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- PDB-9dti: F33Y CuBMb -

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Basic information

Entry
Database: PDB / ID: 9dti
TitleF33Y 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 / DI(HYDROXYETHYL)ETHER / Myoglobin
Similarity search - Component
Biological speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.681 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
Revision 1.1Oct 29, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2525
Polymers17,3981
Non-polymers8544
Water4,918273
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.139, 32.009, 69.655
Angle α, β, γ (deg.)90.000, 102.720, 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

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 277 molecules

#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-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.45 Å3/Da / Density % sol: 49.72 % / Description: Long needles, brown color
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: F33Y CuBMb (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: F33Y CuBMb (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: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 8, 2024
RadiationMonochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.681→38.18 Å / Num. obs: 16635 / % possible obs: 85.29 % / Redundancy: 3.1 % / Biso Wilson estimate: 17.13 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.05966 / Rpim(I) all: 0.03978 / Rrim(I) all: 0.0721 / Net I/σ(I): 14
Reflection shellResolution: 1.681→1.741 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 1.66 / Num. unique obs: 584 / CC1/2: 0.76 / CC star: 0.929 / Rpim(I) all: 0.3582 / Rrim(I) all: 0.5398 / % possible all: 30.67

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.681→38.18 Å / Cross valid method: FREE R-VALUE / σ(F): 1.34
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1921 837 5.09 %
Rwork0.1705 28890 -
obs0.1716 16635 81.14 %
Solvent computationSolvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.33 Å2
Refinement stepCycle: LAST / Resolution: 1.681→38.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1227 0 56 273 1556
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011369
X-RAY DIFFRACTIONf_angle_d1.05871861
X-RAY DIFFRACTIONf_chiral_restr0.0626191
X-RAY DIFFRACTIONf_plane_restr0.01231
X-RAY DIFFRACTIONf_dihedral_angle_d18.6931506
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.681-1.730.4024570.3302760X-RAY DIFFRACTION24.38
1.74-1.80.38361050.28681755X-RAY DIFFRACTION53.98
1.8-1.870.2881280.24662345X-RAY DIFFRACTION72.27
1.87-1.950.27271230.23492709X-RAY DIFFRACTION83.79
1.95-2.060.21371880.19183014X-RAY DIFFRACTION93.11
2.06-2.190.21581660.1873027X-RAY DIFFRACTION93.61
2.19-2.350.20131330.17462977X-RAY DIFFRACTION91.9
2.35-2.590.21151940.16543069X-RAY DIFFRACTION95.33
2.59-2.970.18711600.16763141X-RAY DIFFRACTION96.15
2.97-3.740.13461290.14273007X-RAY DIFFRACTION92.4
3.74-38.180.15021670.14243086X-RAY DIFFRACTION94.92

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