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- PDB-3rj6: Crystal Structure of Horse heart ferric myoglobin; K45E/K63E/K96E... -

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Basic information

Entry
Database: PDB / ID: 3rj6
TitleCrystal Structure of Horse heart ferric myoglobin; K45E/K63E/K96E mutant
ComponentsMyoglobin
KeywordsOXYGEN TRANSPORT
Function / homology
Function and homology information


nitrite reductase activity / Oxidoreductases; Acting on other nitrogenous compounds as donors / sarcoplasm / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / oxygen transport / removal of superoxide radicals / peroxidase activity / oxygen carrier activity / oxygen binding / heme binding / metal ion binding
Similarity search - Function
Myoglobin / Globins / Globin family profile. / Globin-like / Globin / Globin / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Myoglobin
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.23 Å
AuthorsSmith, S.M. / Rosenzweig, A.C.
CitationJournal: J.Am.Chem.Soc. / Year: 2016
Title: Charge-Disproportionation Symmetry Breaking Creates a Heterodimeric Myoglobin Complex with Enhanced Affinity and Rapid Intracomplex Electron Transfer.
Authors: Trana, E.N. / Nocek, J.M. / Woude, J.V. / Span, I. / Smith, S.M. / Rosenzweig, A.C. / Hoffman, B.M.
History
DepositionApr 15, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2020Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Myoglobin
B: Myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3926
Polymers33,9672
Non-polymers1,4254
Water3,891216
1
A: Myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6963
Polymers16,9831
Non-polymers7132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6963
Polymers16,9831
Non-polymers7132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)28.341, 123.565, 34.986
Angle α, β, γ (deg.)90.00, 89.73, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Myoglobin /


Mass: 16983.316 Da / Num. of mol.: 2 / Mutation: K45E, K63E, K96E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Equus caballus (horse) / Gene: MB / Production host: Escherichia coli (E. coli) / References: UniProt: P68082
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 216 / 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: 1.8 Å3/Da / Density % sol: 31.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.3
Details: 3.3 M ammonium sulfate, 0.02 M tris, 0.001 M EDTA, , pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.07809 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 13, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07809 Å / Relative weight: 1
ReflectionResolution: 1.23→61.78 Å / Num. all: 66112 / Num. obs: 64506 / % possible obs: 97.57 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.6 %
Reflection shellResolution: 1.23→1.261 Å / % possible all: 92.85

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.23→61.78 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.952 / SU B: 0.618 / SU ML: 0.029 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.053 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19737 3442 5.1 %RANDOM
Rwork0.17299 ---
obs0.17425 64506 97.57 %-
all-66112 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.034 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å20 Å2-0.21 Å2
2---0.79 Å20 Å2
3---0.34 Å2
Refinement stepCycle: LAST / Resolution: 1.23→61.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2394 0 96 216 2706
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0222744
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.342.0563750
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3015344
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.45525.517116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.86615493
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.146154
X-RAY DIFFRACTIONr_chiral_restr0.1360.2384
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0212094
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1931.51628
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.87722616
X-RAY DIFFRACTIONr_scbond_it3.2831116
X-RAY DIFFRACTIONr_scangle_it4.2654.51134
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.23→1.261 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 228 -
Rwork0.226 4535 -
obs--92.85 %

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