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- PDB-7spf: Crystal structure of sperm whale myoglobin variant sMb5(pCaaF) -

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Basic information

Entry
Database: PDB / ID: 7spf
TitleCrystal structure of sperm whale myoglobin variant sMb5(pCaaF)
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 / Globin / Globin domain profile. / Globin-like superfamily
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / NITRATE ION / OXYGEN MOLECULE / Myoglobin
Similarity search - Component
Biological speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.17 Å
AuthorsBacik, J.P. / Fasan, R. / Ando, N.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CBET-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
Revision 1.3Oct 16, 2024Group: Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag

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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)18,6249
Polymers17,4331
Non-polymers1,1918
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.408, 55.985, 65.855
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Myoglobin


Mass: 17433.320 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

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Non-polymers , 5 types, 119 molecules

#2: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2
#5: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.27 Å3/Da / Density % sol: 45.73 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 160 nl of protein (3.25 mM) in 20 mM Tris pH 8.4, 1 mM EDTA, was mixed with an equal volume of reservoir solution, 2.2 M ammonium sulfate, 0.2 M sodium nitrate.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 13, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.17→35.655 Å / Num. obs: 53004 / % possible obs: 98.7 % / Redundancy: 12.3 % / Biso Wilson estimate: 13.08 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.014 / Net I/σ(I): 25.3
Reflection shellResolution: 1.17→1.19 Å / Rmerge(I) obs: 1.125 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 2284 / CC1/2: 0.673 / Rpim(I) all: 0.396 / % possible all: 86.6

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Processing

Software
NameVersionClassification
XDSdata scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7SPE

7spe


Resolution: 1.17→35.655 Å / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 15.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1721 2607 4.93 %
Rwork0.1469 50324 -
obs0.1482 52931 98.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 71.48 Å2 / Biso mean: 18.0542 Å2 / Biso min: 9.69 Å2
Refinement stepCycle: final / Resolution: 1.17→35.655 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1215 0 74 111 1400
Biso mean--28.4 31.39 -
Num. residues----152
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.17-1.19130.24341220.2202229787
1.1913-1.21420.26151240.1967246693
1.2142-1.2390.22171290.16662628100
1.239-1.26590.16061450.15732634100
1.2659-1.29540.16241230.14262659100
1.2954-1.32780.18431530.13442674100
1.3278-1.36370.19281160.1291261099
1.3637-1.40380.15931260.1242680100
1.4038-1.44910.15691240.11442655100
1.4491-1.50090.11831140.1072695100
1.5009-1.5610.15931460.10852648100
1.561-1.6320.13691420.1107267299
1.632-1.71810.14771450.11922641100
1.7181-1.82570.15991220.13182705100
1.8257-1.96670.14771390.13522677100
1.9667-2.16460.16351650.1322685100
2.1646-2.47770.14551480.1452709100
2.4777-3.12140.17441490.16452730100
3.1214-35.6550.20051750.16792859100

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