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- PDB-7v5q: The dimeric structure of G80A/H81A/L137E myoglobin -

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Basic information

Entry
Database: PDB / ID: 7v5q
TitleThe dimeric structure of G80A/H81A/L137E myoglobin
ComponentsMyoglobin
KeywordsOXYGEN BINDING / OXYGEN STORAGE
Function / homology
Function and homology information


Oxidoreductases; Acting on other nitrogenous compounds as donors / nitrite reductase activity / oxygen transport / sarcoplasm / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / removal of superoxide radicals / oxygen carrier activity / peroxidase activity / oxygen binding / heme binding / metal ion binding
Similarity search - Function
Myoglobin / Globin / Globin / Globin domain profile. / Globin-like superfamily
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Myoglobin
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 Å
AuthorsXie, C. / Komori, H. / Hirota, S.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP21H02060 Japan
Japan Society for the Promotion of Science (JSPS)JP19K05695 Japan
Japan Science and TechnologyJP20338388 Japan
CitationJournal: Rsc Adv / Year: 2021
Title: Experimental and theoretical study on converting myoglobin into a stable domain-swapped dimer by utilizing a tight hydrogen bond network at the hinge region.
Authors: Xie, C. / Shimoyama, H. / Yamanaka, M. / Nagao, S. / Komori, H. / Shibata, N. / Higuchi, Y. / Shigeta, Y. / Hirota, S.
History
DepositionAug 17, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 29, 2022Provider: 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
B: Myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1264
Polymers33,8932
Non-polymers1,2332
Water5,368298
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8270 Å2
ΔGint-94 kcal/mol
Surface area14340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.460, 63.030, 83.430
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: 16946.426 Da / Num. of mol.: 2 / Mutation: G80A, H81A, L137E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Equus caballus (horse) / Gene: MB / Production host: Escherichia coli (E. coli) / References: UniProt: P68082
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 298 / 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: 2.23 Å3/Da / Density % sol: 44.95 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M Sodium acetate, 0.1 M Tris-HCl, 10% (w/v) PEG 6,000, and 5 % (w/v) PEG 8,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.38→47.32 Å / Num. obs: 62992 / % possible obs: 99.9 % / Redundancy: 1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.131 / Net I/σ(I): 10.9
Reflection shellResolution: 1.38→1.4 Å / Num. unique obs: 3135 / CC1/2: 0.865

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
pointlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VM9

3vm9


Resolution: 1.38→47.32 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.034 / SU ML: 0.053 / Cross valid method: THROUGHOUT / ESU R: 0.065 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20504 3108 4.9 %RANDOM
Rwork0.16481 ---
obs0.16675 59812 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.719 Å2
Baniso -1Baniso -2Baniso -3
1--2.42 Å2-0 Å2-0 Å2
2---1.98 Å20 Å2
3---4.39 Å2
Refinement stepCycle: 1 / Resolution: 1.38→47.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2392 0 86 298 2776
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0132549
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172431
X-RAY DIFFRACTIONr_angle_refined_deg1.4771.6963455
X-RAY DIFFRACTIONr_angle_other_deg1.4651.6215624
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9075306
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.91224.727110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.86515455
X-RAY DIFFRACTIONr_dihedral_angle_4_deg5.007154
X-RAY DIFFRACTIONr_chiral_restr0.0760.2312
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022869
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02541
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.571.2761224
X-RAY DIFFRACTIONr_mcbond_other1.5651222
X-RAY DIFFRACTIONr_mcangle_it1.841.9191527
X-RAY DIFFRACTIONr_mcangle_other1.843.4041527
X-RAY DIFFRACTIONr_scbond_it1.7791.4861325
X-RAY DIFFRACTIONr_scbond_other1.7781323
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.1418.5051927
X-RAY DIFFRACTIONr_long_range_B_refined2.43834.6962996
X-RAY DIFFRACTIONr_long_range_B_other2.40729.9392926
X-RAY DIFFRACTIONr_rigid_bond_restr2.98832549
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.38→1.416 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 213 -
Rwork0.278 4306 -
obs--98.41 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.2728-0.45860.342.283-1.01010.8580.01940.01030.0098-0.1322-0.0312-0.00270.0530.07320.01180.0302-0.01750.02340.0411-0.01710.09864.166719.7972.7891
20.6771-0.76950.34512.105-0.65530.432-0.03140.03730.0839-0.10410.0049-0.1069-0.06570.04410.02650.0619-0.02340.01360.0119-0.01110.09212.482727.6898-0.0503
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 153
2X-RAY DIFFRACTION2B1 - 153

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