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- PDB-1fcs: CRYSTAL STRUCTURE OF A DISTAL SITE DOUBLE MUTANT OF SPERM WHALE M... -

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Basic information

Entry
Database: PDB / ID: 1fcs
TitleCRYSTAL STRUCTURE OF A DISTAL SITE DOUBLE MUTANT OF SPERM WHALE MYOGLOBIN AT 1.6 ANGSTROMS RESOLUTION
ComponentsMYOGLOBIN
KeywordsOXYGEN TRANSPORT
Function / homology
Function and homology information


Oxidoreductases; Acting on other nitrogenous compounds as donors / nitrite reductase activity / sarcoplasm / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / removal of superoxide radicals / oxygen carrier activity / peroxidase activity / oxygen binding / heme binding / extracellular exosome / metal ion binding
Similarity search - Function
Myoglobin / Globins / Globin-like / Globin / Globin / Globin domain profile. / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Myoglobin
Similarity search - Component
Biological speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / Resolution: 1.6 Å
AuthorsRizzi, M. / Bolognesi, M. / Coda, A. / Cutruzzola, F. / Travaglini Allocatelli, C. / Brancaccio, A. / Brunori, M.
Citation
Journal: FEBS Lett. / Year: 1993
Title: Crystal structure of a distal site double mutant of sperm whale myoglobin at 1.6 A resolution.
Authors: Rizzi, M. / Bolognesi, M. / Coda, A. / Cutruzzola, F. / Allocatelli, C.T. / Brancaccio, A. / Brunori, M.
#1: Journal: FEBS Lett. / Year: 1991
Title: Control and Recognition of Anionic Ligands in Myoglobin
Authors: Cutruzzola, F. / Allocatelli, C.T. / Ascenzi, P. / Bolognesi, M. / Sligar, S.G. / Brunori, M.
#2: 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.
History
DepositionApr 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 1.3Feb 7, 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.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

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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)18,1914
Polymers17,3821
Non-polymers8093
Water2,162120
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.300, 91.300, 45.860
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6
Atom site foot note1: ARG 45 AND ARG 67 POINT OUT THE DISTAL SITE AND ARE KEPT IN THIS POSITION BY INTERACTIONS WITH A SULFATE ION LOCATED AMONGST THE TWO ON THE PROTEIN SURFACE.

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Components

#1: Protein MYOGLOBIN


Mass: 17382.238 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physeter catodon (sperm whale) / Gene: SYNTHETIC GENE / References: UniProt: P02185
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#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.: 120 / Source method: isolated from a natural source / Formula: H2O
Compound detailsARG 45 AND ARG 67 POINT OUT THE DISTAL SITE AND ARE KEPT IN THIS POSITION BY INTERACTIONS WITH A ...ARG 45 AND ARG 67 POINT OUT THE DISTAL SITE AND ARE KEPT IN THIS POSITION BY INTERACTIONS WITH A SULFATE ION LOCATED AMONGST THE TWO ON THE PROTEIN SURFACE.
Sequence detailsSEQUENCE ADVISORY NOTICE: DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: ...SEQUENCE ADVISORY NOTICE: DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: MYG_PHYCA SWISS-PROT RESIDUE PDB SEQRES NAME NUMBER NAME CHAIN SEQ/INSERT CODE NONE MET 0 ASP 122 ASN 122

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.17 Å3/Da / Density % sol: 61.24 %
Crystal grow
*PLUS
Method: other / Details: NMR

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 15 Å / Num. obs: 15938 / % possible obs: 53 % / Num. measured all: 62341 / Rmerge(I) obs: 0.052

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Processing

SoftwareName: TNT / Classification: refinement
RefinementResolution: 1.6→15 Å /
RfactorNum. reflection
obs0.197 15938
Refinement stepCycle: LAST / Resolution: 1.6→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1226 0 53 120 1399
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.016
X-RAY DIFFRACTIONt_angle_deg2.06
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: 1.6 Å / Lowest resolution: 15 Å / Num. reflection obs: 15938 / Rfactor obs: 0.197
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_d
X-RAY DIFFRACTIONt_angle_deg
X-RAY DIFFRACTIONt_plane_restr0.016

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