[English] 日本語
Yorodumi
- PDB-8zlc: Crystal Structure of Ankyrin Repeat Protein from Plasmodium falciparum -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8zlc
TitleCrystal Structure of Ankyrin Repeat Protein from Plasmodium falciparum
ComponentsAnkyrin-repeat protein
KeywordsSTRUCTURAL PROTEIN / Protein-Protein interaction / Ankyrin Repeat / invasion Complex
Function / homologyAnkyrin repeats (many copies) / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Ankyrin-repeat protein, putative
Function and homology information
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å
AuthorsKumari, P. / Gautam, A.K. / Gourinath, S. / Malhotra, P.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India) India
CitationJournal: To Be Published
Title: Crystal Structure of Ankyrin Repeat Protein from Plasmodium falciparum
Authors: Kumari, P. / Gautam, A.K. / Gourinath, S. / Malhotra, P.
History
DepositionMay 18, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 21, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ankyrin-repeat protein
B: Ankyrin-repeat protein


Theoretical massNumber of molelcules
Total (without water)31,1602
Polymers31,1602
Non-polymers00
Water2,036113
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.377, 62.742, 91.784
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: GLY / End label comp-ID: GLY / Auth seq-ID: 3 - 135 / Label seq-ID: 3 - 135

Dom-IDComponent-IDAuth asym-IDLabel asym-ID
11AA
22BB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

-
Components

#1: Protein Ankyrin-repeat protein


Mass: 15580.159 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: PF3D7_1410800 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8ILY7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.96 Å3/Da / Density % sol: 37.18 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop
Details: 0.2M Ammonium Acetate, 25% PEG 3350, 0.1M bis-tris pH 5.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87313 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jul 5, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87313 Å / Relative weight: 1
ReflectionResolution: 2.13→51.8 Å / Num. obs: 18741 / % possible obs: 99.94 % / Redundancy: 4.82 % / CC1/2: 0.994 / Net I/σ(I): 5.35
Reflection shellResolution: 2.13→2.185 Å / Num. unique obs: 910 / CC1/2: 0.732

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.13→51.797 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.905 / SU B: 5.455 / SU ML: 0.144 / Cross valid method: FREE R-VALUE / ESU R: 0.277 / ESU R Free: 0.201
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2287 711 4.99 %
Rwork0.1847 13538 -
all0.187 --
obs-14249 99.853 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 27.033 Å2
Baniso -1Baniso -2Baniso -3
1--1.195 Å2-0 Å20 Å2
2--0.939 Å2-0 Å2
3---0.256 Å2
Refinement stepCycle: LAST / Resolution: 2.13→51.797 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2103 0 0 113 2216
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0132140
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162109
X-RAY DIFFRACTIONr_angle_refined_deg1.5391.632894
X-RAY DIFFRACTIONr_angle_other_deg1.3131.5854841
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.65270
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.17424.63295
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.75215402
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.744157
X-RAY DIFFRACTIONr_chiral_restr0.0760.2291
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022412
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02458
X-RAY DIFFRACTIONr_nbd_refined0.2240.2461
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1810.21917
X-RAY DIFFRACTIONr_nbtor_refined0.1560.21095
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.2976
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.271
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1010.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.20.228
X-RAY DIFFRACTIONr_nbd_other0.1950.275
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1450.220
X-RAY DIFFRACTIONr_mcbond_it2.1432.6471080
X-RAY DIFFRACTIONr_mcbond_other2.142.6461079
X-RAY DIFFRACTIONr_mcangle_it3.2093.9571347
X-RAY DIFFRACTIONr_mcangle_other3.2083.9581348
X-RAY DIFFRACTIONr_scbond_it3.13.1261060
X-RAY DIFFRACTIONr_scbond_other3.0993.1261060
X-RAY DIFFRACTIONr_scangle_it4.9284.5041546
X-RAY DIFFRACTIONr_scangle_other4.9284.5031546
X-RAY DIFFRACTIONr_lrange_it6.25132.582462
X-RAY DIFFRACTIONr_lrange_other6.24432.5132451
X-RAY DIFFRACTIONr_ncsr_local_group_10.130.053826
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.12970.05007
12BX-RAY DIFFRACTIONLocal ncs0.12970.05007
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.13-2.1850.208560.2269680.22410270.9370.90999.70790.218
2.185-2.2450.234460.2189850.21810330.9150.92399.80640.206
2.245-2.310.245490.198970.1939460.9170.941000.181
2.31-2.3810.204380.2029230.2039640.9270.92699.68880.195
2.381-2.4590.281460.2018750.2059220.9020.92599.89150.199
2.459-2.5450.223560.2058430.2068990.9240.9311000.206
2.545-2.6410.257450.2048370.2078830.9170.92699.88670.207
2.641-2.7480.301440.2057660.218100.8680.9271000.211
2.748-2.870.228350.2057710.2068080.9140.92999.75250.215
2.87-3.010.265340.1857430.1887770.9310.941000.198
3.01-3.1720.26340.1857000.1887340.9190.9511000.199
3.172-3.3640.2330.1776530.1786860.9470.9551000.196
3.364-3.5950.233350.1636400.1666750.950.9641000.19
3.595-3.8810.21310.165790.1626100.9460.9661000.191
3.881-4.2490.237280.1625520.1655800.9450.9671000.199
4.249-4.7470.195260.1544950.1565210.9740.9671000.197
4.747-5.4730.173240.1814340.184580.9670.9611000.233
5.473-6.6850.202220.1843810.1854030.970.9611000.229
6.685-9.3760.121180.183090.1763270.9610.9411000.257
9.376-51.7970.429110.1971850.2112050.6970.9495.60980.401

+
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