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- PDB-7ddu: Elephant seal myoglobin esMb -

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Basic information

Entry
Database: PDB / ID: 7ddu
TitleElephant seal myoglobin esMb
ComponentsMyoglobin
KeywordsOXYGEN STORAGE / Protein evolution / Ancestral protein / Diving adaptation / Seals
Function / homology
Function and homology information


oxygen carrier activity / oxygen binding / heme binding / metal ion binding
Similarity search - Function
Myoglobin / Globin/Protoglobin / Globin domain profile. / Globin / Globin / Globin-like superfamily
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Myoglobin
Similarity search - Component
Biological speciesMirounga angustirostris (Northern elephant seal)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Myoglobin
C: Myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,91020
Polymers35,1402
Non-polymers2,77018
Water5,242291
1
A: Myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,95510
Polymers17,5701
Non-polymers1,3859
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint-18 kcal/mol
Surface area8100 Å2
MethodPISA
2
C: Myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,95510
Polymers17,5701
Non-polymers1,3859
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-20 kcal/mol
Surface area8190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.090, 29.350, 75.360
Angle α, β, γ (deg.)90.000, 96.200, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-205-

SO4

21A-315-

HOH

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Components

#1: Protein Myoglobin


Mass: 17570.232 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mirounga angustirostris (Northern elephant seal)
Gene: Mb / Production host: Escherichia coli (E. coli) / References: UniProt: R9S002
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 291 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.04 Å3/Da / Density % sol: 39.56 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 3.1M Ammonium sulfate, 5.5% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 22841 / % possible obs: 99.8 % / Redundancy: 2 % / Biso Wilson estimate: 19.77 Å2 / Rmerge(I) obs: 0.024 / Net I/σ(I): 13.1
Reflection shellResolution: 1.9→2 Å / Rmerge(I) obs: 0.104 / Num. unique obs: 3287

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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: 1.9→19.82 Å / SU ML: 0.189 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.2036
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2049 1101 4.87 %
Rwork0.199 21517 -
obs0.1993 22618 98.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.85 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2478 0 166 291 2935
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01342699
X-RAY DIFFRACTIONf_angle_d1.16143662
X-RAY DIFFRACTIONf_chiral_restr0.2782364
X-RAY DIFFRACTIONf_plane_restr0.0067447
X-RAY DIFFRACTIONf_dihedral_angle_d24.1145973
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.990.34461340.31552617X-RAY DIFFRACTION97.45
1.99-2.090.26211350.25742656X-RAY DIFFRACTION98.24
2.09-2.220.2511350.22132662X-RAY DIFFRACTION98.76
2.22-2.390.21321200.19032675X-RAY DIFFRACTION99.32
2.39-2.630.20531530.20072674X-RAY DIFFRACTION99.02
2.63-3.010.18851420.18942687X-RAY DIFFRACTION99.23
3.01-3.790.16061550.17762706X-RAY DIFFRACTION99.27
3.79-19.820.19561270.17812840X-RAY DIFFRACTION99.23

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