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- PDB-1hrm: THE PROXIMAL LIGAND VARIANT HIS93TYR OF HORSE HEART MYOGLOBIN -

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Basic information

Entry
Database: PDB / ID: 1hrm
TitleTHE PROXIMAL LIGAND VARIANT HIS93TYR OF HORSE HEART MYOGLOBIN
ComponentsMYOGLOBIN
KeywordsOXYGEN TRANSPORT
Function / homology
Function and homology information


nitrite reductase activity / Oxidoreductases; Acting on other nitrogenous compounds as donors / oxygen transport / sarcoplasm / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / removal of superoxide radicals / oxygen carrier activity / oxygen binding / peroxidase activity / heme binding ...nitrite reductase activity / Oxidoreductases; Acting on other nitrogenous compounds as donors / oxygen transport / 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
PROTOPORPHYRIN IX CONTAINING FE / Myoglobin
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / Resolution: 1.7 Å
AuthorsBurk, D.L. / Brayer, G.D.
Citation
Journal: Biochemistry / Year: 1995
Title: The proximal ligand variant His93Tyr of horse heart myoglobin.
Authors: Hildebrand, D.P. / Burk, D.L. / Maurus, R. / Ferrer, J.C. / Brayer, G.D. / Mauk, A.G.
#1: Journal: J.Biol.Chem. / Year: 1994
Title: Structural Characterization of Heme Ligation in the His64-->Tyr Variant of Myoglobin
Authors: Maurus, R. / Bogumil, R. / Luo, Y. / Tang, H.L. / Smith, M. / Mauk, A.G. / Brayer, G.D.
#2: Journal: Biochemistry / Year: 1994
Title: Ftir Analysis of the Interaction of Azide with Horse Heart Myoglobin
Authors: Bogumil, R. / Hunter, C.L. / Maurus, R. / Tang, H.L. / Lee, H. / Lloyd, E. / Brayer, G.D. / Smith, M. / Mauk, A.G.
#3: 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.
#4: Journal: J.Mol.Biol. / Year: 1990
Title: High-Resolution Study of the Three-Dimensional Structure of Horse Heart Myoglobin
Authors: Evans, S.V. / Brayer, G.D.
#5: 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.
#6: 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 21, 1994Processing site: BNL
Revision 1.0Jan 26, 1995Provider: 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_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_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)17,7213
Polymers17,0091
Non-polymers7132
Water1,42379
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.360, 28.900, 35.960
Angle α, β, γ (deg.)90.00, 107.06, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein MYOGLOBIN


Mass: 17008.543 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Equus caballus (horse) / Organ: HEART / 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-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.: 79 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCROSS REFERENCE TO SEQUENCE DATABASE DATABASE: SWISS-PROT ENTRY NAME: MYG_HORSE SEQUENCE ADVISORY ...CROSS REFERENCE TO SEQUENCE DATABASE DATABASE: SWISS-PROT ENTRY NAME: MYG_HORSE SEQUENCE ADVISORY NOTICE THE SWISS-PROT DATA BASE IS INCORRECT WITH RESPECT TO THIS SEQUENCE. THE ORIGINAL SEQUENCE DETERMINATION (EUR. J. BIOCHEM. 11, 267 (1969)) DID HAVE AN ASN AT POSITION 122. THIS WAS CORRECTED IN BBA 336, 318 (1974) AND CONFIRMED BY THE AUTHORS, GUILLEMETTE, J.G., MATSUSHIMA-HIBIYA, Y., ATKINSON, T., AND SMITH, M. (1991) PROTEIN ENG. 4, 585 - 592.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.91 Å3/Da / Density % sol: 35.55 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / PH range low: 7.9 / PH range high: 7.7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotein1drop
260 %satammonium sulfate1drop
320 mMTris-HCl1drop
41 mMEDTA1drop
565-66 %satammonium sulfate1reservoir
620 mMTris-HCl1reservoir
71 mMEDTA1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 11147 / % possible obs: 75 % / Observed criterion σ(I): 2
Reflection
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 8 Å / Num. measured all: 29784 / Rmerge(I) obs: 0.057

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.7→5 Å / σ(F): 2 /
RfactorNum. reflection% reflection
obs0.151 9888 72.4 %
Displacement parametersBiso mean: 20.12 Å2
Refinement stepCycle: LAST / Resolution: 1.7→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1201 0 48 79 1328
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0180.02
X-RAY DIFFRACTIONp_angle_d0.0340.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0510.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.6631.5
X-RAY DIFFRACTIONp_mcangle_it2.452.5
X-RAY DIFFRACTIONp_scbond_it2.8262
X-RAY DIFFRACTIONp_scangle_it4.43
X-RAY DIFFRACTIONp_plane_restr0.0140.02
X-RAY DIFFRACTIONp_chiral_restr0.0510.06
X-RAY DIFFRACTIONp_singtor_nbd0.1980.25
X-RAY DIFFRACTIONp_multtor_nbd0.1510.25
X-RAY DIFFRACTIONp_xhyhbond_nbd0.1790.25
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor2.22.5
X-RAY DIFFRACTIONp_staggered_tor16.920
X-RAY DIFFRACTIONp_orthonormal_tor4215
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.151
Solvent computation
*PLUS
Displacement parameters
*PLUS

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