[English] 日本語
Yorodumi
- PDB-6tlb: Plasmodium falciparum lipocalin (PF3D7_0925900) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6tlb
TitlePlasmodium falciparum lipocalin (PF3D7_0925900)
ComponentsSerine/threonine protein kinase
KeywordsUNKNOWN FUNCTION / Lipocalin / Malaria / Infection
Function / homologyCalycin / Parasitophorous vacuolar protein 5, putative
Function and homology information
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SOLUTION SCATTERING / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsBurda, P.C. / Crosskey, T.D. / Lauk, K. / Wilmanns, M. / Gilberger, T.W.
Funding support Germany, 1items
OrganizationGrant numberCountry
European Molecular Biology Organization Germany
CitationJournal: Cell Rep / Year: 2020
Title: Structure-Based Identification and Functional Characterization of a Lipocalin in the Malaria Parasite Plasmodium falciparum.
Authors: Burda, P.C. / Crosskey, T. / Lauk, K. / Zurborg, A. / Sohnchen, C. / Liffner, B. / Wilcke, L. / Pietsch, E. / Strauss, J. / Jeffries, C.M. / Svergun, D.I. / Wilson, D.W. / Wilmanns, M. / Gilberger, T.W.
History
DepositionDec 2, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 24, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 24, 2024Group: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Serine/threonine protein kinase
B: Serine/threonine protein kinase
C: Serine/threonine protein kinase
D: Serine/threonine protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,40211
Polymers88,9654
Non-polymers4377
Water70339
1
B: Serine/threonine protein kinase
D: Serine/threonine protein kinase
hetero molecules

A: Serine/threonine protein kinase
C: Serine/threonine protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,40211
Polymers88,9654
Non-polymers4377
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area9450 Å2
ΔGint-111 kcal/mol
Surface area31910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.993, 92.250, 214.502
Angle α, β, γ (deg.)90.00, 98.35, 90.00
Int Tables number5
Space group name H-MI121

-
Components

#1: Protein
Serine/threonine protein kinase


Mass: 22241.195 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / Gene: PF3D7_0925900 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8I2Q0
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C3H8O3
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

Experiment
MethodNumber of used crystals
X-RAY DIFFRACTION1
SOLUTION SCATTERING

-
Sample preparation

CrystalDensity Matthews: 3.7 Å3/Da / Density % sol: 66.76 %
Crystal growTemperature: 292 K / Method: vapor diffusion / pH: 7
Details: 0.2 M magnesium chloride, 0.1 M Tris pH7, 2.5 M Sodium Chloride

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.85→56.2 Å / Num. obs: 28936 / % possible obs: 99.75 % / Redundancy: 2 % / Biso Wilson estimate: 54.95 Å2 / CC1/2: 0.546 / Rmerge(I) obs: 0.1985 / Rrim(I) all: 0.2943 / Net I/σ(I): 3.69
Reflection shellResolution: 2.85→2.952 Å / Mean I/σ(I) obs: 1.19 / Num. unique obs: 2889 / CC1/2: 0.41 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MBT

3mbt


Resolution: 2.85→56.2 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.909 / SU B: 16.431 / SU ML: 0.291 / Cross valid method: THROUGHOUT / ESU R: 0.734 / ESU R Free: 0.321 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23647 1428 4.9 %RANDOM
Rwork0.18886 ---
obs0.1912 27535 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.494 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å2-0 Å2-0.04 Å2
2--0.09 Å20 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 2.85→56.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5930 0 27 40 5997
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0136106
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175628
X-RAY DIFFRACTIONr_angle_refined_deg1.5391.6378263
X-RAY DIFFRACTIONr_angle_other_deg1.2081.56913114
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.7755739
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.26524.919307
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.812151091
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2761516
X-RAY DIFFRACTIONr_chiral_restr0.0640.2815
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026721
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021203
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.335.5292968
X-RAY DIFFRACTIONr_mcbond_other4.3135.5292967
X-RAY DIFFRACTIONr_mcangle_it6.8958.2893703
X-RAY DIFFRACTIONr_mcangle_other6.8988.293704
X-RAY DIFFRACTIONr_scbond_it4.6546.0833138
X-RAY DIFFRACTIONr_scbond_other4.6046.0823138
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.4688.934561
X-RAY DIFFRACTIONr_long_range_B_refined11.23463.7066355
X-RAY DIFFRACTIONr_long_range_B_other11.25163.7176355
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.85→2.924 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 110 -
Rwork0.329 2058 -
obs--99.59 %

+
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://pdbjlvh1.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