[English] 日本語
Yorodumi
- PDB-5hrj: Crystal structure of the scavenger receptor cysteine-rich domain ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5hrj
TitleCrystal structure of the scavenger receptor cysteine-rich domain 5 (SRCR5) from porcine CD163
ComponentsScavenger receptor cysteine-rich type 1 protein M130
KeywordsENDOCYTOSIS / CD163 / SRCR / PRRSV / BALBES NMR
Function / homology
Function and homology information


acute-phase response / virus receptor activity / external side of plasma membrane / extracellular region
Similarity search - Function
Mac-2 Binding Protein / SRCR-like domain / SRCR domain signature. / Scavenger receptor cysteine-rich domain / SRCR domain profile. / SRCR-like domain superfamily / Scavenger receptor Cys-rich / SRCR domain / Roll / Alpha Beta
Similarity search - Domain/homology
Scavenger receptor cysteine-rich type 1 protein M130
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMa, H. / Jiang, L. / Qiao, S. / Zhang, G. / Li, R.
CitationJournal: To Be Published
Title: Crystal structure of the scavenger receptor cysteine-rich domain 5 (SRCR5) from porcine CD163
Authors: Ma, H. / Jiang, L. / Qiao, S. / Zhang, G. / Li, R.
History
DepositionJan 23, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 19, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.2Nov 8, 2023Group: 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
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Scavenger receptor cysteine-rich type 1 protein M130


Theoretical massNumber of molelcules
Total (without water)11,6371
Polymers11,6371
Non-polymers00
Water1,29772
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.720, 73.010, 87.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-636-

HOH

21A-663-

HOH

-
Components

#1: Protein Scavenger receptor cysteine-rich type 1 protein M130


Mass: 11636.828 Da / Num. of mol.: 1
Fragment: scavenger receptor cysteine-rich domain 5 (SRCR5), UNP residues 477-577
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: CD163, M130 / Plasmid: pPICZ-alpha-A / Production host: Pichia pastoris (fungus) / Strain (production host): X-33 / References: UniProt: Q2VL90
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.96 Å3/Da / Density % sol: 37.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 25% (w/v) PEG 4000, 200mM (NH4)2SO4, 100mM sodium acetate, pH 4.6

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→29.1 Å / Num. obs: 8953 / % possible obs: 97.7 % / Redundancy: 13.1 % / Net I/σ(I): 29.1

-
Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-3000data collection
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BY2

1by2


Resolution: 1.8→29.1 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.873 / SU B: 2.888 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.156 / ESU R Free: 0.145 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25341 443 5 %RANDOM
Rwork0.213 ---
obs0.21495 8487 97.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 16.37 Å2
Baniso -1Baniso -2Baniso -3
1--0.57 Å20 Å2-0 Å2
2---0.95 Å20 Å2
3---1.52 Å2
Refinement stepCycle: 1 / Resolution: 1.8→29.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms737 0 0 72 809
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.019757
X-RAY DIFFRACTIONr_bond_other_d0.0030.02669
X-RAY DIFFRACTIONr_angle_refined_deg1.3331.9331030
X-RAY DIFFRACTIONr_angle_other_deg0.92531548
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5795100
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.72223.93933
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.78215109
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.037155
X-RAY DIFFRACTIONr_chiral_restr0.080.2112
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021880
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02171
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_it1.081.494403
X-RAY DIFFRACTIONr_mcbond_other1.0751.492402
X-RAY DIFFRACTIONr_mcangle_it1.8762.236502
X-RAY DIFFRACTIONr_mcangle_other1.8762.238503
X-RAY DIFFRACTIONr_scbond_it1.1051.637354
X-RAY DIFFRACTIONr_scbond_other1.1041.637354
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.8142.415529
X-RAY DIFFRACTIONr_long_range_B_refined5.11412.915864
X-RAY DIFFRACTIONr_long_range_B_other4.34912.185831
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.211 34 -
Rwork0.194 597 -
obs--95.61 %

+
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