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- PDB-2vly: Crystal structure of myoglobin compound III (radiation-induced) -

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Basic information

Entry
Database: PDB / ID: 2vly
TitleCrystal structure of myoglobin compound III (radiation-induced)
ComponentsMYOGLOBIN
KeywordsOXYGEN TRANSPORT / OXYGEN STORAGE-TRANSPORT COMPLEX / 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 / OXYGEN MOLECULE / HYDROGEN PEROXIDE / Myoglobin
Similarity search - Component
Biological speciesEQUUS CABALLUS (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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

Downloads & links

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Assembly

Deposited unit
A: MYOGLOBIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0769
Polymers16,9841
Non-polymers1,0938
Water2,900161
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.760, 28.730, 35.440
Angle α, β, γ (deg.)90.00, 105.83, 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)OO- / FE(II)OO / Source: (natural) EQUUS CABALLUS (horse) / Organ: HEART / References: UniProt: P68082

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Non-polymers , 6 types, 169 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-OXY / OXYGEN MOLECULE


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.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-PEO / HYDROGEN PEROXIDE


Mass: 34.015 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H2O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 1.5 Å3/Da / Density % sol: 33.09 % / Description: NONE
Crystal growpH: 6.8
Details: CRYSTALLIZATION CONDITIONS: 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 6.8)

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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: 1.5→21.97 Å / Num. obs: 16256 / % possible obs: 98.1 % / Observed criterion σ(I): 0 / Redundancy: 2.74 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 6.74
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 2.73 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 1.14 / % possible all: 99.5

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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: 1.6→21.94 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.94 / SU B: 4.394 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THIS STRUCTURE IS FIRST OF THREE DATASETS COLLECTED ON THE SAME CRYSTAL AS 2VLZ AND 2VM0.
RfactorNum. reflection% reflectionSelection details
Rfree0.209 785 4.8 %RANDOM
Rwork0.167 ---
obs0.169 15416 97.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.96 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å20.09 Å2
2--0.23 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.6→21.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1199 0 71 161 1431
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0560.0531369
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2482.0091823
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4435164
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.75425.18554
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.62315239
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.109152
X-RAY DIFFRACTIONr_chiral_restr0.080.2188
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021001
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2010.2717
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.2920
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.2128
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1940.278
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1610.228
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7311.5812
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.16421266
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.953608
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.9854.5557
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: 1.6→1.64 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.286 49
Rwork0.218 1117

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