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- PDB-8qba: Sperm whale myoblogin mutant H64V V68A in complex with glycine et... -

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Basic information

Entry
Database: PDB / ID: 8qba
TitleSperm whale myoblogin mutant H64V V68A in complex with glycine ethyl ester
ComponentsMyoglobin
KeywordsOXYGEN STORAGE / 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: 1.39 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

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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)18,1354
Polymers17,3561
Non-polymers7793
Water3,657203
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-20 kcal/mol
Surface area7860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.932, 47.759, 77.442
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.: 1 / 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.: 203 / 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: 2.13 Å3/Da / Density % sol: 42.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: SPG buffer (0.1 M 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 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000002 Å / Relative weight: 1
ReflectionResolution: 1.39→38.7 Å / Num. obs: 74976 / % possible obs: 99.9 % / Redundancy: 2 % / CC1/2: 1 / Net I/σ(I): 17.18
Reflection shellResolution: 1.39→1.44 Å / Num. unique obs: 3002 / CC1/2: 0.684 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.39→38.7 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 22.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.199 3733 6.51 %
Rwork0.1462 --
obs0.1495 30519 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.39→38.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1224 0 54 203 1481
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051379
X-RAY DIFFRACTIONf_angle_d0.8031878
X-RAY DIFFRACTIONf_dihedral_angle_d19.111524
X-RAY DIFFRACTIONf_chiral_restr0.063196
X-RAY DIFFRACTIONf_plane_restr0.004235
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.39-1.410.31031400.30191946X-RAY DIFFRACTION97
1.41-1.430.31531380.27111996X-RAY DIFFRACTION100
1.43-1.440.30261430.27162002X-RAY DIFFRACTION99
1.44-1.470.30921340.25811963X-RAY DIFFRACTION100
1.47-1.490.28871430.2452000X-RAY DIFFRACTION100
1.49-1.510.29351330.22971964X-RAY DIFFRACTION100
1.51-1.540.29091440.21732022X-RAY DIFFRACTION100
1.54-1.560.29031380.20951971X-RAY DIFFRACTION100
1.56-1.590.23341390.1972025X-RAY DIFFRACTION99
1.59-1.620.29531370.18991934X-RAY DIFFRACTION100
1.62-1.650.23161400.17722026X-RAY DIFFRACTION100
1.65-1.690.24031330.1771985X-RAY DIFFRACTION100
1.69-1.730.21461440.15762013X-RAY DIFFRACTION100
1.73-1.770.21921370.15421990X-RAY DIFFRACTION100
1.77-1.820.25031380.14621986X-RAY DIFFRACTION100
1.82-1.870.18611360.14271974X-RAY DIFFRACTION100
1.87-1.930.18561420.13351991X-RAY DIFFRACTION99
1.93-20.18721360.12561986X-RAY DIFFRACTION100
2-2.080.23261410.13542000X-RAY DIFFRACTION100
2.08-2.180.21441360.13081951X-RAY DIFFRACTION99
2.18-2.290.1931420.12972009X-RAY DIFFRACTION100
2.29-2.440.21021310.12921965X-RAY DIFFRACTION99
2.44-2.620.18911340.13212005X-RAY DIFFRACTION99
2.63-2.890.19161330.13181986X-RAY DIFFRACTION99
2.89-3.310.15681410.12731986X-RAY DIFFRACTION99
3.31-4.160.16331410.1151983X-RAY DIFFRACTION99
4.17-38.70.17491390.14711989X-RAY DIFFRACTION100

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