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- PDB-2frj: Nitrosyl Horse Heart Myoglobin, Nitrite/Dithionite Method -

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Basic information

Entry
Database: PDB / ID: 2frj
TitleNitrosyl Horse Heart Myoglobin, Nitrite/Dithionite Method
ComponentsMyoglobin
KeywordsOXYGEN STORAGE/TRANSPORT / myoglobin / nitric oxide / nitrite / NO / NO2 / heme / iron / 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
PROTOPORPHYRIN IX CONTAINING FE / NITRIC OXIDE / Myoglobin
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsCopeland, D.M. / Soares, A.S. / West, A.H. / Richter-Addo, G.B.
CitationJournal: J.Inorg.Biochem. / Year: 2006
Title: Crystal structures of the nitrite and nitric oxide complexes of horse heart myoglobin.
Authors: Copeland, D.M. / Soares, A.S. / West, A.H. / Richter-Addo, G.B.
History
DepositionJan 19, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: Myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8225
Polymers16,9841
Non-polymers8394
Water2,468137
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.497, 28.795, 63.257
Angle α, β, γ (deg.)90.00, 105.96, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Myoglobin /


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


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#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.: 137 / 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: 1.8 Å3/Da / Density % sol: 32.4 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: Ammonium Sulfate, Tris-HCl, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 1, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. all: 30537 / Num. obs: 28869 / % possible obs: 91.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 17.8
Reflection shellResolution: 1.3→1.333 Å / % possible all: 70.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NPF
Resolution: 1.3→9.78 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.817 / SU ML: 0.052 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.073 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22012 1469 5.1 %RANDOM
Rwork0.17731 ---
all0.17954 28983 --
obs0.17954 27400 94.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.71 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20 Å2-0.09 Å2
2--0.32 Å20 Å2
3----0.67 Å2
Refinement stepCycle: LAST / Resolution: 1.3→9.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1194 0 55 137 1386
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221280
X-RAY DIFFRACTIONr_angle_refined_deg1.1892.0621734
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3655151
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.72625.09453
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.70615229
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.331152
X-RAY DIFFRACTIONr_chiral_restr0.0890.2178
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02941
X-RAY DIFFRACTIONr_nbd_refined0.2040.2670
X-RAY DIFFRACTIONr_nbtor_refined0.3060.2863
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1220.292
X-RAY DIFFRACTIONr_metal_ion_refined0.0790.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1610.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1220.230
X-RAY DIFFRACTIONr_mcbond_it2.8512766
X-RAY DIFFRACTIONr_mcangle_it3.66231191
X-RAY DIFFRACTIONr_scbond_it6.3478572
X-RAY DIFFRACTIONr_scangle_it8.05212541
X-RAY DIFFRACTIONr_rigid_bond_restr3.85931338
X-RAY DIFFRACTIONr_sphericity_free8.7793139
X-RAY DIFFRACTIONr_sphericity_bonded6.16631247
LS refinement shellResolution: 1.3→1.333 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.406 114 -
Rwork0.359 1973 -
obs--96.26 %

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