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- PDB-9dth: Tyr-His linked F33Y CuBMb -

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Basic information

Entry
Database: PDB / ID: 9dth
TitleTyr-His linked F33Y CuBMb
ComponentsMyoglobin
KeywordsOXIDOREDUCTASE / oxidase / metalloenzyme
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 / Globin / Globin domain profile. / Globin-like superfamily
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / OXYGEN ATOM / Myoglobin
Similarity search - Component
Biological speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLu, Y. / Liu, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM141931 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2025
Title: A Post-translational Histidine-Histidine Cross-Link Enhances Enzymatic Oxygen Reduction Activity with Greater pH Adaptability.
Authors: Liu, Y. / Vilbert, A.C. / Ghosh, B. / Young, R.P. / Merkley, E.D. / Mukherjee, A. / Phan, L. / Van Stappen, C. / Baghi-Damodaran, A. / Miner, K.D. / Adkins, J. / Cort, J. / Lu, Y.
History
DepositionOct 1, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 15, 2025Provider: repository / Type: Initial release

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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)18,0313
Polymers17,3981
Non-polymers6322
Water1,45981
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.886, 31.407, 70.669
Angle α, β, γ (deg.)90.000, 102.540, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Myoglobin / Nitrite reductase MB / Pseudoperoxidase MB


Mass: 17398.109 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physeter catodon (sperm whale) / Gene: MB / Production host: Escherichia coli (E. coli)
References: UniProt: P02185, Oxidoreductases; Acting on other nitrogenous compounds as donors, Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-O / OXYGEN ATOM


Mass: 15.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.11 Å3/Da / Density % sol: 41.7 % / Description: Long needles, dark-red color
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: F33YCuBMb (2.2 mM) in 20 mM tris(hydroxymethyl)aminomethane (tris) pH 8 (pH adjusted H2SO4), was mixed 1:1 with well buffer (0.2 M sodium acetate, 0.1 M tris hydrochloride pH 8.5, with 30% ...Details: F33YCuBMb (2.2 mM) in 20 mM tris(hydroxymethyl)aminomethane (tris) pH 8 (pH adjusted H2SO4), was mixed 1:1 with well buffer (0.2 M sodium acetate, 0.1 M tris hydrochloride pH 8.5, with 30% polyethylene glycol 4000) using the hanging drop method, with 300 uL well buffer in the well of the crystallization tray, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Oct 29, 2023
RadiationMonochromator: Double-crystal Si(111) and multilayer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→33.08 Å / Num. obs: 13045 / % possible obs: 94.69 % / Redundancy: 3.5 % / Biso Wilson estimate: 26.63 Å2 / CC1/2: 0.985 / CC star: 0.996 / Rmerge(I) obs: 0.08634 / Rpim(I) all: 0.05611 / Rrim(I) all: 0.1035 / Net I/σ(I): 11.85
Reflection shellResolution: 1.8→1.8645 Å / Num. unique obs: 1101 / CC1/2: 0.66

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→33.08 Å / SU ML: 0.2032 / Cross valid method: FREE R-VALUE / σ(F): 2.02 / Phase error: 28.8319
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2208 637 4.85 %
Rwork0.2071 23016 -
obs0.2078 13045 91.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.88 Å2
Refinement stepCycle: LAST / Resolution: 1.8→33.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1219 0 44 81 1344
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111307
X-RAY DIFFRACTIONf_angle_d1.31871774
X-RAY DIFFRACTIONf_chiral_restr0.0841183
X-RAY DIFFRACTIONf_plane_restr0.0065220
X-RAY DIFFRACTIONf_dihedral_angle_d20.3567475
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.880.35191200.33042969X-RAY DIFFRACTION92.51
1.88-1.980.331080.29642924X-RAY DIFFRACTION92.52
1.98-2.110.25151560.25072931X-RAY DIFFRACTION92.93
2.11-2.270.2641760.23792804X-RAY DIFFRACTION91.38
2.27-2.50.23751300.2242629X-RAY DIFFRACTION83.99
2.5-2.860.23591570.22132999X-RAY DIFFRACTION95.15
2.86-3.60.22811630.19692947X-RAY DIFFRACTION94.9
3.6-33.080.16761640.16122813X-RAY DIFFRACTION90.18

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