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- PDB-2v1g: Crystal structure of radiation-induced myoglobin compound II - in... -

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Basic information

Entry
Database: PDB / ID: 2v1g
TitleCrystal structure of radiation-induced myoglobin compound II - intermediate H at pH 5.2
ComponentsMYOGLOBIN
KeywordsOXYGEN TRANSPORT / MUSCLE PROTEIN / OXYGEN ACTIVATION / PEROXIDASE / MONOOXYGENASE / METAL-BINDING / REACTION INTERMEDIATE / HEME / FERRYL / TRANSPORT / HAEM / IRON / RADIATION
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 domain profile. / Globin-like / Globin / Globin / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / HYDROXIDE ION / Myoglobin
Similarity search - Component
Biological speciesEQUUS CABALLUS (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsHersleth, H.-P. / Dalhus, B. / Gorbitz, C.H. / Andersson, K.K.
Citation
Journal: J.Biol.Chem. / Year: 2007
Title: Crystallographic and Spectroscopic Studies of Peroxide-Derived Myoglobin Compound II and Occurrence of Protonated Fe(Iv)-O
Authors: Hersleth, H.-P. / Uchida, T. / Rohr, A.K. / Teschner, T. / Schunemann, V. / Kitagawa, T. / Trautwein, A.X. / 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. / Dalhus, B. / Gorbitz, C.H. / Andersson, K.K.
History
DepositionMay 24, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2007Provider: 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)18,0858
Polymers16,9841
Non-polymers1,1027
Water3,423190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.862, 28.650, 35.352
Angle α, β, γ (deg.)90.00, 105.93, 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 / Source method: isolated from a natural source / Details: FE(IV)-OH / Source: (natural) EQUUS CABALLUS (horse) / Organ: HEART / References: UniProt: P68082

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Non-polymers , 5 types, 197 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-OH / HYDROXIDE ION


Mass: 17.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: HO
#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.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 1.44 Å3/Da / Density % sol: 31.74 %
Crystal growpH: 5.2
Details: 6-10 MG/ML PROTEIN, 3.0 M AMMONIUM SULPHATE, 10.8% GLYCEROL PH 5.2, RT.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM1A / Wavelength: 0.873
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 15, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 1.35→21 Å / Num. obs: 26717 / % possible obs: 98.4 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 22
Reflection shellResolution: 1.35→1.38 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 2.7 / % possible all: 85.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1WLA

1wla


Resolution: 1.35→20.81 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.154 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R: 0.073 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THIS IS A RE-REFINEMENT OF 1GJN.
RfactorNum. reflection% reflectionSelection details
Rfree0.174 1277 5 %RANDOM
Rwork0.139 ---
obs0.141 24248 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.23 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å20.7 Å2
2--0.14 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.35→20.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1199 0 72 190 1461
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0520.0541387
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0662.0151859
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1185175
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.54525.27355
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.39615254
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.621152
X-RAY DIFFRACTIONr_chiral_restr0.0720.2197
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021005
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2270.3779
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3230.5928
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2220.5288
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2140.394
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2370.572
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9531.5806
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.4521274
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.3073623
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.314.5573
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

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