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- PDB-8eko: Sperm whale myoglobin mutant L29H F33W F43H (F33W CuBMb) -

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Basic information

Entry
Database: PDB / ID: 8eko
TitleSperm whale myoglobin mutant L29H F33W F43H (F33W CuBMb)
ComponentsMyoglobin
KeywordsOXIDOREDUCTASE / Oxygen reduction reaction / heme-copper oxidase / biosynthetic model
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 / removal of superoxide radicals / peroxidase activity / oxygen carrier activity / oxygen binding / heme binding / metal ion binding
Similarity search - Function
Myoglobin / Globin family profile. / Globin / Globin / Globin-like superfamily
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Myoglobin
Similarity search - Component
Biological speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.34 Å
AuthorsLedray, A.P. / Dwaraknath, S. / Lu, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM141931 United States
CitationJournal: Biochemistry / Year: 2023
Title: Tryptophan Can Promote Oxygen Reduction to Water in a Biosynthetic Model of Heme Copper Oxidases.
Authors: Ledray, A.P. / Dwaraknath, S. / Chakarawet, K. / Sponholtz, M.R. / Merchen, C. / Van Stappen, C. / Rao, G. / Britt, R.D. / Lu, Y.
History
DepositionSep 21, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)17,9062
Polymers17,2901
Non-polymers6161
Water2,504139
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.059, 48.070, 77.739
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Myoglobin /


Mass: 17289.951 Da / Num. of mol.: 1 / Mutation: L29H, F33W, F43H
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 / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2.16 Å3/Da / Density % sol: 43.07 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: F33W CuBMb (1.0 mM) in 100 mM tris pH 8, (pH adjusted H2SO4), was mixed 1:3 with well buffer (0.1 M sodium cacodylate pH 6.5, 0.2 M sodium acetate trihydrate with 30% w/v polyethylene glycol ...Details: F33W CuBMb (1.0 mM) in 100 mM tris pH 8, (pH adjusted H2SO4), was mixed 1:3 with well buffer (0.1 M sodium cacodylate pH 6.5, 0.2 M sodium acetate trihydrate with 30% w/v polyethylene glycol 8000) using the hanging drop method with 300 uL well buffer in the well of the crystallization tray. Crystals obtained by this method were soaked with 10 eq CuSO4 in a mixture of F33W CuBMb and well buffer consistent with the original drop conditions to avoid dissolving the crystals and subsequently with 15eq potassium cyanide, in a mixture of E-F33W-CuBMb and well buffer using pH 7.0 sodium cacodylate

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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: Jun 14, 2019
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: 1.34→35.61 Å / Num. obs: 34356 / % possible obs: 99.91 % / Redundancy: 2 % / Biso Wilson estimate: 9.35 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.1921 / Rrim(I) all: 0.02717 / Net I/σ(I): 19.35
Reflection shellResolution: 1.34→1.39 Å / Redundancy: 2 % / Rmerge(I) obs: 0.05665 / Num. unique obs: 3381 / CC1/2: 0.987 / CC star: 0.997 / Rrim(I) all: 0.08011 / % possible all: 99.71

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FWY

4fwy


Resolution: 1.34→35.61 Å / SU ML: 0.0795 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 13.9685
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1642 1705 4.96 %
Rwork0.1394 32650 -
obs0.1406 34355 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.53 Å2
Refinement stepCycle: LAST / Resolution: 1.34→35.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1217 0 43 139 1399
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00591492
X-RAY DIFFRACTIONf_angle_d0.95892046
X-RAY DIFFRACTIONf_chiral_restr0.0883208
X-RAY DIFFRACTIONf_plane_restr0.0082257
X-RAY DIFFRACTIONf_dihedral_angle_d13.8673219
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.34-1.380.15171550.11572645X-RAY DIFFRACTION99.75
1.38-1.430.17851440.10982697X-RAY DIFFRACTION99.89
1.43-1.480.15121330.11012655X-RAY DIFFRACTION99.93
1.48-1.540.13081290.10772720X-RAY DIFFRACTION99.96
1.54-1.60.14651460.10412700X-RAY DIFFRACTION100
1.6-1.690.16751330.11322693X-RAY DIFFRACTION100
1.69-1.80.15971340.12022694X-RAY DIFFRACTION99.96
1.8-1.930.14881480.12962710X-RAY DIFFRACTION99.97
1.93-2.130.14821270.13192745X-RAY DIFFRACTION100
2.13-2.440.15651430.13882737X-RAY DIFFRACTION99.93
2.44-3.070.16871650.1572749X-RAY DIFFRACTION99.86
3.07-35.610.18731480.16982905X-RAY DIFFRACTION99.84

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