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- PDB-8fdj: Wild-Type Sperm Whale Myoglobin in Complex with Nitrosobenzene -

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Basic information

Entry
Database: PDB / ID: 8fdj
TitleWild-Type Sperm Whale Myoglobin in Complex with Nitrosobenzene
ComponentsMyoglobin
KeywordsOXYGEN STORAGE / myoglobin / nitrosobenzene / iron
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 / Globin domain profile. / Globin / Globin / Globin-like superfamily
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / NITROSOBENZENE / Myoglobin
Similarity search - Component
Biological speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsPowell, S.M. / Wang, B. / Thomas, L.M. / Richter-Addo, G.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
CitationJournal: J.Inorg.Biochem. / Year: 2023
Title: Crystal structural investigations of heme protein derivatives resulting from reactions of aryl- and alkylhydroxylamines with human hemoglobin.
Authors: Powell, S.M. / Wang, B. / Herrera, V.E. / Prather, K.Y. / Nguyen, N.T. / Abucayon, E.G. / Thomas, L.M. / Safo, M.K. / Richter-Addo, G.B.
History
DepositionDec 3, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2023Group: Data collection
Category: chem_comp_atom / chem_comp_bond / pdbx_validate_planes
Item: _pdbx_validate_planes.type
Revision 1.2Oct 25, 2023Group: Refinement description / Category: pdbx_initial_refinement_model / Item: _pdbx_initial_refinement_model.details
Revision 1.3May 1, 2024Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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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)18,1854
Polymers17,3651
Non-polymers8203
Water52229
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.529, 30.049, 64.622
Angle α, β, γ (deg.)90.00, 104.55, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Myoglobin


Mass: 17365.164 Da / Num. of mol.: 1 / Mutation: D122N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physeter catodon (sperm whale) / Gene: MB / Production host: Escherichia coli BL21(DE3) (bacteria) / 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-NBE / NITROSOBENZENE


Mass: 107.110 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5NO / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 34.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 2.56 M ammonium sulfate, 100 mM Tris-HCl, 1 mM EDTA

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Nov 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 13162 / % possible obs: 99.7 % / Redundancy: 3.1 % / CC1/2: 0.9 / Rmerge(I) obs: 0.036 / Net I/σ(I): 29.1
Reflection shellResolution: 1.75→1.78 Å / Rmerge(I) obs: 0.347 / Num. unique obs: 632 / CC1/2: 0.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2MBW

2mbw


Resolution: 1.75→33.44 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.926 / SU B: 3.695 / SU ML: 0.118 / Cross valid method: THROUGHOUT / ESU R: 0.173 / ESU R Free: 0.16 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27612 590 4.6 %RANDOM
Rwork0.22875 ---
obs0.23098 12365 98.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 21.128 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å20 Å20.05 Å2
2--0.16 Å20 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.75→33.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1203 0 56 29 1288
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0151293
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171214
X-RAY DIFFRACTIONr_angle_refined_deg1.5781.7151751
X-RAY DIFFRACTIONr_angle_other_deg1.0191.682825
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9385150
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.36923.15857
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.64915234
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.871154
X-RAY DIFFRACTIONr_chiral_restr0.0810.2156
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021415
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02253
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_it1.7021.94604
X-RAY DIFFRACTIONr_mcbond_other1.6741.937602
X-RAY DIFFRACTIONr_mcangle_it2.3892.901752
X-RAY DIFFRACTIONr_mcangle_other2.3882.903753
X-RAY DIFFRACTIONr_scbond_it2.3082.279689
X-RAY DIFFRACTIONr_scbond_other2.3112.285686
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5873.309994
X-RAY DIFFRACTIONr_long_range_B_refined4.44223.4951530
X-RAY DIFFRACTIONr_long_range_B_other4.43723.4831528
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.796 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.393 51 -
Rwork0.312 765 -
obs--85.99 %

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