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- PDB-9p1e: Myoglobin variant RR22 -

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Basic information

Entry
Database: PDB / ID: 9p1e
TitleMyoglobin variant RR22
ComponentsMyoglobin
KeywordsOXYGEN STORAGE / METALLOPROTEIN / MYOGLOBIN / HEME
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 / Myoglobin
Similarity search - Component
Biological speciesPhyseter macrocephalus (sperm whale)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.15 Å
AuthorsDayananda, T. / Jenkins, J.L. / Fasan, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM098628 United States
CitationJournal: Nat Commun / Year: 2026
Title: Computational design of generalist cyclopropanases with stereodivergent selectivity
Authors: Shen, Z. / Siriboe, M.G. / Ren, X. / Dayananda, T. / Jenkins, J.L. / Khare, S.D. / Fasan, R.
History
DepositionJun 9, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 4, 2026Provider: repository / Type: Initial release

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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)18,6029
Polymers17,3131
Non-polymers1,2898
Water7,026390
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.311, 90.311, 45.279
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number168
Space group name H-MP6
Space group name HallP6
Components on special symmetry positions
IDModelComponents
11A-608-

HOH

21A-617-

HOH

31A-664-

HOH

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Components

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


Mass: 17313.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physeter macrocephalus (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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 390 / 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: 3.1 Å3/Da / Density % sol: 60.35 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 20 mM Tris-HCl pH 9.6, 0.1 mM EDTA, 2.2 M Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97001 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 27, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97001 Å / Relative weight: 1
ReflectionResolution: 1.15→31.97 Å / Num. obs: 142011 / % possible obs: 99.9 % / Redundancy: 9.3 % / CC1/2: 0.981 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.029 / Χ2: 0.69 / Net I/σ(I): 11.9
Reflection shellResolution: 1.15→1.17 Å / Redundancy: 5 % / Rmerge(I) obs: 0.37 / Num. unique obs: 3581 / CC1/2: 0.898 / Rpim(I) all: 0.178 / Χ2: 0.33

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimless0.7.8data scaling
XDSJan 10, 2022data reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.15→31.97 Å / SU ML: 0.0745 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 11.6689
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1362 7164 5.04 %
Rwork0.1135 134847 -
obs0.1146 142011 96.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.05 Å2
Refinement stepCycle: LAST / Resolution: 1.15→31.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1209 0 78 390 1677
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00741453
X-RAY DIFFRACTIONf_angle_d1.01281996
X-RAY DIFFRACTIONf_chiral_restr0.0712201
X-RAY DIFFRACTIONf_plane_restr0.0092247
X-RAY DIFFRACTIONf_dihedral_angle_d15.0076544
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.15-1.160.19672290.22594200X-RAY DIFFRACTION89.87
1.16-1.180.23722340.18354345X-RAY DIFFRACTION94.51
1.18-1.190.20242320.16294431X-RAY DIFFRACTION94.47
1.19-1.210.182260.15594427X-RAY DIFFRACTION95.56
1.21-1.220.14382340.13944420X-RAY DIFFRACTION95.29
1.22-1.240.17372260.13324443X-RAY DIFFRACTION95.6
1.24-1.260.14192140.12254427X-RAY DIFFRACTION95.45
1.26-1.280.16472470.12094438X-RAY DIFFRACTION95.98
1.28-1.30.13672510.12264485X-RAY DIFFRACTION95.48
1.3-1.320.13692790.12034408X-RAY DIFFRACTION96.42
1.32-1.340.13622220.11824454X-RAY DIFFRACTION95.86
1.34-1.360.13312320.11844500X-RAY DIFFRACTION96.55
1.36-1.390.14112050.11464546X-RAY DIFFRACTION96.41
1.39-1.420.12392310.11164479X-RAY DIFFRACTION96.4
1.42-1.450.11332310.10624463X-RAY DIFFRACTION96.7
1.45-1.480.10582330.09774537X-RAY DIFFRACTION97.11
1.48-1.520.13052270.09994532X-RAY DIFFRACTION96.96
1.52-1.560.1142760.09934481X-RAY DIFFRACTION96.92
1.56-1.610.1112060.09834563X-RAY DIFFRACTION97.61
1.61-1.660.1242750.10274502X-RAY DIFFRACTION97.65
1.66-1.720.13452350.10034520X-RAY DIFFRACTION97.58
1.72-1.790.11392480.10924539X-RAY DIFFRACTION97.67
1.79-1.870.12742680.10644548X-RAY DIFFRACTION97.99
1.87-1.970.13122320.10724575X-RAY DIFFRACTION98.22
1.97-2.090.13872420.10284554X-RAY DIFFRACTION98.7
2.09-2.250.12482300.10024607X-RAY DIFFRACTION98.51
2.25-2.480.11922250.09954603X-RAY DIFFRACTION98.71
2.48-2.840.1252700.11394573X-RAY DIFFRACTION98.78
2.84-3.570.14742530.10974613X-RAY DIFFRACTION99.41
3.57-31.970.15312510.12624634X-RAY DIFFRACTION99.41

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