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- PDB-1pmb: THE DETERMINATION OF THE CRYSTAL STRUCTURE OF RECOMBINANT PIG MYO... -

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Basic information

Entry
Database: PDB / ID: 1pmb
TitleTHE DETERMINATION OF THE CRYSTAL STRUCTURE OF RECOMBINANT PIG MYOGLOBIN BY MOLECULAR REPLACEMENT AND ITS REFINEMENT
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: 2.5 Å
AuthorsSmerdon, S.J. / Oldfield, T.J. / Dodson, E.J. / Dodson, G.G. / Hubbard, R.E. / Wilkinson, A.J.
Citation
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.
#1: Journal: Protein Eng. / Year: 1988
Title: Apomyoglobin as a Molecular Recognition Surface. Expression, Reconstitution and Crystallisation of Recombinant Porcine Myoglobin in Escherichia Coli
Authors: Dodson, G. / Hubbard, R.E. / Oldfield, T.J. / Smerdon, S.J. / Wilkinson, A.J.
History
DepositionNov 27, 1989Processing site: BNL
Revision 1.0Jan 15, 1990Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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

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Assembly

Deposited unit
A: MYOGLOBIN
B: MYOGLOBIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2004
Polymers33,9672
Non-polymers1,2332
Water1,02757
1
A: MYOGLOBIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6002
Polymers16,9831
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: MYOGLOBIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6002
Polymers16,9831
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)124.910, 42.630, 92.200
Angle α, β, γ (deg.)90.00, 92.16, 90.00
Int Tables number5
Space group name H-MI1211
Atom site foot note1: RESIDUES 152 AND 153 ARE DISORDERED AND NOT DEFINED IN THE ELECTRON DENSITY MAPS.
2: HOH 5 AND HOH 18 ARE WATER MOLECULES IN THE HEME POCKET BUT THEY ARE NOT LIGATED TO THE HEME IRON.

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Components

#1: Protein MYOGLOBIN


Mass: 16983.445 Da / Num. of mol.: 2
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.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 3.61 Å3/Da / Density % sol: 65.93 %
Crystal grow
*PLUS
Temperature: 15 ℃ / pH: 7.1 / Method: vapor diffusion, hanging drop
Details: taken from Dodson, G.(1988). Protein. Eng., 2, 233-237.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
18 mg/mlprotein1drop
250 mMsodium phosphate1reservoir
380 %ammonium sulphate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.5 Å / Num. obs: 15941 / Rmerge(I) obs: 0.059 / Biso Wilson estimate: 33 Å2 / Num. measured all: 49979

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2.5→10 Å /
RfactorNum. reflection
obs0.185 14481
Refinement stepCycle: LAST / Resolution: 2.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2394 0 86 57 2537
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0240.02
X-RAY DIFFRACTIONp_angle_d0.0750.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.090.06
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_restr0.020.02
X-RAY DIFFRACTIONp_chiral_restr0.1760.12
X-RAY DIFFRACTIONp_singtor_nbd0.2390.5
X-RAY DIFFRACTIONp_multtor_nbd0.2510.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2060.5
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
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 10 Å / Num. reflection obs: 14481 / Rfactor obs: 0.185
Solvent computation
*PLUS
Displacement parameters
*PLUS

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