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- PDB-8qbc: Reactive amide intermediate in sperm whale myoglobin mutant H64V V68A -

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Basic information

Entry
Database: PDB / ID: 8qbc
TitleReactive amide intermediate in sperm whale myoglobin mutant H64V V68A
ComponentsMyoglobin
KeywordsOXYGEN STORAGE / amine complex
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
ACETATE ION / ethyl glycinate / PROTOPORPHYRIN IX CONTAINING FE / Myoglobin
Similarity search - Component
Biological speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.23 Å
AuthorsTinzl, M. / Mittl, P.R.E. / Hilvert, D.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Other government Switzerland
CitationJournal: J.Am.Chem.Soc. / Year: 2024
Title: Myoglobin-Catalyzed Azide Reduction Proceeds via an Anionic Metal Amide Intermediate.
Authors: Tinzl, M. / Diedrich, J.V. / Mittl, P.R.E. / Clemancey, M. / Reiher, M. / Proppe, J. / Latour, J.M. / Hilvert, D.
History
DepositionAug 24, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 13, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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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)18,1945
Polymers17,3561
Non-polymers8384
Water4,306239
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1430 Å2
ΔGint-20 kcal/mol
Surface area7780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.842, 47.157, 76.241
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Myoglobin


Mass: 17356.131 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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#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: Chemical ChemComp-GEE / ethyl glycinate


Type: L-peptide linking / Mass: 103.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H9NO2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / 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: 40.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M SPG buffer (succinic acid, sodium dihydrogen phosphate glycine molar ratio 2:7:7) at pH 6.8-7.2 containing 28-32% (w/v) PEG 1500
PH range: 6.8-7.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.000002 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Mar 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000002 Å / Relative weight: 1
ReflectionResolution: 1.23→38.1 Å / Num. obs: 69141 / % possible obs: 99.5 % / Redundancy: 1.9 % / CC1/2: 1 / Net I/σ(I): 1.9
Reflection shellResolution: 1.23→1.274 Å / Num. unique obs: 3019 / CC1/2: 0.471 / % possible all: 72.09

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Processing

Software
NameVersionClassification
PHENIXvrefinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.23→38.1 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 0.19 / Phase error: 19.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.18 3682 4.86 %
Rwork0.1451 --
obs0.1468 40993 93.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.23→38.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1223 0 58 239 1520
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131417
X-RAY DIFFRACTIONf_angle_d1.3011935
X-RAY DIFFRACTIONf_dihedral_angle_d20.207542
X-RAY DIFFRACTIONf_chiral_restr0.086203
X-RAY DIFFRACTIONf_plane_restr0.008244
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.23-1.24580.3602700.3011401X-RAY DIFFRACTION47
1.2458-1.26290.3870.28091763X-RAY DIFFRACTION60
1.2629-1.28090.30581020.27482011X-RAY DIFFRACTION68
1.2809-1.30.26931280.26352348X-RAY DIFFRACTION80
1.3-1.32040.29441480.25132804X-RAY DIFFRACTION95
1.3204-1.3420.28111460.23122884X-RAY DIFFRACTION98
1.342-1.36520.24991490.21412915X-RAY DIFFRACTION99
1.3652-1.390.26211450.21942896X-RAY DIFFRACTION99
1.39-1.41670.28651540.20192949X-RAY DIFFRACTION100
1.4167-1.44560.22251520.18672969X-RAY DIFFRACTION100
1.4456-1.47710.20481460.16732962X-RAY DIFFRACTION100
1.4771-1.51140.18171480.14692925X-RAY DIFFRACTION100
1.5114-1.54920.21041460.13982931X-RAY DIFFRACTION100
1.5492-1.59110.18581520.12932965X-RAY DIFFRACTION100
1.5911-1.63790.17161500.12452923X-RAY DIFFRACTION100
1.6379-1.69080.18691560.12722974X-RAY DIFFRACTION100
1.6908-1.75120.17991540.12322942X-RAY DIFFRACTION100
1.7512-1.82140.16331520.12592946X-RAY DIFFRACTION100
1.8214-1.90420.18381470.12252937X-RAY DIFFRACTION100
1.9042-2.00460.15191440.11522965X-RAY DIFFRACTION100
2.0046-2.13020.15971530.12122933X-RAY DIFFRACTION99
2.1302-2.29470.15451520.11832910X-RAY DIFFRACTION99
2.2947-2.52560.15751520.13652930X-RAY DIFFRACTION100
2.5256-2.89090.1771500.13922969X-RAY DIFFRACTION100
2.8909-3.64190.13071500.13142955X-RAY DIFFRACTION99
3.6419-38.10.18441490.1462916X-RAY DIFFRACTION100

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