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- PDB-2cmm: STRUCTURAL ANALYSIS OF THE MYOGLOBIN RECONSTITUTED WITH IRON PORPHINE -

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Basic information

Entry
Database: PDB / ID: 2cmm
TitleSTRUCTURAL ANALYSIS OF THE MYOGLOBIN RECONSTITUTED WITH IRON PORPHINE
ComponentsMYOGLOBIN
KeywordsOXYGEN TRANSPORT
Function / homology
Function and homology information


nitrite reductase activity / Oxidoreductases; Acting on other nitrogenous compounds as donors / sarcoplasm / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / removal of superoxide radicals / oxygen carrier activity / oxygen binding / peroxidase activity / 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
CYANIDE ION / PORPHYRIN FE(III) / Myoglobin
Similarity search - Component
Biological speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsSato, T. / Tanaka, N. / Moriyama, H. / Igarashi, N. / Neya, S. / Funasaki, N. / Iizuka, T. / Shiro, Y.
Citation
Journal: J.Biol.Chem. / Year: 1993
Title: Structural analysis of the myoglobin reconstituted with iron porphine.
Authors: Neya, S. / Funasaki, N. / Sato, T. / Igarashi, N. / Tanaka, N.
#1: Journal: Bull.Chem.Soc.Jpn. / Year: 1992
Title: The Crystal Structures of Cyanide Metmyoglobins Reconstituted with Iron(III) Complexes of Porphyrin, 5,10,15,20-Tetramethylporphyrin, and 5, 10,15,20-Tetraetylporphyrin
Authors: Sato, T. / Tanaka, N. / Moriyama, H. / Matsumoto, O. / Takenaka, A. / Neya, S. / Funasaki, N.
#2: Journal: Biochim.Biophys.Acta / Year: 1992
Title: Kinetic Studies on Co Binding to Reconstituted Myoglobins with Four Synthetic Hemes; Structural Control in Ligand Binding to Myoglobin
Authors: Sato, T. / Tanaka, N. / Neya, S. / Funasaki, N. / Iizuka, T. / Shiro, Y.
History
DepositionDec 24, 1993Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 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_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.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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6253
Polymers17,2351
Non-polymers3902
Water1,06359
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.620, 76.230, 33.260
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: 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-CYN / CYANIDE ION


Mass: 26.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CN
#3: Chemical ChemComp-POR / PORPHYRIN FE(III)


Mass: 364.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H12FeN4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 2.12 Å3/Da / Density % sol: 41.94 %
Crystal grow
*PLUS
Method: other / Details: NMR

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Data collection

Reflection
*PLUS
Highest resolution: 1.8 Å / Num. obs: 12640 / % possible obs: 89.5 % / Num. measured all: 37599 / Rmerge(I) obs: 0.0726

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Processing

Software
NameClassification
X-PLORmodel building
PROFFTrefinement
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.187 / Rfactor obs: 0.187 / Highest resolution: 1.8 Å
Details: THE SIDE GROUPS OF THE HEME WERE REMOVED COMPLETELY. ARG 45 IS DISPLACED LARGELY FROM THAT IN THE NATIVE AND MAKES OPEN A CHANNEL FOR THE LIGAND PENETRATION FORMED BY HIS 64, THR 67, VAL 68 AND HEME.
Refinement stepCycle: LAST / Highest resolution: 1.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1217 0 27 59 1303
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 7 Å / Num. reflection obs: 11808 / σ(F): 3 / Rfactor all: 0.187
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.0230.02
X-RAY DIFFRACTIONx_angle_d0.0460.03
X-RAY DIFFRACTIONx_planar_d0.060.05
X-RAY DIFFRACTIONx_plane_restr0.0170.02
X-RAY DIFFRACTIONx_chiral_restr0.2270.15

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