[English] 日本語
Yorodumi
- PDB-2hlr: Crystal Structure of the Extracellular Domain of the Type II BMP ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2hlr
TitleCrystal Structure of the Extracellular Domain of the Type II BMP Receptor
ComponentsBone morphogenetic protein receptor type-2
KeywordsTRANSFERASE / three-finger toxin / bmp receptor / tgf-beta
Function / homology
Function and homology information


transmembrane receptor protein serine/threonine kinase activity / ATP binding / membrane
Similarity search - Function
Activin types I and II receptor domain / Activin types I and II receptor domain / CD59 / CD59 / Ser/Thr protein kinase, TGFB receptor / Snake toxin-like superfamily / Ribbon / Mainly Beta
Similarity search - Domain/homology
Bone morphogenetic protein type II receptor
Similarity search - Component
Biological speciesOvis aries (sheep)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.2 Å
AuthorsMace, P.D. / Cutfield, J.F. / Cutfield, S.M.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2006
Title: High resolution structures of the bone morphogenetic protein type II receptor in two crystal forms: Implications for ligand binding
Authors: Mace, P.D. / Cutfield, J.F. / Cutfield, S.M.
History
DepositionJul 10, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 28, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Bone morphogenetic protein receptor type-2


Theoretical massNumber of molelcules
Total (without water)11,1461
Polymers11,1461
Non-polymers00
Water1,31573
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.063, 35.063, 121.057
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein Bone morphogenetic protein receptor type-2 / Bone morphogenetic receptor type II / BMPRII


Mass: 11146.431 Da / Num. of mol.: 1 / Fragment: residues 32-131
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ovis aries (sheep) / Gene: BMPRII / Plasmid: pet21a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q91WY9, receptor protein serine/threonine kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 1.67 Å3/Da / Density % sol: 26.28 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1M Na Citrate, 25% PEG2000 MME, 0.8M Sodium Formate, pH 6.0, vapor diffusion, hanging drop, temperature 290K

-
Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 10, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.2→24.29 Å / Num. obs: 23947 / % possible obs: 98.1 % / Redundancy: 29.5 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 15.2
Reflection shellResolution: 1.2→1.232 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.585 / Mean I/σ(I) obs: 13.6 / % possible all: 88.2

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.2→24.29 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.48 / SU ML: 0.031 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.05 / ESU R Free: 0.045 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2291 1254 5.1 %RANDOM
Rwork0.22018 ---
obs0.22061 23343 99.89 %-
all-24597 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.349 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å20 Å2
2---0.09 Å20 Å2
3---0.18 Å2
Refinement stepCycle: LAST / Resolution: 1.2→24.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms533 0 0 73 606
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.022550
X-RAY DIFFRACTIONr_bond_other_d0.0010.02364
X-RAY DIFFRACTIONr_angle_refined_deg1.2141.919747
X-RAY DIFFRACTIONr_angle_other_deg0.7563.023872
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.707565
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.9382526
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.9171584
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.816151
X-RAY DIFFRACTIONr_chiral_restr0.0730.279
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02603
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02112
X-RAY DIFFRACTIONr_nbd_refined0.2110.273
X-RAY DIFFRACTIONr_nbd_other0.1910.2341
X-RAY DIFFRACTIONr_nbtor_refined0.1870.2249
X-RAY DIFFRACTIONr_nbtor_other0.0850.2272
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.252
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2540.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1620.220
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2910.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.441.5435
X-RAY DIFFRACTIONr_mcbond_other0.5521.5141
X-RAY DIFFRACTIONr_mcangle_it1.7422535
X-RAY DIFFRACTIONr_scbond_it2.7883293
X-RAY DIFFRACTIONr_scangle_it2.8514.5212
X-RAY DIFFRACTIONr_rigid_bond_restr4.58531249
X-RAY DIFFRACTIONr_sphericity_free3.801373
X-RAY DIFFRACTIONr_sphericity_bonded3.9733897
LS refinement shellResolution: 1.2→1.232 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 105 -
Rwork0.277 1654 -
obs--99.83 %

+
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