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- PDB-2zsr: Carbonmonoxy Sperm Whale Myoglobin at 120 K: Laser on [450 min] -

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Basic information

Entry
Database: PDB / ID: 2zsr
TitleCarbonmonoxy Sperm Whale Myoglobin at 120 K: Laser on [450 min]
ComponentsMyoglobin
KeywordsOXYGEN TRANSPORT / haem protein / myoglobin / ligand migration / photodissociation / Heme / Iron / Metal-binding / Muscle protein / Transport
Function / homology
Function and homology information


oxygen carrier activity / oxygen binding / heme binding / metal ion binding
Similarity search - Function
Myoglobin / Globin family profile. / Globins / Globin / Globin / Globin-like / 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
DepositionSep 17, 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

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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)18,0725
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)34.446, 30.721, 63.891
Angle α, β, γ (deg.)90.000, 105.570, 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 / Heme B


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


Mass: 28.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / 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: 34.9 %
Description: Structure determined using identical crystal among these related series
Mosaicity: 0.399 °
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 27, 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: 38766 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.049 / Χ2: 0.967 / Net I/σ(I): 11.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.21-1.252.80.36232810.73884.9
1.25-1.33.60.32239530.63899.9
1.3-1.363.70.25339300.687100
1.36-1.433.70.19539160.703100
1.43-1.523.70.12739150.763100
1.52-1.643.70.09439430.809100
1.64-1.813.80.06939540.915100
1.81-2.073.80.04939581.117100
2.07-2.613.80.03939801.415100
2.61-503.60.03339361.77996.7

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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: PDB ENTRY 1MBC
Resolution: 1.21→17.22 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.958 / WRfactor Rfree: 0.18 / WRfactor Rwork: 0.141 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.909 / SU B: 1.22 / SU ML: 0.025 / SU R Cruickshank DPI: 0.043 / SU Rfree: 0.045 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.043 / ESU R Free: 0.045 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.183 1950 5 %RANDOM
Rwork0.142 ---
obs0.144 38747 98.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 48.2 Å2 / Biso mean: 15.001 Å2 / Biso min: 7.03 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å2-0.01 Å2
2--0.01 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.21→17.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1217 0 55 167 1439
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0221304
X-RAY DIFFRACTIONr_angle_refined_deg1.8632.0641767
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8735152
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.68524.25954
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.20415236
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.73154
X-RAY DIFFRACTIONr_chiral_restr0.1340.2182
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02958
X-RAY DIFFRACTIONr_nbd_refined0.3070.2672
X-RAY DIFFRACTIONr_nbtor_refined0.320.2877
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.110.2113
X-RAY DIFFRACTIONr_metal_ion_refined0.5330.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1550.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1390.236
X-RAY DIFFRACTIONr_mcbond_it2.1261.5759
X-RAY DIFFRACTIONr_mcangle_it3.07921207
X-RAY DIFFRACTIONr_scbond_it4.5743545
X-RAY DIFFRACTIONr_scangle_it6.0354.5560
X-RAY DIFFRACTIONr_rigid_bond_restr3.13731304
X-RAY DIFFRACTIONr_sphericity_free9.9593171
X-RAY DIFFRACTIONr_sphericity_bonded5.67731270
LS refinement shellResolution: 1.212→1.243 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 116 -
Rwork0.2 2214 -
all-2330 -
obs--81.61 %

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