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- PDB-2mye: HIGH RESOLUTION X-RAY STRUCTURES OF MYOGLOBIN-AND HEMOGLOBIN-ALKY... -

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Basic information

Entry
Database: PDB / ID: 2mye
TitleHIGH RESOLUTION X-RAY STRUCTURES OF MYOGLOBIN-AND HEMOGLOBIN-ALKYL ISOCYANIDE COMPLEXES
ComponentsMYOGLOBIN (ETHYL ISOCYANIDE)
KeywordsOXYGEN STORAGE
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 domain profile. / Globin-like / Globin / Globin / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ETHYL ISOCYANIDE / PROTOPORPHYRIN IX CONTAINING FE / Myoglobin
Similarity search - Component
Biological speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / Resolution: 1.68 Å
AuthorsJohnson, K.A. / Olson, J.S. / Phillips Jr., G.N.
Citation
Journal: Thesis / Year: 1993
Title: High Resolution X-Ray Structures of Myoglobin-and Hemoglobin-Alkyl Isocyanide Complexes
Authors: Johnson, K.A.
#1: Journal: J.Mol.Biol. / Year: 1989
Title: Structure of Myoglobin-Ethyl Isocyanide: Histidine as a Swinging Door for Ligand Entry
Authors: Johnson, K.A. / Olson, J.S. / Phillips Jr., G.N.
History
DepositionAug 4, 1993Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 21, 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_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_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

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Assembly

Deposited unit
A: MYOGLOBIN (ETHYL ISOCYANIDE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0044
Polymers17,2351
Non-polymers7693
Water3,333185
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.640, 30.950, 34.950
Angle α, β, γ (deg.)90.00, 106.08, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein MYOGLOBIN (ETHYL ISOCYANIDE)


Mass: 17234.951 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physeter catodon (sperm whale) / References: UniProt: P02185
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / 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: Chemical ChemComp-ENC / ETHYL ISOCYANIDE


Mass: 56.086 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H6N
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 1.95 Å3/Da / Density % sol: 36.88 %
Crystal growDetails: THE PH IN THIS CRYSTAL IS WEAKLY BUFFERED (10 MM PHOSPHATE) AND THE STRUCTURE INDICATES THAT THE PH MAY HAVE FALLEN TO PH 6 OR BELOW. THE RESIDUE HIS 64 MAY BE DOUBLY PROTONATED. COMPARE ...Details: THE PH IN THIS CRYSTAL IS WEAKLY BUFFERED (10 MM PHOSPHATE) AND THE STRUCTURE INDICATES THAT THE PH MAY HAVE FALLEN TO PH 6 OR BELOW. THE RESIDUE HIS 64 MAY BE DOUBLY PROTONATED. COMPARE THIS STRUCTURE WITH THE WELL-BUFFERED (100 MM PHOSPHATE) PH 7.0 MYOGLOBIN-ETHYL ISOCYANIDE STRUCTURE (PROTEIN DATA BANK ENTRY 2MYB).

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
RefinementResolution: 1.68→5 Å / Rfactor Rwork: 0.172 / Rfactor obs: 0.172 / σ(F): 0
Details: WATERS WERE RETAINED FROM THE STARTING STRUCTURE OF OXYMYOGLOBIN (PROTEIN DATA BANK ENTRY 1MBO). ADDITIONAL WATERS WERE ADDED IF THEY LAY IN 3.5 - 4.O SIGMA PEAKS IN FO-FC ELECTRON DENSITY ...Details: WATERS WERE RETAINED FROM THE STARTING STRUCTURE OF OXYMYOGLOBIN (PROTEIN DATA BANK ENTRY 1MBO). ADDITIONAL WATERS WERE ADDED IF THEY LAY IN 3.5 - 4.O SIGMA PEAKS IN FO-FC ELECTRON DENSITY MAPS AND 1 SIGMA PEAKS IN 2FO-FC MAPS. CONCURRENTLY, A WATER WOULD BE DELETED IF ITS OCCUPANCY (Q) AND TEMPERATURE FACTOR (B) COMBINED TO MAKE THE VALUE Q*EXP(-B/36)*100% FALL BELOW 10%. A PEAK NUMBER OF 341 WATERS WAS REACHED. THIS WAS REDUCED TO 185 WATERS OVER THE LAST FEW REFINEMENT CYCLES BY DELETING WATERS WHICH FELL BELOW A 20% THRESHOLD.
Refinement stepCycle: LAST / Resolution: 1.68→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1217 0 52 185 1454
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.02
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.751
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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