[English] 日本語
Yorodumi
- PDB-6qhj: High-resolution crystal structure of calcium- and sodium-bound mo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6qhj
TitleHigh-resolution crystal structure of calcium- and sodium-bound mouse Olfactomedin-1 beta-propeller domain
ComponentsNoelin
KeywordsSIGNALING PROTEIN / Calcium / Beta-propeller / Secreted / Brain
Function / homology
Function and homology information


atrioventricular valve formation / neuronal signal transduction / cardiac epithelial to mesenchymal transition / regulation of axon extension / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / positive regulation of epithelial to mesenchymal transition / axonal growth cone / nervous system development / perikaryon / positive regulation of apoptotic process ...atrioventricular valve formation / neuronal signal transduction / cardiac epithelial to mesenchymal transition / regulation of axon extension / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / positive regulation of epithelial to mesenchymal transition / axonal growth cone / nervous system development / perikaryon / positive regulation of apoptotic process / negative regulation of gene expression / axon / neuronal cell body / positive regulation of gene expression / synapse / endoplasmic reticulum / signal transduction / :
Similarity search - Function
Noelin domain / Neurogenesis glycoprotein / : / Olfactomedin-like domain / Olfactomedin-like domain / Olfactomedin-like domain profile. / Olfactomedin-like domains / Quinoprotein amine dehydrogenase, beta chain-like / Endoplasmic reticulum targeting sequence.
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsPronker, M.F. / van den Hoek, H.G. / Janssen, B.J.C.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research723.012.002 Netherlands
CitationJournal: BMC Mol Cell Biol / Year: 2019
Title: Design and structural characterisation of olfactomedin-1 variants as tools for functional studies.
Authors: Pronker, M.F. / van den Hoek, H. / Janssen, B.J.C.
History
DepositionJan 16, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2019Provider: repository / Type: Initial release
Revision 2.0Oct 16, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / cell / computing / entity / entity_src_gen / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / pdbx_validate_close_contact / pdbx_validate_rmsd_angle / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / software / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _cell.angle_alpha / _cell.angle_beta ..._cell.angle_alpha / _cell.angle_beta / _cell.angle_gamma / _entity.pdbx_number_of_molecules / _entity_src_gen.host_org_common_name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_close_contact.dist / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_low / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_R_free / _refine.ls_percent_reflns_obs / _refine.overall_SU_ML / _refine.pdbx_ls_cross_valid_method / _refine.pdbx_ls_sigma_F / _refine.pdbx_method_to_determine_struct / _refine.pdbx_overall_phase_error / _refine.pdbx_solvent_shrinkage_radii / _refine.pdbx_solvent_vdw_probe_radii / _refine.pdbx_starting_model / _refine_hist.cycle_id / _refine_hist.d_res_low / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_B_iso_mean_solvent / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_residues_total / _reflns.B_iso_Wilson_estimate / _software.classification / _software.name / _software.version / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Missing anisotropic B-factor / Provider: author / Type: Coordinate replacement
Revision 2.1Nov 20, 2019Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.year
Revision 2.2Nov 27, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 2.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / citation ...chem_comp / citation / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _citation.country / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.4Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Noelin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3149
Polymers30,1821
Non-polymers1,1328
Water5,368298
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1500 Å2
ΔGint-13 kcal/mol
Surface area10750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.794, 79.631, 111.719
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-664-

HOH

21A-684-

HOH

-
Components

-
Protein / Sugars , 2 types, 5 molecules A

#1: Protein Noelin / Neuronal olfactomedin-related ER localized protein / Olfactomedin-1


Mass: 30181.529 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OLFM1, NOE1, NOEL1 / Plasmid: pUPE107.03
Details (production host): Secretion signal and C-terminal His6-tag
Cell line (production host): HEK293 EBNA1 GntI-/- / Organ (production host): Kidney / Production host: Homo sapiens (human) / References: UniProt: Q99784
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 4 types, 302 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 298 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.35 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M Tris pH 8.5 8 % (w/v) PEG 8000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Apr 18, 2016 / Details: CRL
RadiationMonochromator: C(110) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.25→36.76 Å / Num. obs: 72028 / % possible obs: 94.6 % / Redundancy: 5.8 % / Biso Wilson estimate: 11.19 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.037 / Rrim(I) all: 0.092 / Net I/σ(I): 13.7
Reflection shellResolution: 1.25→1.29 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.908 / Mean I/σ(I) obs: 1 / Num. unique obs: 4675 / CC1/2: 0.445 / Rpim(I) all: 0.751 / Rrim(I) all: 1.188 / % possible all: 63.9

-
Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
XDSdata reduction
Aimlessdata scaling
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5AMO

5amo


Resolution: 1.25→33.733 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 14.79
RfactorNum. reflection% reflection
Rfree0.1413 3623 5.03 %
Rwork0.1241 --
obs0.125 72013 94.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 91.76 Å2 / Biso mean: 17.7964 Å2 / Biso min: 6.19 Å2
Refinement stepCycle: final / Resolution: 1.25→33.733 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2038 0 142 299 2479
Biso mean--33.95 33.71 -
Num. residues----252
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012400
X-RAY DIFFRACTIONf_angle_d1.1683308
X-RAY DIFFRACTIONf_chiral_restr0.097350
X-RAY DIFFRACTIONf_plane_restr0.008434
X-RAY DIFFRACTIONf_dihedral_angle_d12.286882
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.25-1.26640.3426880.3081151655
1.2664-1.28380.30161070.2866177866
1.2838-1.30210.26081100.2764206675
1.3021-1.32160.26181090.2676229082
1.3216-1.34220.28781430.2472246589
1.3422-1.36420.25531490.2362256795
1.3642-1.38780.24241320.2253266095
1.3878-1.4130.23171580.2131268499
1.413-1.44020.28251420.2084276699
1.4402-1.46960.18171400.16582759100
1.4696-1.50150.17511520.13592769100
1.5015-1.53650.15451480.1192769100
1.5365-1.57490.14241280.1082760100
1.5749-1.61750.12011350.09832774100
1.6175-1.6650.12421330.09282797100
1.665-1.71880.11471460.09392787100
1.7188-1.78020.14381370.09522780100
1.7802-1.85150.121620.09282772100
1.8515-1.93570.12091510.09212806100
1.9357-2.03780.11091320.09182791100
2.0378-2.16540.10451380.09322808100
2.1654-2.33260.11751490.10152792100
2.3326-2.56730.13081430.1092280699
2.5673-2.93860.12631590.1152826100
2.9386-3.70160.12411520.11332848100
3.7016-33.7330.12331800.13262954100

+
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