: 4.043 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.139 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE FOLLOWING SEGMENTS WERE NOT MODELLED A171 TO 176, A204 TO A206, A210 TO A215, A297 TO A334, A403 TO A413, A476 TO A487.
RfactorNum. reflection% reflectionSelection details
Rfree0.269 2070 5.1 %RANDOM
Rwork0.219 ---
obs0.222 38819 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.09 Å2
Baniso -1Baniso -2Baniso -3
1-0.65 Å20 Å21.73 Å2
2---1.97 Å20 Å2
3---2.68 Å2
Refinement stepCycle: LAST / Resolution: 1.8→19.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2932 0 5 213 3150
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0223004
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9261.9424045
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1545355
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.424.452155
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.13115540
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9691521
X-RAY DIFFRACTIONr_chiral_restr0.130.2425
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022286
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2210.21342
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3170.22011
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2280.2206
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1690.228
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.240.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3842.51869
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.4733.52926
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.93541292
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.5865.51119
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.361 148
Rwork0.318 2786

+
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