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- PDB-5ych: Ancestral myoglobin aMbWb of Basilosaurus relative (monophyly) -

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Basic information

Entry
Database: PDB / ID: 5ych
TitleAncestral myoglobin aMbWb of Basilosaurus relative (monophyly)
ComponentsAncestral myoglobin aMbWb of Basilosaurus relative (monophyly)
KeywordsOXYGEN STORAGE / Globin / Molecular Archaeology / Ancient protein / Protein evolution / Deep-sea adaptation
Function / homology
Function and homology information


hydrogen peroxide mediated signaling pathway / oxygen carrier activity / oxygen binding / heme binding / metal ion binding
Similarity search - Function
Myoglobin / Globins / Globin family profile. / Globin-like / Globin / Globin / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Myoglobin
Similarity search - Component
Biological speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.354 Å
AuthorsIsogai, Y. / Imamura, H. / Nakae, S. / Sumi, T. / Takahashi, K. / Nakagawa, T. / Tsuneshige, A. / Shirai, T.
Funding support Japan, 2items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)JP17H01818 Japan
Japan Agency for Medical Research and Development17am0101069j0001 Japan
CitationJournal: Sci Rep / Year: 2018
Title: Tracing whale myoglobin evolution by resurrecting ancient proteins.
Authors: Isogai, Y. / Imamura, H. / Nakae, S. / Sumi, T. / Takahashi, K.I. / Nakagawa, T. / Tsuneshige, A. / Shirai, T.
History
DepositionSep 7, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ancestral myoglobin aMbWb of Basilosaurus relative (monophyly)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0504
Polymers17,2411
Non-polymers8093
Water3,207178
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1350 Å2
ΔGint-37 kcal/mol
Surface area7760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.370, 30.430, 63.330
Angle α, β, γ (deg.)90.00, 105.81, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ancestral myoglobin aMbWb of Basilosaurus relative (monophyly)


Mass: 17240.959 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physeter catodon (sperm whale) / Production host: Escherichia coli (E. coli) / References: UniProt: P02185*PLUS
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 178 / Source method: isolated from a natural source / Formula: H2O

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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: 1.85 Å3/Da / Density % sol: 33.45 %
Crystal growTemperature: 291 K / Method: batch mode
Details: 76% saturated ammonium sulfate solution containing 2% (w/v) aMbWb by micro-seeding the crashed SWMb crystal

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.35→22.4 Å / Num. obs: 26897 / % possible obs: 97.3 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.013 / Net I/σ(I): 41.2
Reflection shellResolution: 1.35→1.43 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.052 / Mean I/σ(I) obs: 18.6 / Num. unique obs: 3828 / % possible all: 95.4

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
iMOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YCJ
Resolution: 1.354→22.399 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2073 1351 5.04 %
Rwork0.1707 --
obs0.1726 26832 96.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.354→22.399 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1211 0 53 178 1442
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121314
X-RAY DIFFRACTIONf_angle_d1.2841783
X-RAY DIFFRACTIONf_dihedral_angle_d25.105476
X-RAY DIFFRACTIONf_chiral_restr0.077183
X-RAY DIFFRACTIONf_plane_restr0.006221
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.354-1.40240.2581360.20522448X-RAY DIFFRACTION94
1.4024-1.45860.23721340.18582465X-RAY DIFFRACTION95
1.4586-1.52490.19871160.18012541X-RAY DIFFRACTION95
1.5249-1.60530.21941260.17382492X-RAY DIFFRACTION96
1.6053-1.70580.20951190.16982576X-RAY DIFFRACTION96
1.7058-1.83750.20981450.17782519X-RAY DIFFRACTION97
1.8375-2.02230.21661320.16762575X-RAY DIFFRACTION98
2.0223-2.31470.18591420.15452583X-RAY DIFFRACTION98
2.3147-2.91520.21151320.16482633X-RAY DIFFRACTION99
2.9152-22.40160.2011690.17282649X-RAY DIFFRACTION98

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