[English] 日本語
Yorodumi
- PDB-4jle: Structure of the P. falciparum PFI1780w PHIST domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4jle
TitleStructure of the P. falciparum PFI1780w PHIST domain
ComponentsPHIST
KeywordsPROTEIN BINDING / 3-helix bundle / Protein interaction module / PfEMP1 ATS domain / Human P. falciparum-infected erythrocytes
Function / homology
Function and homology information


Maurer's cleft / host cell cytosol / membrane => GO:0016020 / host cell plasma membrane
Similarity search - Function
Plasmodium RESA, N-terminal helical domain / Exported protein, PHISTa/b/c, conserved domain, Plasmodium / Plasmodium RESA, N-terminal / Plasmodium RESA N-terminal / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Helix non-globular / Special
Similarity search - Domain/homology
ACETATE ION / PRESAN domain-containing protein
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.35 Å
AuthorsSlater, L. / Vakonakis, I.
CitationJournal: Faseb J. / Year: 2014
Title: A Plasmodium falciparum PHIST protein binds the virulence factor PfEMP1 and comigrates to knobs on the host cell surface.
Authors: Oberli, A. / Slater, L.M. / Cutts, E. / Brand, F. / Mundwiler-Pachlatko, E. / Rusch, S. / Masik, M.F. / Erat, M.C. / Beck, H.P. / Vakonakis, I.
History
DepositionMar 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 16, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references
Revision 1.2Mar 11, 2015Group: Structure summary
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PHIST
B: PHIST
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3099
Polymers41,0372
Non-polymers2727
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11380 Å2
ΔGint-161 kcal/mol
Surface area19370 Å2
MethodPISA
2
B: PHIST
hetero molecules

B: PHIST
hetero molecules

A: PHIST
hetero molecules

A: PHIST
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,61818
Polymers82,0754
Non-polymers54414
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_675x-y+1,-y+2,-z+2/31
crystal symmetry operation3_564-x+y,-x+1,z-1/31
crystal symmetry operation4_566y,x+1,-z+11
Buried area8310 Å2
ΔGint-146 kcal/mol
Surface area53190 Å2
MethodPISA
3
A: PHIST
B: PHIST
hetero molecules

A: PHIST
B: PHIST
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,61818
Polymers82,0754
Non-polymers54414
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_675x-y+1,-y+2,-z+2/31
Buried area26810 Å2
ΔGint-343 kcal/mol
Surface area34690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.030, 71.030, 146.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsThe asymmetric unit contains one helix-swapped protein dimer, however in solution under physiological conditions the protein is a monomer

-
Components

#1: Protein PHIST


Mass: 20518.676 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: P. falciparum 3D7 / Gene: PFI1780w / Plasmid: PGEX-6P-2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8I2F2
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 2.0M Sodium Chloride 0.1M Sodium Acetate 22.5% Glycerol, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 10, 2011
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.35→146.4 Å / Num. all: 18438 / Num. obs: 18438 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 53.38 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 11.8
Reflection shellResolution: 2.35→2.48 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.494 / Mean I/σ(I) obs: 2.4 / Num. unique all: 2646 / Rsym value: 0.494 / % possible all: 100

-
Processing

SoftwareName: BUSTER / Version: 2.10.0 / Classification: refinement
RefinementMethod to determine structure: SAD / Resolution: 2.35→56.71 Å / Cor.coef. Fo:Fc: 0.9337 / Cor.coef. Fo:Fc free: 0.8976 / SU R Cruickshank DPI: 0.295
Isotropic thermal model: Isotropic thermal model with 1 TLS group per chain
Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2553 947 5.14 %RANDOM
Rwork0.2068 ---
all0.2092 18437 --
obs0.2092 18437 99.82 %-
Displacement parametersBiso mean: 66.53 Å2
Baniso -1Baniso -2Baniso -3
1--7.5734 Å20 Å20 Å2
2---7.5734 Å20 Å2
3---15.1469 Å2
Refine analyzeLuzzati coordinate error obs: 0.369 Å
Refinement stepCycle: LAST / Resolution: 2.35→56.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2678 0 10 47 2735
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012756HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.963664HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1371SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes84HARMONIC2
X-RAY DIFFRACTIONt_gen_planes380HARMONIC5
X-RAY DIFFRACTIONt_it2756HARMONIC20
X-RAY DIFFRACTIONt_omega_torsion2.5
X-RAY DIFFRACTIONt_other_torsion3.4
X-RAY DIFFRACTIONt_chiral_improper_torsion329SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact3261SEMIHARMONIC4
LS refinement shellResolution: 2.35→2.49 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2579 137 4.68 %
Rwork0.2285 2790 -
all0.23 2927 -
obs-2927 99.82 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4129-0.501-0.06350.66350.45161.62840.01160.00110.06610.05030.1695-0.1481-0.19280.1944-0.1811-0.2315-0.03750.0859-0.4673-0.0129-0.4453.205757.545767.1634
20.1177-0.15770.36010.19310.02751.83350.24180.05540.0628-0.02260.00720.03550.036-0.2024-0.249-0.46540.00610.0287-0.59490.0339-0.6492-10.675844.999352.4065
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|19 - A|167 }A19 - 167
2X-RAY DIFFRACTION2{ B|6 - B|164 }B6 - 164

+
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