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- PDB-3mba: APLYSIA LIMACINA MYOGLOBIN. CRYSTALLOGRAPHIC ANALYSIS AT 1.6 ANGS... -

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Basic information

Entry
Database: PDB / ID: 3mba
TitleAPLYSIA LIMACINA MYOGLOBIN. CRYSTALLOGRAPHIC ANALYSIS AT 1.6 ANGSTROMS RESOLUTION
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-like / Globin / Globin / Globin domain profile. / Globin-like superfamily ...Globin, lamprey/hagfish type / Erythrocruorin / Myoglobin-like, M family globin domain / Globin/Protoglobin / Globins / Globin-like / Globin / Globin / Globin domain profile. / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
FLUORIDE ION / PROTOPORPHYRIN IX CONTAINING FE / Globin
Similarity search - Component
Biological speciesAplysia limacina (slug sea hare)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsBolognesi, M. / Onesti, S. / Gatti, G. / Coda, A. / Ascenzi, P. / Brunori, M.
Citation
Journal: J.Mol.Biol. / Year: 1989
Title: Aplysia limacina myoglobin. Crystallographic analysis at 1.6 A resolution.
Authors: Bolognesi, M. / Onesti, S. / Gatti, G. / Coda, A. / Ascenzi, P. / Brunori, M.
#1: Journal: To be Published
Title: Aplysia Limacina Myoglobin. Molecular Bases for Ligand Binding and Reversible Unfolding
Authors: Bolognesi, M. / Gatti, G. / Guanziroli, M.G. / Mattevi, A. / Onesti, S. / Coda, A. / Ascenzi, P. / Brunori, M.
#2: Journal: J.Mol.Biol. / Year: 1985
Title: Crystal Structure of Ferric Aplysia Limacina Myoglobin at 2.0 Angstroms Resolution
Authors: Bolognesi, M. / Coda, A. / Gatti, G. / Ascenzi, P. / Brunori, M.
#3: 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.
#4: Journal: Acta Crystallogr.,Sect.A (Supplement) / Year: 1978
Title: The Structure of Aplysia Limacina Myoglobin at 3.6 Angstroms Resolution
Authors: Bolognesi, M. / Cannillo, E. / Oberti, R. / Rossi, G. / Ungaretti, L.
#5: Journal: Acta Crystallogr.,Sect.B / Year: 1978
Title: The Crystal Structure of met-Myoglobin from Aplysia Limacina at 5 Angstroms Resolution
Authors: Ungaretti, L. / Bolognesi, M. / Cannillo, E. / Oberti, R. / Rossi, G.
#6: Journal: J.Mol.Biol. / Year: 1975
Title: Crystallization and Preliminary X-Ray Diffraction Studies on met-Myoglobin from Aplysia Limacina
Authors: Blundell, T.L. / Brunori, M. / Curti, B. / Bolognesi, M. / Coda, A. / Fumagalli, M. / Ungaretti, L.
#7: Journal: Int.J.Pept.Protein Res. / Year: 1973
Title: The Amino Acid Sequence of Myoglobin from the Mollusc Aplysia Limacina
Authors: Tentori, L. / Vivaldi, G. / Carta, S. / Marinucci, M. / Massa, A. / Antonini, E. / Brunori, M.
History
DepositionFeb 22, 1989Processing site: BNL
Revision 1.0Jan 15, 1990Provider: repository / Type: Initial release
Revision 1.1Mar 25, 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_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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 23, 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)15,9853
Polymers15,3491
Non-polymers6352
Water3,621201
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
Atom site foot note1: ARG 66 IS SALT-LINKED TO THE FLUORIDE ION.

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Components

#1: Protein MYOGLOBIN


Mass: 15349.438 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-F / FLUORIDE ION


Mass: 18.998 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: F
#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.: 201 / Source method: isolated from a natural source / Formula: H2O
Compound detailsARG 66 IS SALT-LINKED TO THE FLUORIDE ION.
Has protein modificationY
Nonpolymer detailsFLUORIDE IS COORDINATED TO THE THE HEME IRON AT THE DISTAL SITE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.98 Å3/Da / Density % sol: 37.94 %
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
130 mg/mlprotein1drop
22.8 Mammonium sulfate1drop
30.05 Mphosphate1drop
43.2 Mammonium sulphate1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 5 Å / Num. obs: 14740 / % possible obs: 92 %

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Processing

SoftwareName: TNT / Classification: refinement
RefinementRfactor obs: 0.142 / Highest resolution: 2 Å
Refinement stepCycle: LAST / Highest resolution: 2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1086 0 44 201 1331
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.013
X-RAY DIFFRACTIONt_angle_deg2.53
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
Refinement
*PLUS
Highest resolution: 2 Å / Rfactor obs: 0.142
Solvent computation
*PLUS
Displacement parameters
*PLUS

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