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- PDB-1gjn: Hydrogen Peroxide Derived Myoglobin Compound II at pH 5.2 -

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Basic information

Entry
Database: PDB / ID: 1gjn
TitleHydrogen Peroxide Derived Myoglobin Compound II at pH 5.2
ComponentsMYOGLOBIN
KeywordsOXYGEN TRANSPORT / REACTION INTERMEDIATE / HAEM / HEME / OXYGEN ACTIVATION / PEROXIDASE / MONOOXYGENASE / FERRYL / HYDROXY RADICAL
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 / Globin/Protoglobin / Globins / Globin-like / Globin / Globin / Globin domain profile. / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / HYDROXIDE ION / Myoglobin / 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.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.
#1: Journal: Biochim.Biophys.Acta / Year: 1997
Title: A Myoglobin Variant with a Polar Substitution in a Conserved Hydrophobic Cluster in the Heme Binding Pocket
Authors: Maurus, R. / Overall, C.M. / Bogumil, R. / Luo, Y. / Mauk, A.G. / Smith, M. / Brayer, G.D.
#2: Journal: J.Mol.Biol. / Year: 1987
Title: Crystallization and Preliminary Diffraction Data for Horse Heart Metmyoglobin
Authors: Sherwood, C. / Mauk, A.G. / Brayer, G.D.
History
DepositionJul 27, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 1, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 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

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Assembly

Deposited unit
A: MYOGLOBIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8095
Polymers16,9841
Non-polymers8264
Water2,864159
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

#1: Protein MYOGLOBIN


Mass: 16983.514 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: A FE(III)-BONDED HYDROXYL RADICAL / Source: (natural) EQUUS CABALLUS (horse) / Organ: HEART / References: UniProt: P02188, UniProt: P68082*PLUS
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / 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: 31.76 %
Crystal growpH: 5.2
Details: 6-10 MG/ML PROTEIN 3.0 M AMMONIUM SULPHATE, 10.8% GLYCEROL PH 5.2, RT.
Crystal grow
*PLUS
Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
16-10 mg/mlprotein11
23.0 Mammonium sulfate11
310.8 %glycerol11pH5.2

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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 % / Biso Wilson estimate: 11.5 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 22
Reflection shellResolution: 1.35→1.38 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.305 / Mean I/σ(I) obs: 2.7 / % possible all: 85.4
Reflection
*PLUS
Lowest resolution: 21 Å / Num. measured all: 296944
Reflection shell
*PLUS
% possible obs: 85.4 %

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WLA

1wla


Resolution: 1.35→20.79 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2057058.11 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.205 1277 5 %RANDOM
Rwork0.178 ---
obs0.178 25526 94.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 71.5094 Å2 / ksol: 0.438879 e/Å3
Displacement parametersBiso mean: 15.6 Å2
Baniso -1Baniso -2Baniso -3
1--3.55 Å20 Å21.13 Å2
2--2.27 Å20 Å2
3---1.28 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.16 Å0.14 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.35→20.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1199 0 54 159 1412
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d18.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.11
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.35→1.43 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.308 210 5.5 %
Rwork0.259 3575 -
obs--85 %
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg18.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.11

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