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- PDB-2o5q: Manganese horse heart myoglobin, nitric oxide modified -

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Database: PDB / ID: 2o5q
TitleManganese horse heart myoglobin, nitric oxide modified
KeywordsOXYGEN STORAGE/TRANSPORT / Manganese protoporphyrin IX / manganese myoglobin / nitric oxide / horse heart / OXYGEN STORAGE-TRANSPORT COMPLEX
Function / homology
Function and homology information

oxygen transport / oxygen carrier activity / oxygen binding / heme binding / metal ion binding
Similarity search - Function
Myoglobin / Globin family profile. / Globins / Globin / Globin / Globin-like / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Similarity search - Component
Biological speciesEquus caballus (horse)
AuthorsRichter-Addo, G.B. / Zahran, Z.N. / Chooback, L. / Copeland, D.M. / West, A.H.
CitationJournal: J.Inorg.Biochem. / Year: 2008
Title: Crystal structures of manganese- and cobalt-substituted myoglobin in complex with NO and nitrite reveal unusual ligand conformations.
Authors: Zahran, Z.N. / Chooback, L. / Copeland, D.M. / West, A.H. / Richter-Addo, G.B.
DepositionDec 6, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

Structure visualization

Structure viewerMolecule:

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Deposited unit
X: Myoglobin
hetero molecules

Theoretical massNumber of molelcules
Total (without water)17,8215

  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.468, 28.637, 63.193
Angle α, β, γ (deg.)90.00, 105.70, 90.00
Int Tables number4
Space group name H-MP1211


#1: Protein Myoglobin /

Mass: 16983.514 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Equus caballus (horse) / Organ: Heart / References: UniProt: P68082
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate

Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4

Mass: 615.580 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32MnN4O4
#4: Chemical ChemComp-NO / NITRIC OXIDE / Nitrogen monoxide / Nitric oxide

Mass: 30.006 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO
#5: Water ChemComp-HOH / water / Water

Mass: 18.015 Da / Num. of mol.: 163 / Source method: isolated from a natural source / Formula: H2O

Experimental details


ExperimentMethod: X-RAY DIFFRACTION

Sample preparation

CrystalDensity Matthews: 1.82 Å3/Da / Density % sol: 32.37 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: Ammonium sulfate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Temp details: Room temperature

Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 1, 2005
RadiationMonochromator: Osmic mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.9→34.14 Å / Num. obs: 9669 / Rmerge(I) obs: 0.095


CrystalCleardata collection
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→26.57 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.937 / SU B: 4.726 / SU ML: 0.139 / Cross valid method: THROUGHOUT / ESU R: 0.218 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23543 461 4.8 %RANDOM
Rwork0.17733 ---
obs0.18029 9205 97.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.563 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.9→26.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1194 0 55 163 1412
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0211281
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.6722.0081736
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7335151
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.42225.09453
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.12915229
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.673152
X-RAY DIFFRACTIONr_chiral_restr0.1330.2178
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02951
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2570.2715
X-RAY DIFFRACTIONr_nbtor_refined0.2950.2850
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.210.2131
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1960.259
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2910.229
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1261.5785
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.67721193
X-RAY DIFFRACTIONr_scbond_it2.8683605
X-RAY DIFFRACTIONr_scangle_it3.9184.5541
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.457 34 -
Rwork0.307 660 -
obs--100 %

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