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- PDB-1mbd: X-ray structure of sperm whale deoxymoglobin refined at 1.4A reso... -

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Basic information

Entry
Database: PDB / ID: 1mbd
TitleX-ray structure of sperm whale deoxymoglobin refined at 1.4A resolution
ComponentsMYOGLOBIN
KeywordsOXYGEN STORAGE
Function / homology
Function and homology information


Oxidoreductases; Acting on other nitrogenous compounds as donors / nitrite reductase activity / sarcoplasm / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / removal of superoxide radicals / oxygen carrier activity / peroxidase activity / oxygen binding / 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 speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / Resolution: 1.4 Å
AuthorsPhillips, S.E.V.
Citation
Journal: to be published
Title: X-ray structure of sperm whale deoxymoglobin refined at 1.4A resolution
Authors: Phillips, S.E.
#1: Journal: J.Mol.Biol. / Year: 1980
Title: Structure and Refinement of Oxymyoglobin at 1.6 Angstroms Resolution
Authors: Phillips, S.E.V.
#2: Journal: Nature / Year: 1978
Title: Structure of Oxymyoglobin
Authors: Phillips, S.E.V.
#3: Journal: Acta Crystallogr.,Sect.A (Supplement) / Year: 1978
Title: The Structure of Oxy-Myoglobin
Authors: Phillips, S.E.V.
History
DepositionAug 27, 1981Processing site: BNL
Revision 1.0Feb 3, 1982Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 8, 2017Group: Database references / Other / Structure summary
Category: citation / citation_author ...citation / citation_author / pdbx_database_status / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_database_status.process_site / _struct.title
Revision 2.0Feb 8, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / database_2 ...atom_site / database_2 / database_PDB_matrix / pdbx_struct_conn_angle / pdbx_validate_close_contact / pdbx_validate_main_chain_plane / pdbx_validate_planes / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_symm_contact / pdbx_validate_torsion / struct_conn / struct_site
Item: _atom_site.Cartn_x / _atom_site.Cartn_z ..._atom_site.Cartn_x / _atom_site.Cartn_z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _database_PDB_matrix.origx[1][1] / _database_PDB_matrix.origx[1][3] / _database_PDB_matrix.origx[2][2] / _database_PDB_matrix.origx[3][1] / _database_PDB_matrix.origx[3][3] / _pdbx_struct_conn_angle.value / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_close_contact.dist / _pdbx_validate_planes.rmsd / _pdbx_validate_rmsd_angle.angle_deviation / _pdbx_validate_rmsd_angle.angle_standard_deviation / _pdbx_validate_rmsd_angle.angle_target_value / _pdbx_validate_rmsd_angle.angle_value / _pdbx_validate_rmsd_angle.auth_atom_id_1 / _pdbx_validate_rmsd_angle.auth_atom_id_2 / _pdbx_validate_rmsd_angle.auth_atom_id_3 / _pdbx_validate_rmsd_angle.auth_comp_id_1 / _pdbx_validate_rmsd_angle.auth_comp_id_2 / _pdbx_validate_rmsd_angle.auth_comp_id_3 / _pdbx_validate_rmsd_angle.auth_seq_id_1 / _pdbx_validate_rmsd_angle.auth_seq_id_2 / _pdbx_validate_rmsd_angle.auth_seq_id_3 / _pdbx_validate_rmsd_bond.bond_deviation / _pdbx_validate_rmsd_bond.bond_value / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _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
Details: Coordinates and associated ncs operations (if present) transformed into standard crystal frame
Provider: repository / Type: Remediation
Revision 2.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)17,9483
Polymers17,2351
Non-polymers7132
Water6,990388
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.660, 31.120, 35.060
Angle α, β, γ (deg.)90.00, 105.78, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: INSPECTION OF MAPS AT VARIOUS STAGES OF REFINEMENT INDICATED THAT SEVERAL SIDE-CHAINS AND THE C- AND N-TERMINAL RESIDUES WERE DISORDERED TO SOME DEGREE. IN MOST CASES, ONE CONFORMATION WAS VERY ...1: INSPECTION OF MAPS AT VARIOUS STAGES OF REFINEMENT INDICATED THAT SEVERAL SIDE-CHAINS AND THE C- AND N-TERMINAL RESIDUES WERE DISORDERED TO SOME DEGREE. IN MOST CASES, ONE CONFORMATION WAS VERY MUCH STRONGER THAN THE OTHER, BUT THREE SIDE-CHAINS WERE INCLUDED IN THE MODEL WITH TWO ALTERNATE CONFORMATIONS (VAL 13, LEU 86, LEU 89).
2: HOH 305 IS A FULLY OCCUPIED WATER MOLECULE IN THE HEME POCKET. IN OXYMYOGLOBIN IT IS PRESENT IN LOW OCCUPANCY CLOSE TO ATOM O1 OF THE HEME. SEE PAPER CITED AS REFERENCE 1 ABOVE.

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Components

#1: Protein MYOGLOBIN


Mass: 17234.951 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physeter catodon (sperm whale) / References: UniProt: P02185
#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.: 388 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsHOH 305 IS A FULLY OCCUPIED WATER MOLECULE IN THE HEME POCKET. IN OXYMYOGLOBIN IT IS PRESENT IN LOW ...HOH 305 IS A FULLY OCCUPIED WATER MOLECULE IN THE HEME POCKET. IN OXYMYOGLOBIN IT IS PRESENT IN LOW OCCUPANCY CLOSE TO ATOM O1 OF THE HEME. SEE PAPER CITED AS REFERENCE 1 ABOVE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.97 Å3/Da / Density % sol: 37.53 %
Crystal grow
*PLUS
Method: unknown

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Data collection

Reflection
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 2 Å / Num. obs: 14411 / Rmerge(I) obs: 0.141

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Processing

SoftwareName: CONSTRAINED / Version: RECIPROCAL-SPACE LEAST-SQUARES / Classification: refinement
RefinementHighest resolution: 1.4 Å
Refinement stepCycle: LAST / Highest resolution: 1.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1230 0 48 388 1666
Refinement
*PLUS
Rfactor obs: 0.188
Solvent computation
*PLUS
Displacement parameters
*PLUS

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