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- PDB-6qhj: High-resolution crystal structure of calcium- and sodium-bound mo... -

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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 / axonal growth cone / positive regulation of epithelial to mesenchymal transition / nervous system development / perikaryon / positive regulation of apoptotic process / axon ...atrioventricular valve formation / neuronal signal transduction / cardiac epithelial to mesenchymal transition / regulation of axon extension / axonal growth cone / positive regulation of epithelial to mesenchymal transition / nervous system development / perikaryon / positive regulation of apoptotic process / axon / negative regulation of gene expression / neuronal cell body / synapse / positive regulation of gene expression / endoplasmic reticulum / signal transduction / extracellular space
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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Components

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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

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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

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Details

Has ligand of interestY

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Experimental details

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Experiment

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

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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

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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

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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

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