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- PDB-3ecz: Carbonmonoxy Sperm Whale Myoglobin at 120 K: Laser on [30 min] -

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Basic information

Entry
Database: PDB / ID: 3ecz
TitleCarbonmonoxy Sperm Whale Myoglobin at 120 K: Laser on [30 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 / 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. / Adachi, S.
History
DepositionSep 2, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 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
Water3,009167
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.425, 30.720, 63.843
Angle α, β, γ (deg.)90.000, 105.540, 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.: 167 / 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: 1.89 Å3/Da / Density % sol: 34.82 %
Description: Structure determined using identical crystal among these related series
Mosaicity: 0.353 °
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: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW14A / Wavelength: 0.827 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 26, 2007
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: 38789 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.052 / Χ2: 1.223 / Net I/σ(I): 13.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.21-1.2530.25633180.73585.5
1.25-1.33.70.22139440.693100
1.3-1.363.70.17439410.724100
1.36-1.433.70.1439250.757100
1.43-1.523.70.10139170.882100
1.52-1.643.70.0839470.988100
1.64-1.813.80.06639541.23100
1.81-2.073.80.05139631.528100
2.07-2.613.80.04439801.99299.9
2.61-503.60.0439002.55195.7

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Processing

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

1mbc


Resolution: 1.21→15.66 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.959 / WRfactor Rfree: 0.179 / WRfactor Rwork: 0.141 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.91 / SU B: 1.16 / SU ML: 0.024 / SU R Cruickshank DPI: 0.043 / SU Rfree: 0.045 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.044 / ESU R Free: 0.045 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.182 1945 5 %RANDOM
Rwork0.143 ---
obs0.145 38771 98.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 42.77 Å2 / Biso mean: 14.571 Å2 / Biso min: 7.36 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å2-0.01 Å2
2--0.01 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.21→15.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1217 0 55 167 1439
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221304
X-RAY DIFFRACTIONr_angle_refined_deg1.7872.0641767
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8785152
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.88124.25954
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.06915236
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.099154
X-RAY DIFFRACTIONr_chiral_restr0.1310.2182
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02958
X-RAY DIFFRACTIONr_nbd_refined0.3080.2680
X-RAY DIFFRACTIONr_nbtor_refined0.3190.2881
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1030.2108
X-RAY DIFFRACTIONr_metal_ion_refined0.5970.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1430.237
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1440.236
X-RAY DIFFRACTIONr_mcbond_it2.0031.5759
X-RAY DIFFRACTIONr_mcangle_it2.86821207
X-RAY DIFFRACTIONr_scbond_it4.1523545
X-RAY DIFFRACTIONr_scangle_it5.5744.5560
X-RAY DIFFRACTIONr_rigid_bond_restr2.65931304
X-RAY DIFFRACTIONr_sphericity_free9.6093172
X-RAY DIFFRACTIONr_sphericity_bonded5.36831270
LS refinement shellResolution: 1.212→1.244 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.216 119 -
Rwork0.161 2360 -
all-2479 -
obs--86.62 %

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