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- PDB-1ycb: DISTAL POCKET POLARITY IN LIGAND BINDING TO MYOGLOBIN: DEOXY AND ... -

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Basic information

Entry
Database: PDB / ID: 1ycb
TitleDISTAL POCKET POLARITY IN LIGAND BINDING TO MYOGLOBIN: DEOXY AND CARBONMONOXY FORMS OF A THREONINE68 (E11) MUTANT INVESTIGATED BY X-RAY CRYSTALLOGRAPHY AND INFRARED SPECTROSCOPY
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: 2.1 Å
AuthorsCameron, A.D. / Smerdon, S.J. / Wilkinson, A.J. / Habash, J. / Helliwell, J.R.
Citation
Journal: Biochemistry / Year: 1993
Title: Distal pocket polarity in ligand binding to myoglobin: deoxy and carbonmonoxy forms of a 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.
#1: 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.
#2: Journal: Biochemistry / Year: 1991
Title: Distal Polarity in Ligand Binding to Myoglobin: Structural and Functional Characterization of a Threonine68(E11) Mutant
Authors: Smerdon, S.J. / Dodson, G.G. / Wilkinson, A.J. / Gibson, Q.H. / Blackmore, R.S. / Carver, T.E. / Olson, J.S.
#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.
#4: 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.G. / Hubbard, R.E. / Oldfield, T.J. / Smerdon, S.J. / Wilkinson, A.J.
History
DepositionAug 10, 1993Processing site: BNL
Revision 1.0Jan 31, 1994Provider: 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 / 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

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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)35,2044
Polymers33,9712
Non-polymers1,2332
Water1,964109
1
A: MYOGLOBIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6022
Polymers16,9851
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: MYOGLOBIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6022
Polymers16,9851
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)124.600, 42.500, 92.000
Angle α, β, γ (deg.)90.00, 92.00, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: PHE A 151 - GLN A 152 OMEGA ANGLE = 146.397 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION

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Components

#1: Protein MYOGLOBIN


Mass: 16985.418 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.: 109 / 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

Crystal grow
*PLUS
pH: 7.1 / Method: vapor diffusion, hanging drop / Details: under 1 atm of argon
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
1100 mMsodium phosphate1drop
270-80 %ammonium sulfate1drop
35-6 mg/mlprotein1drop
4sodium dithionite1drop50-fold molar excess

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Data collection

Reflection
*PLUS
Highest resolution: 2.1 Å / Num. obs: 18251 / Rmerge(I) obs: 0.111

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2.1→8 Å / σ(F): 0
Details: THIS STRUCTURE WAS REFINED AGAINST LAUE DATA TO 2.1 ANGSTROMS RESOLUTION. THE DATA SET IS 63% COMPLETE OVERALL BUT ONLY 38% OF REFLECTIONS ARE PRESENT BELOW 2DMIN. AS A RESULT THE ELECTRON ...Details: THIS STRUCTURE WAS REFINED AGAINST LAUE DATA TO 2.1 ANGSTROMS RESOLUTION. THE DATA SET IS 63% COMPLETE OVERALL BUT ONLY 38% OF REFLECTIONS ARE PRESENT BELOW 2DMIN. AS A RESULT THE ELECTRON DENSITY MAPS HAVE BREAKS PERIODICALLY ALONG THE MAIN CHAIN. THOSE ATOMS WHICH COULD NOT BE OBSERVED IN ANY MAP HAVE BEEN ASSIGNED AN OCCUPANCY OF 0.0. DURING THE COURSE OF REFINEMENT REASONABLY TIGHT RESTRAINTS WERE APPLIED TO THE GEOMETRY WHILE MOST ATTENTION WAS PAID TO THE HAEM GROUP AND ITS ENVIRONMENT. THIS STRATEGY WAS ADOPTED AS THE PURPOSE OF THE STUDY WAS TO DEFINE THE LOCATION OF WATER MOLECULES IN THE DISTAL POCKET.
RfactorNum. reflection
obs0.198 18200
Refinement stepCycle: LAST / Resolution: 2.1→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2394 0 86 109 2589
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.020.02
X-RAY DIFFRACTIONp_angle_d0.0550.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0810.06
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.8561
X-RAY DIFFRACTIONp_mcangle_it1.3871.5
X-RAY DIFFRACTIONp_scbond_it1.6731.5
X-RAY DIFFRACTIONp_scangle_it2.5032
X-RAY DIFFRACTIONp_plane_restr0.0160.02
X-RAY DIFFRACTIONp_chiral_restr0.1380.12
X-RAY DIFFRACTIONp_singtor_nbd0.2270.5
X-RAY DIFFRACTIONp_multtor_nbd0.2390.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2490.5
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor2.84320
X-RAY DIFFRACTIONp_staggered_tor20.9420
X-RAY DIFFRACTIONp_orthonormal_tor40.0620
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 8 Å / Num. reflection all: 18200 / σ(F): 0 / Rfactor all: 0.198
Solvent computation
*PLUS
Displacement parameters
*PLUS

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