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- PDB-3lr9: X-ray photogenerated ferrous horse heart myoglobin, nitrite adduct -

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Basic information

Entry
Database: PDB / ID: 3lr9
TitleX-ray photogenerated ferrous horse heart myoglobin, nitrite adduct
ComponentsMyoglobin
KeywordsOXYGEN TRANSPORT / Myoglobin / Heme / Nitrite / X-ray photogenerated / Iron / Metal-binding / Muscle protein / Transport
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 / NITRITE ION / Myoglobin
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsYi, J. / Orville, A.M. / Richter-Addo, G.B.
CitationJournal: Biochemistry / Year: 2010
Title: Synchrotron X-ray-Induced Photoreduction of Ferric Myoglobin Nitrite Crystals Gives the Ferrous Derivative with Retention of the O-Bonded Nitrite Ligand.
Authors: Yi, J. / Orville, A.M. / Skinner, J.M. / Skinner, M.J. / Richter-Addo, G.B.
History
DepositionFeb 10, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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_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)17,9768
Polymers16,9841
Non-polymers9937
Water2,216123
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.327, 28.691, 62.911
Angle α, β, γ (deg.)90.00, 105.64, 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: horse heart / Source: (natural) Equus caballus (horse) / References: UniProt: P68082
#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-NO2 / NITRITE ION


Mass: 46.005 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: NO2
#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.: 123 / 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: 1.81 Å3/Da / Density % sol: 31.96 %
Crystal growTemperature: 295 K / Method: seeding / pH: 7.4
Details: 2.74 M ammonium sulfate, 100 mM TrisHCl, 1 mM EDTA, pH 7.4, seeding, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 26, 2009
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→26.74 Å / Num. obs: 17892 / % possible obs: 99.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.85 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 15.7
Reflection shellResolution: 1.55→1.61 Å / Redundancy: 2.87 % / Rmerge(I) obs: 0.186 / Mean I/σ(I) obs: 3.9 / % possible all: 95.3

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.5_2)refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry: 1dwr

1dwr


Resolution: 1.55→26.74 Å / SU ML: 0.22 / Isotropic thermal model: isotropic / σ(F): 1.39 / Phase error: 20.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2118 925 5.21 %
Rwork0.1785 --
obs0.1803 17757 98.81 %
all-17892 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.243 Å2 / ksol: 0.389 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.0697 Å2-0 Å20.0485 Å2
2---0.0001 Å20 Å2
3----0.0696 Å2
Refinement stepCycle: LAST / Resolution: 1.55→26.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1194 0 65 123 1382
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061294
X-RAY DIFFRACTIONf_angle_d0.9941748
X-RAY DIFFRACTIONf_dihedral_angle_d16.956461
X-RAY DIFFRACTIONf_chiral_restr0.063179
X-RAY DIFFRACTIONf_plane_restr0.004215
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.63170.28581410.18472281X-RAY DIFFRACTION96
1.6317-1.73390.25281210.18532374X-RAY DIFFRACTION98
1.7339-1.86780.26831180.17952421X-RAY DIFFRACTION99
1.8678-2.05570.23451260.1792420X-RAY DIFFRACTION100
2.0557-2.3530.20541150.16882425X-RAY DIFFRACTION100
2.353-2.96390.20781450.17362428X-RAY DIFFRACTION100
2.9639-26.74810.16881590.15372483X-RAY DIFFRACTION99

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