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- PDB-2fam: X-RAY CRYSTAL STRUCTURE OF FERRIC APLYSIA LIMACINA MYOGLOBIN IN D... -

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Basic information

Entry
Database: PDB / ID: 2fam
TitleX-RAY CRYSTAL STRUCTURE OF FERRIC APLYSIA LIMACINA MYOGLOBIN IN DIFFERENT LIGANDED STATES
ComponentsMYOGLOBIN
KeywordsOXYGEN STORAGE
Function / homology
Function and homology information


hemoglobin complex / oxygen carrier activity / oxygen binding / oxidoreductase activity / iron ion binding / heme binding / extracellular region
Similarity search - Function
Globin, lamprey/hagfish type / Erythrocruorin / Myoglobin-like, M family globin domain / Globin/Protoglobin / Globins / Globin domain profile. / Globin-like / Globin / Globin / Globin-like superfamily ...Globin, lamprey/hagfish type / Erythrocruorin / Myoglobin-like, M family globin domain / Globin/Protoglobin / Globins / Globin domain profile. / Globin-like / Globin / Globin / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / THIOCYANATE ION / Globin
Similarity search - Component
Biological speciesAplysia limacina (slug sea hare)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsConti, E. / Moser, C. / Rizzi, M. / Mattevi, A. / Lionetti, C. / Coda, A. / Ascenzi, P. / Brunori, M. / Bolognesi, M.
Citation
Journal: J.Mol.Biol. / Year: 1993
Title: X-ray crystal structure of ferric Aplysia limacina myoglobin in different liganded states.
Authors: Conti, E. / Moser, C. / Rizzi, M. / Mattevi, A. / Lionetti, C. / Coda, A. / Ascenzi, P. / Brunori, M. / Bolognesi, M.
#1: Journal: J.Mol.Biol. / Year: 1991
Title: X-Ray Crystal Structure of the Ferric Sperm Whale Myoglobin: Imidazole Complex at 2.0 Angstroms Resolution
Authors: Lionetti, C. / Guanziroli, M.G. / Frigerio, F. / Ascenzi, P. / Bolognesi, M.
#2: Journal: Structure and Function of Invertebrate Oxygen Carriers
Year: 1991
Title: Aplysia Limacina Myoglobin: Molecular Bases for Ligand Binding
Authors: Bolognesi, M. / Frigerio, F. / Lionetti, C. / Rizzi, M. / Ascenzi, P. / Brunori, M.
#3: Journal: J.Mol.Recog. / Year: 1991
Title: Binding Mode of Azide to Ferric Aplysia Limacina Myoglobin: Crystallographic Analysis at 1.9 Angstroms Resolution
Authors: Mattevi, A. / Gatti, G. / Coda, A. / Rizzi, M. / Ascenzi, P. / Brunori, M. / Bolognesi, M.
#4: Journal: J.Mol.Biol. / Year: 1990
Title: X-Ray Crystal Structure of the Fluoride Derivative of Aplysia Limacina Myoglobin at 2.0 Angstroms Resolution: Stabilization of the Fluoride by Hydrogen Bonding to Arg66 (E10)
Authors: Bolognesi, M. / Coda, A. / Frigerio, F. / Gatti, G. / Ascenzi, P. / Brunori, M.
#5: Journal: J.Mol.Biol. / Year: 1989
Title: Aplysia Limacina Myoglobin. Crystallographic Analysis at 1.6 Angstroms Resolution
Authors: Bolognesi, M. / Onesti, S. / Gatti, G. / Coda, A. / Ascenzi, P. / Brunori, M.
#6: Journal: J.Mol.Biol. / Year: 1982
Title: Reactivity of Ferric Aplysia and Sperm Whale Myoglobins Towards Imidazole. X-Ray and Binding Study
Authors: Bolognesi, M. / Cannillo, E. / Ascenzi, P. / Giacometti, G.M. / Merli, A. / Brunori, M.
History
DepositionJul 20, 1993Processing 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 1.3Jun 5, 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_conn_type / struct_ref_seq_dif / 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.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.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.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_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MYOGLOBIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0823
Polymers15,4081
Non-polymers6752
Water1,67593
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.980, 70.700, 32.500
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 MYOGLOBIN


Mass: 15407.539 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aplysia limacina (slug sea hare) / References: UniProt: P02210
#2: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CNS
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsBASED ON ANALYSIS OF THE ELECTRON DENSITY MAPS, SEVERAL AMINO ACIDS HAVE BEEN REASSIGNED IN THIS ...BASED ON ANALYSIS OF THE ELECTRON DENSITY MAPS, SEVERAL AMINO ACIDS HAVE BEEN REASSIGNED IN THIS ENTRY COMPARED TO THE SEQUENCE PUBLISHED IN 1973. THE CHANGES ARE AS FOLLOWS: RESIDUE 1973 ENTRY 26 ALA LEU LEU ELECTRON DENSITY SEEN AFTER SEVERAL OMIT MAPS 77 ASP ASN MORE APPROPRIATE AS ASN OWING TO THE APOLAR ENVIRONMENT (MET 84) 129 EXTRA ALA CONFIRMED BY SEVERAL OMIT MAPS C-TERMINAL LYS ALA ELECTRON DENSITY ALWAYS MISSING AFTER CB - MAY BE LYS

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.97 Å3/Da / Density % sol: 37.71 %
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion
Components of the solutions
*PLUS
Common name: ammonium sulfate

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Processing

SoftwareName: TNT / Classification: refinement
RefinementRfactor obs: 0.161 / Highest resolution: 2 Å
Refinement stepCycle: LAST / Highest resolution: 2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1086 0 46 93 1225
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.018
X-RAY DIFFRACTIONt_angle_deg2.9
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 10 Å / Rfactor obs: 0.161
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 25.7 Å2
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONt_angle_d
X-RAY DIFFRACTIONt_angle_deg

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