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- PDB-7ddt: Ancestral myoglobin aMbSe of Enaliarctos relative (imidazol ligand) -

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Entry
Database: PDB / ID: 7ddt
TitleAncestral myoglobin aMbSe of Enaliarctos relative (imidazol ligand)
ComponentsAncestral myoglobin aMbSe
KeywordsOXYGEN STORAGE / Protein evolution / Ancestral protein / Diving adaptation / Seals
Function / homologyPROTOPORPHYRIN IX CONTAINING FE / IMIDAZOLE
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsIsogai, Y. / Imamura, H. / Nakae, S. / Sumi, T. / Takahashi, K. / Shirai, T.
Funding support Japan, 2items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)17H01818 Japan
Japan Agency for Medical Research and Development (AMED)JP20am0101111j0004 Japan
CitationJournal: Iscience / Year: 2021
Title: Common and unique strategies of myoglobin evolution for deep-sea adaptation of diving mammals.
Authors: Isogai, Y. / Imamura, H. / Nakae, S. / Sumi, T. / Takahashi, K.I. / Shirai, T.
History
DepositionOct 29, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 8, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

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Assembly

Deposited unit
A: Ancestral myoglobin aMbSe
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,87512
Polymers17,3251
Non-polymers1,55011
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1070 Å2
ΔGint-18 kcal/mol
Surface area8030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.360, 115.360, 35.000
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

#1: Protein Ancestral myoglobin aMbSe


Mass: 17325.008 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#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 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 3.88 Å3/Da / Density % sol: 68.3 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 2.5M AmSO4, 80mM di-Sodium tartrate, 4% (v/v) methanol, 20mM sodium malonate dibasic monohydrate, 30mM boric acid, 35mM imidazole, pH 9.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 4M / Detector: PIXEL / Date: Nov 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→20 Å / Num. obs: 6086 / % possible obs: 99.7 % / Redundancy: 2 % / Biso Wilson estimate: 30.37 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 15.3
Reflection shellResolution: 2.9→3.06 Å / Rmerge(I) obs: 0.159 / Num. unique obs: 874

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Processing

Software
NameVersionClassification
PHENIX1.17rc5_3630refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIX1.17rc5_3630phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YCE

5yce


Resolution: 2.9→20 Å / SU ML: 0.467 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 17.2406
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2581 285 4.89 %
Rwork0.1879 5538 -
obs0.1915 5823 95.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.45 Å2
Refinement stepCycle: LAST / Resolution: 2.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1213 0 93 27 1333
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01591336
X-RAY DIFFRACTIONf_angle_d1.77951809
X-RAY DIFFRACTIONf_chiral_restr0.0817178
X-RAY DIFFRACTIONf_plane_restr0.0096220
X-RAY DIFFRACTIONf_dihedral_angle_d26.5235482
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.650.34371440.23842679X-RAY DIFFRACTION93.97
3.65-19.980.20551410.15752859X-RAY DIFFRACTION97.56

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