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- PDB-2mb5: HYDRATION IN PROTEIN CRYSTALS. A NEUTRON DIFFRACTION ANALYSIS OF ... -

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Basic information

Entry
Database: PDB / ID: 2mb5
TitleHYDRATION IN PROTEIN CRYSTALS. A NEUTRON DIFFRACTION ANALYSIS OF CARBONMONOXYMYOGLOBIN
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-like / Globin / Globin / Globin domain profile. / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
CARBON MONOXIDE / DEUTERATED WATER / PROTOPORPHYRIN IX CONTAINING FE / AMMONIUM CATION WITH D / Myoglobin
Similarity search - Component
Biological speciesPhyseter catodon (sperm whale)
MethodNEUTRON DIFFRACTION / Resolution: 1.8 Å
AuthorsSchoenborn, B.P. / Cheng, X.
Citation
Journal: Acta Crystallogr.,Sect.B / Year: 1990
Title: Hydration in Protein Crystals. A Neutron Diffraction Analysis of Carbonmonoxymyoglobin
Authors: Cheng, X. / Schoenborn, B.P.
#1: Journal: J.Mol.Biol. / Year: 1981
Title: Real Space Refinement of Neutron Diffraction Data from Sperm Whale Carbonmonoxymyoglobin
Authors: Hanson, J.C. / Schoenborn, B.P.
#2: Journal: Acs Symp.Ser. / Year: 1980
Title: The Determination of Structural Water by Neutron Protein Crystallography. An Analysis of the Carbon Monoxide Myoglobin Water Structure
Authors: Schoenborn, B.P. / Hanson, J.C.
#3: Journal: Acta Crystallogr.,Sect.A (Supplement) / Year: 1975
Title: Neutron Diffraction Analysis and Real Space Refinement of met and Carbon Monoxide Myoglobin
Authors: Schoenborn, B.P. / Norvell, J.C.
#4: Journal: Brookhaven Symposia in Biology / Year: 1975
Title: Neutron Diffraction Analysis of Metmyoglobin
Authors: Schoenborn, B.P. / Diamond, R.
#5: Journal: Science / Year: 1975
Title: Neutron Diffraction Analysis of Myoglobin. Structure of the Carbon Monoxide Derivative
Authors: Norvell, J.C. / Nunes, A.C. / Schoenborn, B.P.
#6: Journal: Cold Spring Harbor Symp.Quant.Biol. / Year: 1972
Title: A Neutron Diffraction Analysis of Myoglobin. III. Hydrogen-Deuterium Bonding in Side Chains
Authors: Schoenborn, B.P.
#7: Journal: Nature / Year: 1969
Title: Neutron Diffraction Analysis of Myoglobin
Authors: Schoenborn, B.P.
#8: Journal: Atlas of Protein Sequence and Structure (Data Section)
Year: 1972
History
DepositionOct 11, 1989Processing site: BNL
SupersessionJan 15, 1991ID: 1MB5
Revision 1.0Apr 15, 1991Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Version format compliance
Revision 1.3Feb 21, 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
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_alt_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_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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

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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)18,0869
Polymers17,2351
Non-polymers8518
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.610, 30.950, 34.860
Angle α, β, γ (deg.)90.00, 105.78, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 97 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-ND4 / AMMONIUM CATION WITH D


Mass: 22.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: N
#4: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#5: Chemical ChemComp-CMO / CARBON MONOXIDE


Mass: 28.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO
#6: Chemical ChemComp-DOD / water


Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: D2O

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Experimental details

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Experiment

ExperimentMethod: NEUTRON DIFFRACTION

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Sample preparation

Crystal grow
*PLUS
Method: unknown

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementHighest resolution: 1.8 Å
Refinement stepCycle: LAST / Highest resolution: 1.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1217 0 55 89 1361
Refine LS restraints
Refine-IDTypeDev ideal
NEUTRON DIFFRACTIONp_bond_d0.006
NEUTRON DIFFRACTIONp_angle_d0.039

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