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- PDB-3ba2: Cyanide bound Chlorin substituted Myoglobin -

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Basic information

Entry
Database: PDB / ID: 3ba2
TitleCyanide bound Chlorin substituted Myoglobin
ComponentsMyoglobin
KeywordsTRANSPORT PROTEIN / Myoglobin / Heme / Chlorin / Cyanide / CN / reconstituted / Iron / Metal-binding / Muscle protein / Oxygen transport / Transport
Function / homology
Function and homology information


Oxidoreductases; Acting on other nitrogenous compounds as donors / nitrite reductase activity / oxygen transport / sarcoplasm / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / removal of superoxide radicals / oxygen carrier activity / peroxidase activity / oxygen binding / heme binding / 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
CYANIDE ION / Fe(III) pyropheophorbide-a methyl ester / Myoglobin
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsYi, J. / Copeland, D.M. / Richter-Addo, G.B.
CitationJournal: To be Published
Title: Cyanide bound Chlorin substituted Myoglobin
Authors: Yi, J. / Copeland, D.M. / West, A.H. / Richter-Addo, G.B.
History
DepositionNov 7, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_chiral / 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)17,9006
Polymers16,9841
Non-polymers9175
Water1,964109
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.123, 30.389, 64.499
Angle α, β, γ (deg.)90.000, 106.010, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Myoglobin


Mass: 16983.514 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Horse Heart / Source: (natural) Equus caballus (horse) / References: UniProt: P68082
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CYN / CYANIDE ION


Mass: 26.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CN
#4: Chemical ChemComp-HKL / Fe(III) pyropheophorbide-a methyl ester


Mass: 602.504 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 35.01 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 3.1M ammonium sulfate, 100mM Tris HCl, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 12, 2007 / Details: Osmic blue
RadiationMonochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→22.35 Å / Num. all: 12043 / Num. obs: 11926 / % possible obs: 99 % / Redundancy: 3.44 % / Rmerge(I) obs: 0.034 / Χ2: 0.98 / Net I/σ(I): 21.9 / Scaling rejects: 310
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
1.8-1.863.330.137.3390811601.0898.9
1.86-1.943.310.1088.6386911591.0497.4
1.94-2.033.390.07611.5405511930.9298.4
2.03-2.133.440.0615.9408911821.0299.6
2.13-2.273.440.05517.2408311801.0299
2.27-2.443.480.04121.6415511910.9199.6
2.44-2.693.510.03824.9425712080.9499.5
2.69-3.083.520.03128.6425612020.9199.6
3.08-3.873.510.02637.3428512030.9699.3
3.87-22.353.420.02242.7432912481.0599.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.343 / Cor.coef. Fo:Fc: 0.703
Highest resolutionLowest resolution
Rotation3 Å22.35 Å
Translation3 Å22.35 Å

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Processing

Software
NameVersionClassificationNB
d*TREK9.2Ddata scaling
MOLREPphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.004data extraction
CrystalCleardata collection
d*TREKdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→22.35 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.923 / SU B: 2.8 / SU ML: 0.089 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.158 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.231 571 4.8 %RANDOM
Rwork0.179 ---
obs0.181 11924 99.01 %-
all-12043 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.551 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.8→22.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1194 0 59 109 1362
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0211285
X-RAY DIFFRACTIONr_angle_refined_deg2.8732.0111744
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9985151
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.31125.09453
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.35715230
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.528152
X-RAY DIFFRACTIONr_chiral_restr0.0920.2181
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02946
X-RAY DIFFRACTIONr_nbd_refined0.2680.2712
X-RAY DIFFRACTIONr_nbtor_refined0.3030.2863
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.281
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2030.256
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1690.217
X-RAY DIFFRACTIONr_mcbond_it0.8991.5750
X-RAY DIFFRACTIONr_mcangle_it1.67421191
X-RAY DIFFRACTIONr_scbond_it2.7083537
X-RAY DIFFRACTIONr_scangle_it4.1294.5553
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 46 -
Rwork0.255 804 -
all-850 -
obs--99.42 %

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