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- PDB-2z6s: Crystal structure of the oxy myoglobin free from X-ray-induced ph... -

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Basic information

Entry
Database: PDB / ID: 2z6s
TitleCrystal structure of the oxy myoglobin free from X-ray-induced photoreduction
ComponentsMyoglobin
KeywordsOXYGEN BINDING / heme / oxygen transport / Microspectrophotometer / X-ray-induced-photoreduction / Iron / Metal-binding / Muscle protein
Function / homology
Function and homology information


Oxidoreductases; Acting on other nitrogenous compounds as donors / nitrite reductase activity / sarcoplasm / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / removal of superoxide radicals / oxygen carrier activity / peroxidase activity / oxygen binding / heme binding / extracellular exosome / 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 / OXYGEN MOLECULE / Myoglobin
Similarity search - Component
Biological speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsUnno, M. / Kusama, S. / Chen, H. / Shaik, S. / Ikeda-Saito, M.
CitationJournal: J.Am.Chem.Soc. / Year: 2007
Title: Structural Characterization of the Fleeting Ferric Peroxo Species in Myoglobin: Experiment and Theory
Authors: Unno, M. / Chen, H. / Kusama, S. / Shaik, S. / Ikeda-Saito, M.
History
DepositionAug 8, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 6, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)18,0765
Polymers17,2351
Non-polymers8414
Water3,189177
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.338, 30.699, 63.674
Angle α, β, γ (deg.)90.00, 105.46, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Myoglobin


Mass: 17234.951 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Physeter catodon (sperm whale) / References: UniProt: P02185
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / 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: 1.88 Å3/Da / Density % sol: 34.46 %
Crystal growTemperature: 293 K / Method: liquid diffusion / pH: 6
Details: ammonium sulfate, pH6.0, LIQUID DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 0.6 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 15, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6 Å / Relative weight: 1
ReflectionResolution: 1.25→50 Å / Num. obs: 35414 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rsym value: 0.048 / Net I/σ(I): 24.4
Reflection shellResolution: 1.25→1.29 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 2.53 / Rsym value: 0.44 / % possible all: 96.6

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AM6

1am6


Resolution: 1.25→8 Å / Cross valid method: Conjugated gradient / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Shelx
RfactorNum. reflection% reflectionSelection details
Rfree0.187 1765 -Random
Rwork0.136 ---
all0.187 33525 --
obs0.187 33525 99.2 %-
Refinement stepCycle: LAST / Resolution: 1.25→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1297 0 55 177 1529

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