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- PDB-1mnh: INTERACTIONS AMONG RESIDUES CD3, E7, E10 AND E11 IN MYOGLOBINS: A... -

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Basic information

Entry
Database: PDB / ID: 1mnh
TitleINTERACTIONS AMONG RESIDUES CD3, E7, E10 AND E11 IN MYOGLOBINS: ATTEMPTS TO SIMULATE THE O2 AND CO BINDING PROPERTIES OF APLYSIA MYOGLOBIN
ComponentsMYOGLOBIN
KeywordsOXYGEN STORAGE
Function / homology
Function and homology information


Intracellular oxygen transport / 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 ...Intracellular oxygen transport / 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 speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsDavies, G.J. / Wilkinson, A.J.
Citation
Journal: Biochemistry / Year: 1995
Title: Interactions among residues CD3, E7, E10, and E11 in myoglobins: attempts to simulate the ligand-binding properties of Aplysia myoglobin.
Authors: Smerdon, S.J. / Krzywda, S. / Brzozowski, A.M. / Davies, G.J. / Wilkinson, A.J. / Brancaccio, A. / Cutruzzola, F. / Allocatelli, C.T. / Brunori, M. / Li, T. / Brantley Jr., R.E. / Carver, T. ...Authors: Smerdon, S.J. / Krzywda, S. / Brzozowski, A.M. / Davies, G.J. / Wilkinson, A.J. / Brancaccio, A. / Cutruzzola, F. / Allocatelli, C.T. / Brunori, M. / Li, T. / Brantley Jr., R.E. / Carver, T.E. / Eich, R.F. / Singleton, E. / Olson, J.S.
#1: Journal: Biochemistry / Year: 1993
Title: Distal Pocket Polarity in Ligand Binding to Myoglobin: Deoxy and Carbonmonoxy Forms of Threonine68(E11) Mutant Investigated by X-Ray Crystallography and Infrared Spectroscopy
Authors: Cameron, A.D. / Smerdon, S.J. / Wilkinson, A.J. / Habash, J. / Helliwell, J.R. / Li, T. / Olson, J.S.
#2: Journal: Biochemistry / Year: 1992
Title: High Resolution X-Ray Structures of Pig Metmyoglobin and Two Cd3 Mutants Mb(Lys45-->Arg) and Mb(Lys45-->Ser)
Authors: Oldfield, T.J. / Smerdon, S.J. / Dauter, Z. / Petratos, K. / Wilson, K.S. / Wilkinson, A.J.
#3: Journal: Acta Crystallogr.,Sect.B / Year: 1990
Title: Determination of the Crystal Structure of Recombinant Pig Myoglobin by Molecular Replacement and its Refinement
Authors: Smerdon, S.J. / Oldfield, T.J. / Dodson, E.J. / Dodson, G.G. / Hubbard, R.E. / Wilkinson, A.J.
History
DepositionJan 11, 1995Processing site: BNL
Revision 1.0May 8, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 22, 2012Group: Database references
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_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 / _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

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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)17,6172
Polymers17,0011
Non-polymers6161
Water2,090116
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)29.700, 119.510, 58.180
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein MYOGLOBIN


Mass: 17000.520 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / References: UniProt: P02189
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 3.04 Å3/Da / Density % sol: 59.49 %
Crystal grow
*PLUS
pH: 7.1 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
150 mMphosphate1reservoir
270-80 %ammonium phosphate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.3 Å / Num. obs: 9174 / % possible obs: 94.2 % / Rmerge(I) obs: 0.07
Reflection shell
*PLUS
Rmerge(I) obs: 0.084

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Processing

Software
NameClassification
ARP/wARPmodel building
PROLSQrefinement
RefinementResolution: 2.3→10 Å /
RfactorNum. reflection
obs0.185 9174
Refinement stepCycle: LAST / Resolution: 2.3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1198 0 43 116 1357
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0140.02
X-RAY DIFFRACTIONp_angle_d0.0450.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0530.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it3.8424
X-RAY DIFFRACTIONp_mcangle_it5.1396
X-RAY DIFFRACTIONp_scbond_it9.7668
X-RAY DIFFRACTIONp_scangle_it13.55710
X-RAY DIFFRACTIONp_plane_restr0.0130.02
X-RAY DIFFRACTIONp_chiral_restr0.0380.06
X-RAY DIFFRACTIONp_singtor_nbd0.190.3
X-RAY DIFFRACTIONp_multtor_nbd0.2680.3
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2360.3
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor2.2673
X-RAY DIFFRACTIONp_staggered_tor19.91515
X-RAY DIFFRACTIONp_orthonormal_tor40.94620
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Rfactor Rfree: 0.251
Solvent computation
*PLUS
Displacement parameters
*PLUS

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