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- PDB-1xch: MYOGLOBIN (HORSE HEART) MUTANT WITH LEU 104 REPLACED BY ASN (L104N) -

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Basic information

Entry
Database: PDB / ID: 1xch
TitleMYOGLOBIN (HORSE HEART) MUTANT WITH LEU 104 REPLACED BY ASN (L104N)
ComponentsMYOGLOBIN
KeywordsOXYGEN TRANSPORT / HEME / RESPIRATORY PROTEIN / MUSCLE
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
PROTOPORPHYRIN IX CONTAINING FE / Myoglobin
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / Resolution: 1.7 Å
AuthorsMaurus, R. / Brayer, G.D.
Citation
Journal: Biochim.Biophys.Acta / Year: 1997
Title: A myoglobin variant with a polar substitution in a conserved hydrophobic cluster in the heme binding pocket.
Authors: Maurus, R. / Overall, C.M. / Bogumil, R. / Luo, Y. / Mauk, A.G. / Smith, M. / Brayer, G.D.
#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 Variants
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 Metmyoglobin
Authors: Evans, S.V. / Brayer, G.D.
#5: Journal: J.Biol.Chem. / Year: 1988
Title: Horse Heart Metmyoglobin. A 2.8-A 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
DepositionJun 6, 1997Processing site: BNL
Revision 1.0Sep 17, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...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
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)17,6973
Polymers16,9841
Non-polymers7132
Water1,13563
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.566, 28.872, 35.882
Angle α, β, γ (deg.)90.00, 107.17, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein MYOGLOBIN


Mass: 16984.459 Da / Num. of mol.: 1 / Mutation: L104N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Equus caballus (horse) / Organ: HEART / Production host: Escherichia coli (E. coli) / Strain (production host): LE392 / 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.: 63 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.88 Å3/Da / Density % sol: 34.61 %
Crystal growpH: 8.4
Details: 20 MM TRIS/HCL, 1MM EDTA, PH 8.4, 8 MG/ML PROTEIN 69% AMMONIUM SULFATE
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
18 mg/mlprotein1drop
260-62 %satammonium sulfate1drop
320 mMTris-HCl1drop
41 mMEDTA1drop
568-70 %satammonium sulfate1reservoir
620 mMTris-HCl1reservoir
71 mMEDTA1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Feb 17, 1992
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→35 Å / Num. obs: 12442 / % possible obs: 83 % / Observed criterion σ(I): 2 / Redundancy: 3.91 % / Biso Wilson estimate: 16.6 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 8.5

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Processing

Software
NameClassification
GPRLSArefinement
RIGAKUdata reduction
RIGAKUdata scaling
RefinementResolution: 1.7→6 Å / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.179 --
all-11726 -
obs-11725 83 %
Displacement parametersBiso mean: 18.3 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 1.7→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1195 0 47 62 1304
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0140.015
X-RAY DIFFRACTIONp_angle_d0.0370.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0550.05
X-RAY DIFFRACTIONp_hb_or_metal_coord0.1950.06
X-RAY DIFFRACTIONp_mcbond_it1.71.5
X-RAY DIFFRACTIONp_mcangle_it2.52.5
X-RAY DIFFRACTIONp_scbond_it3.12
X-RAY DIFFRACTIONp_scangle_it4.62
X-RAY DIFFRACTIONp_plane_restr0.0150.02
X-RAY DIFFRACTIONp_chiral_restr0.0130.025
X-RAY DIFFRACTIONp_singtor_nbd0.1990.2
X-RAY DIFFRACTIONp_multtor_nbd0.1730.2
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1660.2
X-RAY DIFFRACTIONp_planar_tor1.91.5
X-RAY DIFFRACTIONp_staggered_tor17.220
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: GPRLSA / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.179
Solvent computation
*PLUS
Displacement parameters
*PLUS

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