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- PDB-1omd: STRUCTURE OF ONCOMODULIN REFINED AT 1.85 ANGSTROMS RESOLUTION. AN... -

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Basic information

Entry
Database: PDB / ID: 1omd
TitleSTRUCTURE OF ONCOMODULIN REFINED AT 1.85 ANGSTROMS RESOLUTION. AN EXAMPLE OF EXTENSIVE MOLECULAR AGGREGATION VIA CA2+
ComponentsONCOMODULIN
KeywordsCALCIUM BINDING PROTEIN
Function / homology
Function and homology information


cuticular plate / stereocilium / ion binding / supramolecular fiber / cochlea development / response to wounding / vesicle / calcium ion binding / protein-containing complex binding / protein homodimerization activity ...cuticular plate / stereocilium / ion binding / supramolecular fiber / cochlea development / response to wounding / vesicle / calcium ion binding / protein-containing complex binding / protein homodimerization activity / protein-containing complex / extracellular space / identical protein binding / cytoplasm
Similarity search - Function
Parvalbumin / EF hand / EF-hand / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain ...Parvalbumin / EF hand / EF-hand / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / Resolution: 1.85 Å
AuthorsAhmed, F.R. / Przybylska, M. / Rose, D.R. / Birnbaum, G.I. / Pippy, M.E. / Macmanus, J.P.
Citation
Journal: J.Mol.Biol. / Year: 1990
Title: Structure of oncomodulin refined at 1.85 A resolution. An example of extensive molecular aggregation via Ca2+.
Authors: Ahmed, F.R. / Przybylska, M. / Rose, D.R. / Birnbaum, G.I. / Pippy, M.E. / MacManus, J.P.
#1: Journal: J.Mol.Biol. / Year: 1988
Title: Crystallization and Preliminary Crystallographic Data for Oncomodulin
Authors: Przybylska, M. / Ahmed, F.R. / Birnbaum, G.I. / Rose, D.R.
#2: Journal: J.Biol.Chem. / Year: 1987
Title: A Complete Complementary DNA for the Oncodevelopmental Calcium-Binding Protein, Oncomodulin
Authors: Gillen, M.F. / Banville, D. / Rutledge, R.G. / Narang, S. / Seligy, V.L. / Whitfield, J.F. / Macmanus, J.P.
#3: Journal: Eur.J.Biochem. / Year: 1983
Title: The Complete Amino Acid Sequence of Oncomodulin-A Parvalbumin-Like Calcium-Binding Protein from Morris Hepatoma 5123Tc
Authors: Macmanus, J.P. / Watson, D.C. / Yaguchi, M.
History
DepositionApr 19, 1990Processing site: BNL
Revision 1.0Jul 15, 1991Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ONCOMODULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1874
Polymers12,0671
Non-polymers1203
Water1,56787
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.590, 64.280, 33.070
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ONCOMODULIN


Mass: 12067.064 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / References: UniProt: P02631
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsCALCIUM 135 IS INTERMOLECULAR. IT IS BONDED DIRECTLY TO THREE DIFFERENT ONCOMODULIN MOLECULES AND ...CALCIUM 135 IS INTERMOLECULAR. IT IS BONDED DIRECTLY TO THREE DIFFERENT ONCOMODULIN MOLECULES AND INDIRECTLY (THROUGH TWO HYDROGEN BONDS) TO A FOURTH, TO FORM ZIGZAG SHEETS OF ONCOMODULIN NORMAL TO THE B AXIS.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.74 Å3/Da / Density % sol: 29.45 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 5.2 / Method: vapor diffusion, hanging drop / Details: took Przybylska et al., from original paper
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11.4 %protein1drop
25 mMcacodylate1drop
310 mM1dropCaCl2
40.5 mMdithiothreitol1drop
511 %PEG60001drop
633 %(w/v)PEG60001reservoir
710 mMcacodylate1reservoir
81 mMdithiothreitol1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.85 Å / Num. obs: 5965 / Rmerge(I) obs: 3

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.85→6 Å /
RfactorNum. reflection
obs0.166 5770
Refinement stepCycle: LAST / Resolution: 1.85→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms840 0 3 87 930
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0280.03
X-RAY DIFFRACTIONp_angle_d0.0450.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0440.04
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.32.8
X-RAY DIFFRACTIONp_mcangle_it3.25.6
X-RAY DIFFRACTIONp_scbond_it12.312.6
X-RAY DIFFRACTIONp_scangle_it14.312.6
X-RAY DIFFRACTIONp_plane_restr0.0180.025
X-RAY DIFFRACTIONp_chiral_restr0.1790.125
X-RAY DIFFRACTIONp_singtor_nbd0.1880.5
X-RAY DIFFRACTIONp_multtor_nbd0.3090.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2340.5
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor3.34
X-RAY DIFFRACTIONp_staggered_tor18.215
X-RAY DIFFRACTIONp_orthonormal_tor27.220
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.166
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_dihedral_angle_d0.0440.04
X-RAY DIFFRACTIONp_planar_d

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