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

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Basic information

Entry
Database: PDB / ID: 1mnj
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 / oxygen transport / oxygen carrier activity / oxygen binding / heme binding / metal ion binding
Similarity search - Function
Myoglobin / Globins / Globin family 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 speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsKrzywda, S. / 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 1.0Apr 20, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 25, 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

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Assembly

Deposited unit
A: MYOGLOBIN
B: MYOGLOBIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1504
Polymers33,9172
Non-polymers1,2332
Water3,171176
1
A: MYOGLOBIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5752
Polymers16,9581
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: MYOGLOBIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5752
Polymers16,9581
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)124.290, 42.560, 92.450
Angle α, β, γ (deg.)90.00, 92.65, 90.00
Int Tables number5
Space group name H-MI1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.992808, 0.024012, 0.117285), (0.021597, -0.999529, 0.021819), (0.117754, -0.019129, -0.992859)
Vector: -3.53654, 50.00204, 39.56234)
DetailsMTRIX THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE VARIOUS DOMAINS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. APPLIED TO TRANSFORMED TO MTRIX CHAIN RESIDUES CHAIN RESIDUES RMSD M1 A 1 - A 153 B 1 - B 153 0.424

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Components

#1: Protein MYOGLOBIN /


Mass: 16958.455 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 / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 3.6 Å3/Da / Density % sol: 65.83 %
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 sulfate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.2 Å / Num. obs: 21170 / % possible obs: 85 % / Rmerge(I) obs: 0.046
Reflection shell
*PLUS
Rmerge(I) obs: 0.147

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Processing

Software
NameClassification
ARP/wARPmodel building
PROLSQrefinement
RefinementResolution: 2.2→10 Å / Details: GLN A 152 AND GLY A 153 ARE DISORDERED. /
RfactorNum. reflection
obs0.162 21170
Refinement stepCycle: LAST / Resolution: 2.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2376 0 86 176 2638
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0210.02
X-RAY DIFFRACTIONp_angle_d0.0590.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0630.06
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.0411
X-RAY DIFFRACTIONp_mcangle_it1.8031.5
X-RAY DIFFRACTIONp_scbond_it5.8712.5
X-RAY DIFFRACTIONp_scangle_it9.3565
X-RAY DIFFRACTIONp_plane_restr0.0140.02
X-RAY DIFFRACTIONp_chiral_restr0.120.14
X-RAY DIFFRACTIONp_singtor_nbd0.2110.5
X-RAY DIFFRACTIONp_multtor_nbd0.2180.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2340.5
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor2.5445
X-RAY DIFFRACTIONp_staggered_tor20.4115
X-RAY DIFFRACTIONp_orthonormal_tor37.49515
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Rfactor Rfree: 0.24
Solvent computation
*PLUS
Displacement parameters
*PLUS

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