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- PDB-1ymc: THREE-DIMENSIONAL STRUCTURE OF CYANOMET-SULFMYOGLOBIN C -

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Basic information

Entry
Database: PDB / ID: 1ymc
TitleTHREE-DIMENSIONAL STRUCTURE OF CYANOMET-SULFMYOGLOBIN C
ComponentsCYANOMET-SULFMYOGLOBIN
KeywordsOXYGEN TRANSPORT
Function / homology
Function and homology information


Oxidoreductases; Acting on other nitrogenous compounds as donors / nitrite reductase activity / oxygen transport / sarcoplasm / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / removal of superoxide radicals / oxygen carrier activity / peroxidase activity / oxygen binding / heme binding / 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
SULFUR SUBSTITUTED PROTOPORPHYRIN IX / CYANIDE ION / Myoglobin
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsEvans, S.V. / Brayer, G.D.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1994
Title: Three-dimensional structure of cyanomet-sulfmyoglobin C.
Authors: Evans, S.V. / Sishta, B.P. / Mauk, A.G. / Brayer, G.D.
#1: Journal: J.Mol.Biol. / Year: 1990
Title: High-Resolution Study of the Three-Dimensional Structure of Horse Heart Metmyoglobin
Authors: Evans, S.V. / Brayer, G.D.
#2: Journal: J.Biol.Chem. / Year: 1988
Title: Horse Heart Metmyoglobin: A 2.8-Angstroms Resolution Three-Dimensional Structure Determination
Authors: Evans, S.V. / Brayer, G.D.
#3: Journal: J.Mol.Biol. / Year: 1987
Title: Crystallization and Preliminary Diffraction Data for Horse Heart Metmyoglobin
Authors: Sherwood, C. / Mauk, A.G. / Brayer, G.D.
History
DepositionSep 27, 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 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: CYANOMET-SULFMYOGLOBIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7544
Polymers16,9841
Non-polymers7713
Water3,117173
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.500, 28.910, 35.660
Angle α, β, γ (deg.)90.00, 107.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein CYANOMET-SULFMYOGLOBIN


Mass: 16983.514 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Equus caballus (horse) / References: UniProt: P68082
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CYN / CYANIDE ION


Mass: 26.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CN
#4: Chemical ChemComp-CLN / SULFUR SUBSTITUTED PROTOPORPHYRIN IX


Mass: 648.552 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 1.87 Å3/Da / Density % sol: 34.28 %
Crystal grow
*PLUS
Method: batch method / Details: can also be done with hanging drop vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
18 mg/mlprotein11
20.1 Msodium acetate11

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Data collection

Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 6 Å / Num. obs: 7946

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2→6 Å / σ(F): 2 /
RfactorNum. reflection
obs0.129 5369
Refinement stepCycle: LAST / Resolution: 2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1199 0 51 173 1423
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.036
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 6 Å / Num. reflection obs: 5369 / σ(F): 2 / Rfactor obs: 0.129
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: p_angle_d / Dev ideal: 0.06

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