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- PDB-1rro: REFINEMENT OF RECOMBINANT ONCOMODULIN AT 1.30 ANGSTROMS RESOLUTION -

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Basic information

Entry
Database: PDB / ID: 1rro
TitleREFINEMENT OF RECOMBINANT ONCOMODULIN AT 1.30 ANGSTROMS RESOLUTION
ComponentsRAT ONCOMODULIN
KeywordsCALCIUM-BINDING PROTEIN
Function / homology
Function and homology information


cuticular plate / stereocilium / supramolecular fiber / cochlea development / response to wounding / vesicle / calcium ion binding / protein-containing complex binding / protein homodimerization activity / protein-containing complex ...cuticular plate / stereocilium / 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 rattus (black rat)
MethodX-RAY DIFFRACTION / Resolution: 1.3 Å
AuthorsAhmed, F.R. / Rose, D.R. / Evans, S.V. / Pippy, M.E. / To, R.
Citation
Journal: J.Mol.Biol. / Year: 1993
Title: Refinement of recombinant oncomodulin at 1.30 A resolution.
Authors: Ahmed, F.R. / Rose, D.R. / Evans, S.V. / Pippy, M.E. / To, R.
#1: Journal: J.Mol.Biol. / Year: 1990
Title: Structure of Oncomodulin Refined at 1.85 Angstroms 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.
#2: 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.
#3: Journal: Cancer Res. / Year: 1979
Title: Occurrence of a Low-Molecular-Weight Calcium-Binding Protein in Neoplastic Liver
Authors: Macmanus, J.P.
#4: Journal: Biochim.Biophys.Acta / Year: 1980
Title: The Purification of a Unique Calcium-Binding Protein from Morris Hepatoma 5123 Tc
Authors: Macmanus, J.P.
History
DepositionAug 27, 1992Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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

Downloads & links

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Assembly

Deposited unit
A: RAT ONCOMODULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,2275
Polymers12,0671
Non-polymers1604
Water1,856103
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.700, 65.120, 32.940
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: RESIDUES SER 7, GLU 25, MET 38, SER 41, GLN 42, ARG 48, ASP 59, SER 84, ASP 100 AND GLN 103 ARE DISORDERED.
2: RESIDUE LYS 64 IS POORLY DEFINED.

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Components

#1: Protein RAT ONCOMODULIN


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


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.76 Å3/Da / Density % sol: 30.28 %
Crystal grow
*PLUS
pH: 5.2 / Method: vapor diffusion, hanging drop
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: 1.24 Å / Lowest resolution: 9999 Å / Num. obs: 22446 / Num. measured all: 115881 / Rmerge(I) obs: 0.051

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.3→10 Å
Details: RESIDUES SER 7, GLU 25, MET 38, SER 41, GLN 42, ARG 48, ASP 59, SER 84, ASP 100 AND GLN 103 ARE DISORDERED. RESIDUE LYS 64 IS POORLY DEFINED.
RfactorNum. reflection
obs0.176 20186
Refinement stepCycle: LAST / Resolution: 1.3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms846 0 4 103 953
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.024
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 1.3 Å / Lowest resolution: 10 Å / Num. reflection obs: 20186 / Rfactor obs: 0.176
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONp_bond_d0.025
X-RAY DIFFRACTIONp_angle_d0.040.038
X-RAY DIFFRACTIONp_dihedral_angle_d0.0250.041
X-RAY DIFFRACTIONp_plane_restr0.0250.018
X-RAY DIFFRACTIONp_chiral_restr0.1250.125
X-RAY DIFFRACTIONp_mcbond_it21.3
X-RAY DIFFRACTIONp_scbond_it2.53.2
X-RAY DIFFRACTIONp_mcangle_it2.51.9
X-RAY DIFFRACTIONp_scangle_it3.54.7

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