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- PDB-7spe: Crystal structure of sperm whale myoglobin variant sMb5(O2beY) -

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Basic information

Entry
Database: PDB / ID: 7spe
TitleCrystal structure of sperm whale myoglobin variant sMb5(O2beY)
ComponentsMyoglobin
KeywordsOXYGEN STORAGE / HEME / METALLOPROTEIN / THIOETHER / MYOGLOBIN
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 domain 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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsBacik, J.P. / Fasan, R. / Ando, N.
Funding support United States, 1items
OrganizationGrant numberCountry
Not fundedCBET-1929256 United States
CitationJournal: Biochemistry / Year: 2022
Title: Tuning Enzyme Thermostability via Computationally Guided Covalent Stapling and Structural Basis of Enhanced Stabilization.
Authors: Iannuzzelli, J.A. / Bacik, J.P. / Moore, E.J. / Shen, Z. / Irving, E.M. / Vargas, D.A. / Khare, S.D. / Ando, N. / Fasan, R.
History
DepositionNov 2, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
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)18,4216
Polymers17,4201
Non-polymers1,0015
Water2,522140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.436, 54.339, 76.583
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Myoglobin


Mass: 17420.322 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
#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-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 140 / 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: 2.06 Å3/Da / Density % sol: 40.19 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 160 nl of protein (1 mM) in 20 mM Tris pH 8.4, 1 mM EDTA, was mixed with an equal volume of reservoir solution, 3.0 M ammonium sulfate, 10% w/v glycerol.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: DECTRIS PILATUS3 R 300K / Detector: PIXEL / Date: Oct 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. obs: 14910 / % possible obs: 89.9 % / Redundancy: 2.9 % / Biso Wilson estimate: 15.75 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.074 / Net I/σ(I): 10.5
Reflection shellResolution: 1.7→1.73 Å / Rmerge(I) obs: 0.578 / Num. unique obs: 430 / CC1/2: 0.634 / Rpim(I) all: 0.542

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6M8F

6m8f


Resolution: 1.7→27.192 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2117 738 4.99 %
Rwork0.1842 14059 -
obs0.1857 14797 90.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 48.74 Å2 / Biso mean: 16.3581 Å2 / Biso min: 5.88 Å2
Refinement stepCycle: final / Resolution: 1.7→27.192 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1205 0 63 140 1408
Biso mean--18.27 25.5 -
Num. residues----154
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7-1.83130.30351000.2605206167
1.8313-2.01550.29161400.2176279891
2.0155-2.3070.21371610.1743303098
2.307-2.90610.20251650.1787304598
2.9061-27.190.18811720.1723312596

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