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- PDB-9p1f: Myoglobin variant RR22 in complex with imidazole -

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Basic information

Entry
Database: PDB / ID: 9p1f
TitleMyoglobin variant RR22 in complex with imidazole
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 / IMIDAZOLE / Myoglobin
Similarity search - Component
Biological speciesPhyseter macrocephalus (sperm whale)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.1 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)18,5759
Polymers17,3131
Non-polymers1,2628
Water6,359353
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.086, 90.086, 45.167
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-206-

SO4

21A-206-

SO4

31A-585-

HOH

41A-594-

HOH

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Components

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


Mass: 17313.105 Da / Num. of mol.: 1 / Mutation: V29, V33, V64, F68
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-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 353 / 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: 3.08 Å3/Da / Density % sol: 60.06 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 20 mM Tris-HCl pH 8.8, 0.1 mM EDTA, 2.3 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: 1.1→39.09 Å / Num. obs: 162182 / % possible obs: 99.2 % / Redundancy: 8.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.028 / Χ2: 0.76 / Net I/σ(I): 12.5
Reflection shellResolution: 1.1→1.12 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.315 / Num. unique obs: 3691 / CC1/2: 0.873 / Rpim(I) all: 0.198 / Χ2: 0.28

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimless0.7.8data scaling
XDSJan 10, 2022data reduction
PHENIX1.20.1_4487phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.1→39.01 Å / SU ML: 0.0806 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 12.823
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1396 8167 5.04 %
Rwork0.1222 154015 -
obs0.1231 162182 97.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.55 Å2
Refinement stepCycle: LAST / Resolution: 1.1→39.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1209 0 78 353 1640
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00841533
X-RAY DIFFRACTIONf_angle_d1.06212115
X-RAY DIFFRACTIONf_chiral_restr0.0702211
X-RAY DIFFRACTIONf_plane_restr0.0091269
X-RAY DIFFRACTIONf_dihedral_angle_d14.6376577
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1-1.110.23572170.24274169X-RAY DIFFRACTION79.54
1.11-1.130.22472520.21314571X-RAY DIFFRACTION87.36
1.13-1.140.23192600.18614887X-RAY DIFFRACTION92.51
1.14-1.150.18952700.16575059X-RAY DIFFRACTION95.28
1.15-1.170.15022820.15185102X-RAY DIFFRACTION97.11
1.17-1.180.17282710.14585111X-RAY DIFFRACTION97.06
1.18-1.20.1482570.14215173X-RAY DIFFRACTION97.84
1.2-1.220.15092670.13935100X-RAY DIFFRACTION97.3
1.22-1.240.1492590.14165170X-RAY DIFFRACTION98.12
1.24-1.260.14462770.13565190X-RAY DIFFRACTION97.76
1.26-1.280.13582790.14015125X-RAY DIFFRACTION98.17
1.28-1.30.1493120.1365120X-RAY DIFFRACTION98.05
1.3-1.330.13862950.12515191X-RAY DIFFRACTION98.14
1.33-1.360.13192590.12655213X-RAY DIFFRACTION98.4
1.36-1.390.14622310.11745249X-RAY DIFFRACTION98.7
1.39-1.420.1192650.11345211X-RAY DIFFRACTION98.31
1.42-1.450.13012810.11495205X-RAY DIFFRACTION98.58
1.45-1.490.12432650.10885163X-RAY DIFFRACTION99.11
1.49-1.540.12772650.10845232X-RAY DIFFRACTION99.24
1.54-1.590.1072770.10855217X-RAY DIFFRACTION99.1
1.59-1.640.11842780.11045270X-RAY DIFFRACTION99.23
1.64-1.710.12172930.11255238X-RAY DIFFRACTION99.25
1.71-1.790.16182870.11825204X-RAY DIFFRACTION99.38
1.79-1.880.14053090.11625222X-RAY DIFFRACTION99.3
1.88-20.13212680.11455253X-RAY DIFFRACTION99.75
2-2.150.11322670.1075274X-RAY DIFFRACTION99.75
2.15-2.370.12782490.10555288X-RAY DIFFRACTION99.93
2.37-2.710.11283100.11455286X-RAY DIFFRACTION99.91
2.71-3.420.16882850.12165225X-RAY DIFFRACTION99.91
3.42-39.010.1472800.12715297X-RAY DIFFRACTION99.93

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