[English] 日本語
Yorodumi
- PDB-4x0j: Trypanosoma brucei haptoglobin-haemoglobin receptor -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4x0j
TitleTrypanosoma brucei haptoglobin-haemoglobin receptor
ComponentsHaptoglobin-hemoglobin receptor
KeywordsPROTEIN TRANSPORT / Trypanosoma brucei / Haptoglobin-haemoglobin receptor
Function / homologyFerritin - #80 / Ferritin / Up-down Bundle / Mainly Alpha / Haptoglobin-hemoglobin receptor
Function and homology information
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsLane-Serff, H. / MacGregor, P. / Lowe, E.D. / Carrington, M. / Higgins, M.K.
CitationJournal: Elife / Year: 2014
Title: Structural basis for ligand and innate immunity factor uptake by the trypanosome haptoglobin-haemoglobin receptor.
Authors: Lane-Serff, H. / MacGregor, P. / Lowe, E.D. / Carrington, M. / Higgins, M.K.
History
DepositionNov 21, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 21, 2015Group: Database references
Revision 1.2Mar 4, 2015Group: Database references
Revision 1.3Jan 10, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Haptoglobin-hemoglobin receptor
B: Haptoglobin-hemoglobin receptor


Theoretical massNumber of molelcules
Total (without water)57,0042
Polymers57,0042
Non-polymers00
Water4,756264
1
A: Haptoglobin-hemoglobin receptor


Theoretical massNumber of molelcules
Total (without water)28,5021
Polymers28,5021
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Haptoglobin-hemoglobin receptor


Theoretical massNumber of molelcules
Total (without water)28,5021
Polymers28,5021
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)27.900, 47.790, 203.380
Angle α, β, γ (deg.)90.00, 92.79, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 0 / Auth seq-ID: 37 - 296 / Label seq-ID: 3 - 262

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

-
Components

#1: Protein Haptoglobin-hemoglobin receptor


Mass: 28502.127 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Gene: HpHbR / Production host: Escherichia coli (E. coli) / References: UniProt: I7BA99
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 264 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.23 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.15 M KBr, 30 % w/v PEG 2000 MME

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 24, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.85→203.14 Å / Num. obs: 44672 / % possible obs: 97.4 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 10.2
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.64 / % possible all: 96.4

-
Processing

Software
NameVersionClassification
REFMAC5.8.0069refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4X0I

4x0i
PDB Unreleased entry


Resolution: 1.85→203.14 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.932 / SU B: 3.942 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R: 0.153 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23998 2250 5 %RANDOM
Rwork0.19863 ---
obs0.20074 42418 96.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.564 Å2
Baniso -1Baniso -2Baniso -3
1-1.64 Å20 Å2-1.29 Å2
2---0.69 Å20 Å2
3----0.82 Å2
Refinement stepCycle: 1 / Resolution: 1.85→203.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3941 0 0 264 4205
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0193991
X-RAY DIFFRACTIONr_bond_other_d0.0060.023947
X-RAY DIFFRACTIONr_angle_refined_deg1.6581.9435373
X-RAY DIFFRACTIONr_angle_other_deg1.24739084
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1340.2629
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024573
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02845
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_it2.3652.6872094
X-RAY DIFFRACTIONr_mcbond_other2.3612.6852093
X-RAY DIFFRACTIONr_mcangle_it3.1074.0142615
X-RAY DIFFRACTIONr_mcangle_other3.1074.0162616
X-RAY DIFFRACTIONr_scbond_it4.1623.271897
X-RAY DIFFRACTIONr_scbond_other4.1613.2711898
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.224.6532757
X-RAY DIFFRACTIONr_long_range_B_refined6.46428.0093601
X-RAY DIFFRACTIONr_long_range_B_other6.41127.9353514
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 14881 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 157 -
Rwork0.306 3053 -
obs--95.99 %

+
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