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- PDB-5mba: BINDING MODE OF AZIDE TO FERRIC APLYSIA LIMACINA MYOGLOBIN. CRYST... -

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Basic information

Entry
Database: PDB / ID: 5mba
TitleBINDING MODE OF AZIDE TO FERRIC APLYSIA LIMACINA MYOGLOBIN. CRYSTALLOGRAPHIC ANALYSIS AT 1.9 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
AZIDE ION / PROTOPORPHYRIN IX CONTAINING FE / Globin
Similarity search - Component
Biological speciesAplysia limacina (slug sea hare)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsBolognesi, M. / Onesti, S. / Gatti, G. / Coda, A. / Ascenzi, P. / Brunori, M.
Citation
Journal: J.Mol.Recog. / Year: 1991
Title: Binding mode of azide to ferric Aplysia limacina myoglobin. Crystallographic analysis at 1.9 A resolution.
Authors: Mattevi, A. / Gatti, G. / Coda, A. / Rizzi, M. / Ascenzi, P. / Brunori, M. / Bolognesi, M.
#1: 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.
#2: 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.
#3: 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.
#4: 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.
#5: 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.
#6: 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.
#7: 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.
#8: 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
DepositionJan 14, 1991Processing site: BNL
SupersessionJul 15, 1992ID: 2MBA
Revision 1.0Jul 15, 1992Provider: 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 / 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 / _struct_conn.pdbx_leaving_atom_flag / _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

Downloads & links

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Assembly

Deposited unit
A: MYOGLOBIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0083
Polymers15,3491
Non-polymers6592
Water2,270126
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: 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-AZI / AZIDE ION


Mass: 42.020 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: N3
#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.: 126 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsAZIDE ION IS BOUND TO THE HEME IRON AT THE DISTAL SITE AND TRIGGERS A LARGE CONFORMATIONAL CHANGE ...AZIDE ION IS BOUND TO THE HEME IRON AT THE DISTAL SITE AND TRIGGERS A LARGE CONFORMATIONAL CHANGE IN THE SIDE CHAIN OF RESIDUE ARG 66. A HYDROGEN BOND OCCURS BETWEEN AZIDE ATOM N1 AND NE1 ARG 66. THIS CONFORMATIONAL CHANGE AT RESIDUE ARG 66 BECAME EVIDENT ONLY IN THE LATER STAGES OF REFINEMENT. THE SIDE CHAIN OF ARG 66 IS NOT FULLY OCCUPIED BEYOND THE CB ATOM.

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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 / Details: took Bolognesi et al., from original paper
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.8 Mammonium sulfate1drop
23.2 Mammonium sulfate1reservior

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Data collection

Reflection
*PLUS
Highest resolution: 1.9 Å

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Processing

SoftwareName: TNT / Classification: refinement
RefinementRfactor obs: 0.139 / Highest resolution: 1.9 Å
Refinement stepCycle: LAST / Highest resolution: 1.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1086 0 46 126 1258
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.015
X-RAY DIFFRACTIONt_angle_deg2.35
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
Lowest resolution: 11 Å / Num. reflection obs: 7487 / Rfactor obs: 0.139
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: t_angle_d / Dev ideal: 2.35

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