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- PDB-7dds: Ancestral myoglobin aMbSp of Puijila Darwini relative -

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Basic information

Entry
Database: PDB / ID: 7dds
TitleAncestral myoglobin aMbSp of Puijila Darwini relative
ComponentsAncestral myoglobin aMbSp
KeywordsOXYGEN STORAGE / Protein evolution / Ancestral protein / Diving adaptation / Seals
Function / homologyPROTOPORPHYRIN IX CONTAINING FE
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ancestral myoglobin aMbSp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7732
Polymers17,1571
Non-polymers6161
Water1,22568
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1150 Å2
ΔGint-20 kcal/mol
Surface area7850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.310, 58.020, 80.200
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Ancestral myoglobin aMbSp


Mass: 17156.768 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


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 1.99 Å3/Da / Density % sol: 38.11 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 1.6M tri-Sodium citrate

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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: May 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 6494 / % possible obs: 99.7 % / Redundancy: 2 % / Biso Wilson estimate: 23.78 Å2 / Rmerge(I) obs: 0.024 / Net I/σ(I): 10.9
Reflection shellResolution: 2.3→2.42 Å / Rmerge(I) obs: 0.037 / Num. unique obs: 930

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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: 2.3→20 Å / SU ML: 0.2996 / Cross valid method: FREE R-VALUE / σ(F): 1.47 / Phase error: 22.8454
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2575 337 5.22 %
Rwork0.1734 6123 -
obs0.1776 6460 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.63 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1209 0 43 68 1320
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01511283
X-RAY DIFFRACTIONf_angle_d1.33351733
X-RAY DIFFRACTIONf_chiral_restr0.0597176
X-RAY DIFFRACTIONf_plane_restr0.0066218
X-RAY DIFFRACTIONf_dihedral_angle_d22.3215473
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.90.29481680.19312983X-RAY DIFFRACTION99.81
2.9-19.970.24011690.16453140X-RAY DIFFRACTION99.64

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