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- PDB-7dgo: The Zn-bound dimeric structure of K79H/G80A/H81A myoglobin -

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Basic information

Entry
Database: PDB / ID: 7dgo
TitleThe Zn-bound dimeric structure of K79H/G80A/H81A myoglobin
ComponentsMyoglobin
KeywordsOXYGEN BINDING / OXYGEN STORAGE
Function / homology
Function and homology information


nitrite reductase activity / Oxidoreductases; Acting on other nitrogenous compounds as donors / sarcoplasm / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / oxygen transport / removal of superoxide radicals / peroxidase activity / oxygen carrier activity / oxygen binding / heme binding / metal ion binding
Similarity search - Function
Myoglobin / Globin family profile. / Globin / Globin / Globin-like superfamily
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / OXYGEN ATOM / Myoglobin
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsNagao, S. / Idomoto, A. / Shibata, N. / Higuchi, Y. / Hirota, S.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP16K17935 Japan
Japan Society for the Promotion of Science (JSPS)JP19K05695 Japan
Japan Society for the Promotion of Science (JSPS)JP26288080 Japan
CitationJournal: J.Inorg.Biochem. / Year: 2021
Title: Rational design of metal-binding sites in domain-swapped myoglobin dimers.
Authors: Nagao, S. / Idomoto, A. / Shibata, N. / Higuchi, Y. / Hirota, S.
History
DepositionNov 12, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 17, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed
Revision 1.2Nov 29, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Myoglobin
B: Myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,47111
Polymers33,8792
Non-polymers1,5929
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9130 Å2
ΔGint-289 kcal/mol
Surface area14310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.738, 63.141, 79.466
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: 0 / Auth seq-ID: 1 - 153 / Label seq-ID: 1 - 153

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Myoglobin /


Mass: 16939.438 Da / Num. of mol.: 2 / Mutation: K79H, G80A, H81A
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 / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-O / OXYGEN ATOM / Oxygen


Mass: 15.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 1.95 Å3/Da / Density % sol: 37.01 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M Sodium acetate, 0.1 M Tris-HCl, 25% (w/v) PEG 6,000

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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: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→43.98 Å / Num. obs: 18568 / % possible obs: 100 % / Redundancy: 6.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.068 / Net I/σ(I): 17.7
Reflection shellResolution: 2→2.05 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.732 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1354 / CC1/2: 0.772 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VM9

3vm9


Resolution: 2→43.98 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.926 / SU B: 5.539 / SU ML: 0.153 / Cross valid method: THROUGHOUT / ESU R: 0.263 / ESU R Free: 0.208 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26504 946 5.1 %RANDOM
Rwork0.21305 ---
obs0.21575 17575 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.233 Å2
Baniso -1Baniso -2Baniso -3
1-1.28 Å20 Å2-0 Å2
2---1.07 Å20 Å2
3----0.21 Å2
Refinement stepCycle: 1 / Resolution: 2→43.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2392 0 93 94 2579
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0132610
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172416
X-RAY DIFFRACTIONr_angle_refined_deg1.521.6993541
X-RAY DIFFRACTIONr_angle_other_deg1.3171.6185615
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.1625.111315
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.81624.513113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.98415452
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.391154
X-RAY DIFFRACTIONr_chiral_restr0.0760.2314
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023061
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02527
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_it2.3693.3791242
X-RAY DIFFRACTIONr_mcbond_other2.3683.3731240
X-RAY DIFFRACTIONr_mcangle_it3.4865.061556
X-RAY DIFFRACTIONr_mcangle_other3.4835.061556
X-RAY DIFFRACTIONr_scbond_it3.1643.6471368
X-RAY DIFFRACTIONr_scbond_other3.153.651361
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.8465.2971985
X-RAY DIFFRACTIONr_long_range_B_refined6.18339.022981
X-RAY DIFFRACTIONr_long_range_B_other6.158392976
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 4402 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.14 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 57 -
Rwork0.28 1292 -
obs--99.78 %

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