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- PDB-9x07: Serial Femtosecond Crystallography Structure of Myoglobin from eq... -

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Basic information

Entry
Database: PDB / ID: 9x07
TitleSerial Femtosecond Crystallography Structure of Myoglobin from equine skeletal muscle
ComponentsMyoglobin
KeywordsOXYGEN STORAGE / myoglobin / SFX / PAL-XFEL / serial crystallography / serial femtosecond crystallography
Function / homology
Function and homology information


Oxidoreductases; Acting on other nitrogenous compounds as donors / nitrite reductase activity / oxygen transport / sarcoplasm / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / removal of superoxide radicals / oxygen carrier activity / peroxidase activity / oxygen binding / heme binding / 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 speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsNam, K.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2021R1I1A1A01050838 Korea, Republic Of
CitationJournal: Crystals / Year: 2025
Title: Preliminary Serial Femtosecond Crystallography Studies of Myoglobin from Equine Skeletal Muscle
Authors: Park, J. / Park, S. / Nam, K.H.
History
DepositionSep 30, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 12, 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)17,5113
Polymers16,7981
Non-polymers7132
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1290 Å2
ΔGint-31 kcal/mol
Surface area7620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.690, 28.620, 35.590
Angle α, β, γ (deg.)90.00, 107.19, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 16798.334 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Equus caballus (horse)
References: UniProt: P68082, 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.: 1 / Source method: isolated from a natural source / 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.: 54 / 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: 1.84 Å3/Da / Density % sol: 33.32 %
Crystal growTemperature: 298 K / Method: small tubes / Details: ammonium sulfate

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: PAL-XFEL / Beamline: NCI / Wavelength: 1.3051 Å
DetectorType: RAYONIX MX225-HS / Detector: CCD / Date: Aug 20, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3051 Å / Relative weight: 1
ReflectionResolution: 2.3→61.72 Å / Num. obs: 5781 / % possible obs: 99.24 % / Redundancy: 11 % / CC1/2: 0.7261 / CC star: 0.917 / Net I/σ(I): 2.07
Reflection shellResolution: 2.3→2.38 Å / Num. unique obs: 577 / CC1/2: 0.4101 / CC star: 0.7627
Serial crystallography sample deliveryMethod: fixed target

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
CrystFELdata scaling
CrystFELdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→60.84 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3174 560 9.99 %
Rwork0.2468 --
obs0.2541 5607 98.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→60.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1185 0 48 54 1287
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091266
X-RAY DIFFRACTIONf_angle_d1.0271716
X-RAY DIFFRACTIONf_dihedral_angle_d13.479162
X-RAY DIFFRACTIONf_chiral_restr0.049177
X-RAY DIFFRACTIONf_plane_restr0.005212
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.530.36361350.24021241X-RAY DIFFRACTION98
2.53-2.90.32181390.23861238X-RAY DIFFRACTION99
2.9-3.650.2941370.22571263X-RAY DIFFRACTION100
3.65-60.840.31381490.26841305X-RAY DIFFRACTION100

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