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- PDB-2vlz: Crystal structure of peroxymyoglobin generated by cryoradiolytic ... -

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Basic information

Entry
Database: PDB / ID: 2vlz
TitleCrystal structure of peroxymyoglobin generated by cryoradiolytic reduction of myoglobin compound III
ComponentsMYOGLOBIN
KeywordsOXYGEN TRANSPORT / HAEM / IRON / HEME / FERRYL / TRANSPORT / PEROXIDASE / OXYGEN ACTIVATION / RADIOLYTIC- REDUCTION / REACTION INTERMEDIATE / MONOOXYGENASE / METAL-BINDING / MUSCLE PROTEIN / X-RAY-INDUCED-PHOTOREDUCTION
Function / homology
Function and homology information


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 / HYDROGEN PEROXIDE / PEROXIDE ION / Myoglobin
Similarity search - Component
Biological speciesEQUUS CABALLUS (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsHersleth, H.-P. / Gorbitz, C.H. / Andersson, K.K.
Citation
Journal: Biochem.J. / Year: 2008
Title: The Crystal Structure of Peroxymyoglobin Generated Through Cryoradiolytic Reduction of Myoglobin Compound III During Data Collection.
Authors: Hersleth, H.-P. / Hsiao, Y. / Ryde, U. / Gorbitz, C.H. / Andersson, K.K.
#1: Journal: J.Biol.Inorg.Chem. / Year: 2002
Title: An Iron Hydroxide Moiety in the 1.35 A Resolution Structure of Hydrogen Peroxide Derived Myoglobin Compound II at Ph 5.2
Authors: Hersleth, H.-P. / Dalhus, B. / Gorbitz, C.H. / Andersson, K.K.
History
DepositionJan 20, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jun 2, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,08611
Polymers16,9841
Non-polymers1,10310
Water3,117173
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.804, 28.714, 35.452
Angle α, β, γ (deg.)90.00, 105.82, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein MYOGLOBIN


Mass: 16983.514 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-154 / Source method: isolated from a natural source / Details: FE(III)OO2- / FE(II)OO- / Source: (natural) EQUUS CABALLUS (horse) / Organ: HEART / References: UniProt: P68082

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Non-polymers , 6 types, 183 molecules

#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-PER / PEROXIDE ION


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-PEO / HYDROGEN PEROXIDE


Mass: 34.015 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: H2O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 1.48 Å3/Da / Density % sol: 16.2 % / Description: NONE
Crystal growpH: 6.8
Details: BATCH METHOD: 6-12 MG/ML MYOGLOBIN, 80-85% OF THE CRYSTALLIZATION STOCK-SOLUTION (3.9 M AMMONIUM SULPHATE, 0.1 M MOPS, 5-10% OF GLYCEROL PH 5.2)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM1A / Wavelength: 0.8
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 17, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.38→34.16 Å / Num. obs: 20072 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 3.59 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 6.41
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 2.96 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 1.45 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GJN

1gjn


Resolution: 1.5→26.87 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.958 / SU B: 3.325 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.084 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THIS STRUCTURE IS SECOND OF THREE DATASETS COLLECTED ON THE SAME CRYSTAL AS 2VLY AND 2VM0.
RfactorNum. reflection% reflectionSelection details
Rfree0.19 973 4.9 %RANDOM
Rwork0.162 ---
obs0.164 19043 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å20.17 Å2
2--0.2 Å20 Å2
3---0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.5→26.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1199 0 71 173 1443
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0550.0531383
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1662.0051845
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3715168
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.19325.27355
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.52515244
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.603152
X-RAY DIFFRACTIONr_chiral_restr0.070.2192
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021021
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1980.2721
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.2938
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.2130
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1690.261
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1460.235
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6681.5824
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.10721289
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.8783610
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.8564.5556
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.54 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.249 80
Rwork0.207 1380

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