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- PDB-1rse: MYOGLOBIN (HORSE HEART) MUTANT WITH SER 92 REPLACED BY ASP (S92D) -

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Basic information

Entry
Database: PDB / ID: 1rse
TitleMYOGLOBIN (HORSE HEART) MUTANT WITH SER 92 REPLACED BY ASP (S92D)
ComponentsHORSE HEART MYOGLOBIN
KeywordsOXYGEN TRANSPORT / HEME / RESPIRATORY PROTEIN
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
AuthorsBurk, D.L. / Brayer, G.D.
Citation
Journal: Biochemistry / Year: 1996
Title: Electrostatic modification of the active site of myoglobin: characterization of the proximal Ser92Asp variant.
Authors: Lloyd, E. / Burk, D.L. / Ferrer, J.C. / Maurus, R. / Doran, J. / Carey, P.R. / Brayer, G.D. / Mauk, A.G.
#1: Journal: Protein Eng. / Year: 1991
Title: Expression in Escherichia Coli of a Synthetic Gene Coding for Horse Heart Myoglobin
Authors: Guillemette, J.G. / Matsushima-Hibiya, Y. / Atkinson, T. / Smith, M.
#2: 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.
#3: 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.
#4: 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 20, 1996Processing site: BNL
Revision 1.0Dec 23, 1996Provider: 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: HORSE HEART MYOGLOBIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7243
Polymers17,0121
Non-polymers7132
Water1,09961
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.420, 28.880, 35.970
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 HORSE HEART MYOGLOBIN


Mass: 17011.525 Da / Num. of mol.: 1 / Mutation: S92D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Equus caballus (horse) / Organ: HEART / Production host: Escherichia coli (E. coli) / 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.: 61 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsHOH 156 IS COVALENTLY BOUND TO THE IRON OF THE HEME.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.88 Å3/Da / Density % sol: 34.59 %
Crystal grow
*PLUS
Temperature: 21 ℃ / pH: 6.8 / Method: vapor diffusion, hanging drop / Details: used to seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotein1drop
259 %satammonium sulfate1drop
320 mMTris-HCl1drop
41 mMEDTA1drop
567 %satammonium sulfate1reservoir
620 mMTris-HCl1reservoir
71 mMEDTA1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: May 28, 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 11967 / % possible obs: 85.6 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.059
Reflection
*PLUS
Num. measured all: 45864

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Processing

Software
NameClassification
PROLSQrefinement
OSCILLdata reduction
RefinementResolution: 1.7→6 Å / σ(F): 0 /
RfactorNum. reflection
Rwork0.188 -
all-11615
obs-11615
Displacement parametersBiso mean: 21.8 Å2
Refinement stepCycle: LAST / Resolution: 1.7→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1244 0 0 66 1310
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0150.02
X-RAY DIFFRACTIONp_angle_d0.0310.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0460.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.3761.5
X-RAY DIFFRACTIONp_mcangle_it2.1072.5
X-RAY DIFFRACTIONp_scbond_it2.3612
X-RAY DIFFRACTIONp_scangle_it3.7693
X-RAY DIFFRACTIONp_plane_restr0.010.02
X-RAY DIFFRACTIONp_chiral_restr0.0480.06
X-RAY DIFFRACTIONp_singtor_nbd0.1930.2
X-RAY DIFFRACTIONp_multtor_nbd0.1590.2
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1470.2
X-RAY DIFFRACTIONp_planar_tor1.31.5
X-RAY DIFFRACTIONp_staggered_tor17.820
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor3715
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.188
Solvent computation
*PLUS
Displacement parameters
*PLUS

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