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- PDB-2zsz: Carbonmonoxy Sperm Whale Myoglobin at 100 K: Laser on [600 min] -

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Basic information

Entry
Database: PDB / ID: 2zsz
TitleCarbonmonoxy Sperm Whale Myoglobin at 100 K: Laser on [600 min]
ComponentsMyoglobin
KeywordsOXYGEN TRANSPORT / haem protein / myoglobin / ligand migration / photodissociation / Heme / Iron / Metal-binding / Muscle protein / Transport
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
CARBON MONOXIDE / PROTOPORPHYRIN IX CONTAINING FE / Myoglobin
Similarity search - Component
Biological speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.21 Å
AuthorsTomita, A. / Sato, T. / Ichiyanagi, K. / Nozawa, S. / Ichikawa, H. / Chollet, M. / Kawai, F. / Park, S.-Y. / Koshihara, S. / Adachi, S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Visualizing breathing motion of internal cavities in concert with ligand migration in myoglobin
Authors: Tomita, A. / Sato, T. / Ichiyanagi, K. / Nozawa, S. / Ichikawa, H. / Chollet, M. / Kawai, F. / Park, S.-Y. / Tsuduki, T. / Yamato, T. / Koshihara, S.Y. / Adachi, S.
History
DepositionSep 18, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 11, 2017Group: Refinement description / Category: software
Revision 1.3Nov 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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)18,0725
Polymers17,2351
Non-polymers8374
Water2,756153
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.350, 30.633, 63.729
Angle α, β, γ (deg.)90.000, 105.370, 90.000
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-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-CMO / CARBON MONOXIDE


Mass: 28.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO
#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.: 153 / 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: 34.43 % / Mosaicity: 0.365 °
Crystal growTemperature: 293 K / Method: batch / pH: 6
Details: 2.4M Ammonium sulfate, 10mM TrisHCl, 100mM Sodium phosphate, pH 6.0, batch, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW14A / Wavelength: 0.827 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 20, 2008
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.827 Å / Relative weight: 1
ReflectionResolution: 1.21→50 Å / Num. obs: 33880 / % possible obs: 85.7 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rmerge(I) obs: 0.052 / Χ2: 0.851 / Net I/σ(I): 10.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.21-1.251.90.44510840.70727.9
1.25-1.32.30.47122010.71556
1.3-1.362.90.49533150.72784.2
1.36-1.433.60.45338200.6997
1.43-1.523.80.28738350.70798.3
1.52-1.643.80.19439130.74898.8
1.64-1.813.80.12239130.7799.2
1.81-2.073.80.06639270.84799.3
2.07-2.613.80.03939771.00699.7
2.61-503.70.0338951.30895.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MBC

1mbc


Resolution: 1.21→19.94 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.949 / WRfactor Rfree: 0.203 / WRfactor Rwork: 0.148 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.884 / SU B: 1.687 / SU ML: 0.034 / SU R Cruickshank DPI: 0.054 / SU Rfree: 0.057 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.054 / ESU R Free: 0.057 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21 1680 5 %RANDOM
Rwork0.153 ---
obs0.156 33863 86.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 43.79 Å2 / Biso mean: 15.62 Å2 / Biso min: 6.53 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å2-0.02 Å2
2---0.02 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.21→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1217 0 55 153 1425
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0221304
X-RAY DIFFRACTIONr_angle_refined_deg2.2292.0641767
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3355152
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.75424.25954
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.19215236
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.62154
X-RAY DIFFRACTIONr_chiral_restr0.1680.2182
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.02958
X-RAY DIFFRACTIONr_nbd_refined0.3060.2674
X-RAY DIFFRACTIONr_nbtor_refined0.3240.2881
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2107
X-RAY DIFFRACTIONr_metal_ion_refined0.2380.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2070.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1710.235
X-RAY DIFFRACTIONr_mcbond_it2.6171.5759
X-RAY DIFFRACTIONr_mcangle_it3.68421207
X-RAY DIFFRACTIONr_scbond_it5.2283545
X-RAY DIFFRACTIONr_scangle_it7.0314.5560
X-RAY DIFFRACTIONr_rigid_bond_restr3.49131304
X-RAY DIFFRACTIONr_sphericity_free11.0683163
X-RAY DIFFRACTIONr_sphericity_bonded6.4331270
LS refinement shellResolution: 1.21→1.241 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 30 -
Rwork0.269 714 -
all-744 -
obs--25.87 %

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