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- PDB-1mdn: WILD TYPE MYOGLOBIN WITH CO -

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Basic information

Entry
Database: PDB / ID: 1mdn
TitleWILD TYPE MYOGLOBIN WITH CO
ComponentsPROTEIN (MYOGLOBIN)
KeywordsOXYGEN STORAGE/TRANSPORT / OXYGEN STORAGE / MYOGLOBIN / V68N / DEOXY / OXYGEN STORAGE-TRANSPORT COMPLEX
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 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 speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 1.98 Å
AuthorsMurshudov, G.N. / Krzywda, S. / Brzozowski, A.M. / Jaskolski, M. / Scott, E.E. / Klizas, S.A. / Gibson, Q.H. / Olson, J.S. / Wilkinson, A.J.
CitationJournal: Biochemistry / Year: 1998
Title: Stabilizing bound O2 in myoglobin by valine68 (E11) to asparagine substitution.
Authors: Krzywda, S. / Murshudov, G.N. / Brzozowski, A.M. / Jaskolski, M. / Scott, E.E. / Klizas, S.A. / Gibson, Q.H. / Olson, J.S. / Wilkinson, A.J.
History
DepositionAug 12, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Sep 30, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...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
Revision 1.4Feb 14, 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: PROTEIN (MYOGLOBIN)
B: PROTEIN (MYOGLOBIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2304
Polymers33,9972
Non-polymers1,2332
Water8,089449
1
A: PROTEIN (MYOGLOBIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6152
Polymers16,9981
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PROTEIN (MYOGLOBIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6152
Polymers16,9981
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)122.000, 42.170, 91.500
Angle α, β, γ (deg.)90.00, 92.73, 90.00
Int Tables number5
Space group name H-MI1211

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Components

#1: Protein PROTEIN (MYOGLOBIN)


Mass: 16998.416 Da / Num. of mol.: 2 / Mutation: V68N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Plasmid: PLCII / Production host: Escherichia coli (E. coli) / 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.: 449 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.46 Å3/Da / Density % sol: 64.42 %
Crystal growpH: 7.1 / Details: 0.1 PHOSPHATE BUFFER PH 7.1 10 MG/ML PROTEIN
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
172-80 %(v/v)satammonium sulfate1drop
20.1 Mphosphate1drop
310 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 150 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→24 Å / Num. obs: 48028 / % possible obs: 96 % / Redundancy: 8 % / Biso Wilson estimate: 26.82 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 19.5
Reflection
*PLUS
Highest resolution: 1.98 Å / Num. obs: 32221 / % possible obs: 96.7 %
Reflection shell
*PLUS
Rmerge(I) obs: 0.22

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Processing

Software
NameClassification
CCP4model building
REFMACrefinement
DENZOdata reduction
CCP4data scaling
CCP4phasing
RefinementMethod to determine structure: OTHER / Resolution: 1.98→24 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.262 1560 5 %RANDOM
Rwork0.198 ---
obs-32221 96 %-
Displacement parametersBiso mean: 33.43 Å2
Baniso -1Baniso -2Baniso -3
1-5.589 Å20 Å22.481 Å2
2--1.157 Å20 Å2
3----6.68 Å2
Refinement stepCycle: LAST / Resolution: 1.98→24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2471 0 86 449 3006
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0140.02
X-RAY DIFFRACTIONp_angle_d0.0330.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0370.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it3.8354
X-RAY DIFFRACTIONp_mcangle_it4.9026
X-RAY DIFFRACTIONp_scbond_it4.4394
X-RAY DIFFRACTIONp_scangle_it6.3456
X-RAY DIFFRACTIONp_plane_restr0.01270.02
X-RAY DIFFRACTIONp_chiral_restr0.1280.15
X-RAY DIFFRACTIONp_singtor_nbd0.2010.3
X-RAY DIFFRACTIONp_multtor_nbd0.3190.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor3.27
X-RAY DIFFRACTIONp_staggered_tor17.115
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor40.920
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.198
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal target
X-RAY DIFFRACTIONp_planar_d0.05
X-RAY DIFFRACTIONp_plane_restr0.02
X-RAY DIFFRACTIONp_chiral_restr0.15
X-RAY DIFFRACTIONp_mcbond_it4
X-RAY DIFFRACTIONp_scbond_it4
X-RAY DIFFRACTIONp_mcangle_it6
X-RAY DIFFRACTIONp_scangle_it6

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