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- PDB-3e4n: Carbonmonoxy Sperm Whale Myoglobin at 40 K: Laser off -

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Basic information

Entry
Database: PDB / ID: 3e4n
TitleCarbonmonoxy Sperm Whale Myoglobin at 40 K: Laser off
ComponentsMyoglobin
KeywordsOXYGEN TRANSPORT / haem protein / 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-like / Globin / Globin / Globin domain profile. / 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. / Adachi, S.
History
DepositionAug 12, 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.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

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
Water3,099172
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.312, 30.618, 63.714
Angle α, β, γ (deg.)90.000, 105.740, 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-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-CMO / CARBON MONOXIDE


Mass: 28.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 1.87 Å3/Da / Density % sol: 34.19 % / Mosaicity: 0.602 °
Crystal growTemperature: 293 K / pH: 6
Details: 2.4M Ammonium Sulfate, 10mM Tris-HCl, 100mM Sodium phosphate, pH 6.0, batch, temperature 293K

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Data collection

DiffractionMean temperature: 40 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW14A / Wavelength: 0.827 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 24, 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: 37292 / % possible obs: 94.7 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rmerge(I) obs: 0.033 / Χ2: 0.817 / Net I/σ(I): 15.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.21-1.253.10.20428170.83873
1.25-1.33.70.17137740.72996.2
1.3-1.363.80.13437930.7496.8
1.36-1.433.80.10938130.78397.1
1.43-1.523.80.07738010.79997.5
1.52-1.643.80.05938520.82197.8
1.64-1.813.80.04438660.83598.2
1.81-2.073.80.03238750.87398.6
2.07-2.613.80.02539370.84499.1
2.61-503.60.02237640.91592.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.38 Å21.67 Å
Translation1.38 Å21.67 Å

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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: PDB ENTRY 1MBC

1mbc


Resolution: 1.21→17.15 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.959 / WRfactor Rfree: 0.182 / WRfactor Rwork: 0.142 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.907 / SU B: 1.203 / SU ML: 0.025 / SU R Cruickshank DPI: 0.045 / SU Rfree: 0.046 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.045 / ESU R Free: 0.046 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.182 1873 5 %RANDOM
Rwork0.142 ---
obs0.144 37268 95.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 44.66 Å2 / Biso mean: 13.241 Å2 / Biso min: 6.16 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.03 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.21→17.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1217 0 55 172 1444
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0221304
X-RAY DIFFRACTIONr_angle_refined_deg1.8622.0641767
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9135152
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.1724.25954
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.82515236
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.297154
X-RAY DIFFRACTIONr_chiral_restr0.1350.2182
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02958
X-RAY DIFFRACTIONr_nbd_refined0.3080.2701
X-RAY DIFFRACTIONr_nbtor_refined0.3190.2881
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1230.2123
X-RAY DIFFRACTIONr_metal_ion_refined0.5860.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1450.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1660.236
X-RAY DIFFRACTIONr_mcbond_it2.0281.5759
X-RAY DIFFRACTIONr_mcangle_it2.87121207
X-RAY DIFFRACTIONr_scbond_it3.9133545
X-RAY DIFFRACTIONr_scangle_it5.3774.5560
X-RAY DIFFRACTIONr_rigid_bond_restr2.331304
X-RAY DIFFRACTIONr_sphericity_free9.6633187
X-RAY DIFFRACTIONr_sphericity_bonded5.43831270
LS refinement shellResolution: 1.213→1.244 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.215 116 -
Rwork0.151 2119 -
all-2235 -
obs--78.26 %

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