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- PDB-6ls8: The monomeric structure of G80A/H81A/H82A myoglobin -

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Basic information

Entry
Database: PDB / ID: 6ls8
TitleThe monomeric structure of G80A/H81A/H82A myoglobin
ComponentsMyoglobin
KeywordsOXYGEN BINDING / OXYGEN STORAGE
Function / homology
Function and homology information


nitrite reductase activity / Oxidoreductases; Acting on other nitrogenous compounds as donors / oxygen transport / sarcoplasm / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / removal of superoxide radicals / peroxidase activity / oxygen carrier activity / oxygen binding / heme binding / metal ion binding
Similarity search - Function
Myoglobin / Globins / Globin family profile. / Globin-like / Globin / Globin / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Myoglobin
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsNagao, S. / Suda, A. / Kobayashi, H. / 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: Chem Asian J / Year: 2020
Title: Thermodynamic Control of Domain Swapping by Modulating the Helical Propensity in the Hinge Region of Myoglobin.
Authors: Nagao, S. / Suda, A. / Kobayashi, H. / Shibata, N. / Higuchi, Y. / Hirota, S.
History
DepositionJan 17, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 6, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Nov 29, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Myoglobin
C: Myoglobin
E: Myoglobin
G: Myoglobin
I: Myoglobin
K: Myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,87912
Polymers101,1806
Non-polymers3,6996
Water75742
1
A: Myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4802
Polymers16,8631
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint-21 kcal/mol
Surface area7730 Å2
MethodPISA
2
C: Myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4802
Polymers16,8631
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint-20 kcal/mol
Surface area7920 Å2
MethodPISA
3
E: Myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4802
Polymers16,8631
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-19 kcal/mol
Surface area8070 Å2
MethodPISA
4
G: Myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4802
Polymers16,8631
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint-21 kcal/mol
Surface area7990 Å2
MethodPISA
5
I: Myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4802
Polymers16,8631
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint-20 kcal/mol
Surface area7740 Å2
MethodPISA
6
K: Myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4802
Polymers16,8631
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint-20 kcal/mol
Surface area7830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.147, 61.490, 70.323
Angle α, β, γ (deg.)78.83, 81.14, 63.12
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Myoglobin /


Mass: 16863.400 Da / Num. of mol.: 6 / Mutation: G80A/H81A/H82A
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.: 6 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 2.21 Å3/Da / Density % sol: 44.23 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1M Tris-HCl buffer, 15% (w/v) PEG 6000

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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: RAYONIX MX225HE / Detector: CCD / Date: Jun 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 37657 / % possible obs: 98 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 10.1
Reflection shellResolution: 2.3→2.34 Å / Rmerge(I) obs: 0.594 / Num. unique obs: 1876 / CC1/2: 0.554

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WLA

1wla


Resolution: 2.3→43.409 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 30.93
RfactorNum. reflection% reflection
Rfree0.2739 1868 4.97 %
Rwork0.2159 --
obs0.2188 37558 97.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→43.409 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7140 0 258 42 7440
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0117602
X-RAY DIFFRACTIONf_angle_d1.3610344
X-RAY DIFFRACTIONf_dihedral_angle_d9.7564398
X-RAY DIFFRACTIONf_chiral_restr0.0621074
X-RAY DIFFRACTIONf_plane_restr0.0081284
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3001-2.36230.38181730.29432674X-RAY DIFFRACTION95
2.3623-2.43180.33791570.27792693X-RAY DIFFRACTION97
2.4318-2.51020.34281380.27022741X-RAY DIFFRACTION98
2.5102-2.60.32021240.27112758X-RAY DIFFRACTION98
2.6-2.7040.32751490.27062763X-RAY DIFFRACTION98
2.704-2.82710.32111360.25642758X-RAY DIFFRACTION98
2.8271-2.97610.36251340.26422751X-RAY DIFFRACTION98
2.9761-3.16250.30861340.26662778X-RAY DIFFRACTION98
3.1625-3.40660.34721690.25352747X-RAY DIFFRACTION98
3.4066-3.74920.2571620.2142720X-RAY DIFFRACTION98
3.7492-4.29140.2151410.17972763X-RAY DIFFRACTION98
4.2914-5.4050.18931300.16392792X-RAY DIFFRACTION98
5.405-43.40.1971210.14692752X-RAY DIFFRACTION98

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