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- PDB-6ltm: The dimeric structure of G80A/H81A/H82A myoglobin -

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Basic information

Entry
Database: PDB / ID: 6ltm
TitleThe dimeric structure of G80A/H81A/H82A 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
Helix Hairpins - #2100 / Helix Hairpins - #2110 / Helix Hairpins / Myoglobin / Globin domain profile. / Globin / Globin / Helix non-globular / Globin-like superfamily / Special
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Myoglobin
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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 22, 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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
B: Myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9604
Polymers33,7272
Non-polymers1,2332
Water2,396133
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8130 Å2
ΔGint-94 kcal/mol
Surface area14240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.225, 62.841, 81.532
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: 16863.400 Da / Num. of mol.: 2 / 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


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.: 133 / 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: 2.1 Å3/Da / Density % sol: 41.35 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M Tris-HCl buffer, 0.1M sodium acetate, 12.5% (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: BL26B1 / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Oct 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 34523 / % possible obs: 99.9 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 23.3
Reflection shellResolution: 1.65→1.68 Å / Num. unique obs: 1682 / CC1/2: 0.784

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VM9

3vm9


Resolution: 1.65→49.77 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.937 / SU B: 3.779 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.109 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2305 1756 5.1 %RANDOM
Rwork0.19174 ---
obs0.19363 32712 99.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 19.351 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20 Å20 Å2
2---0.1 Å20 Å2
3----0.14 Å2
Refinement stepCycle: 1 / Resolution: 1.65→49.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2380 0 86 133 2599
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.022530
X-RAY DIFFRACTIONr_bond_other_d0.0010.022470
X-RAY DIFFRACTIONr_angle_refined_deg1.9332.0483430
X-RAY DIFFRACTIONr_angle_other_deg0.91635700
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8465304
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.27625.294102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.99515454
X-RAY DIFFRACTIONr_dihedral_angle_4_deg5.012154
X-RAY DIFFRACTIONr_chiral_restr0.1430.2362
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022834
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02566
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_it1.0191.091222
X-RAY DIFFRACTIONr_mcbond_other1.0191.0891221
X-RAY DIFFRACTIONr_mcangle_it1.4791.6321524
X-RAY DIFFRACTIONr_mcangle_other1.4791.6331525
X-RAY DIFFRACTIONr_scbond_it1.8621.3371308
X-RAY DIFFRACTIONr_scbond_other1.8571.3371306
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.9251.8991906
X-RAY DIFFRACTIONr_long_range_B_refined3.9139.4013082
X-RAY DIFFRACTIONr_long_range_B_other3.9019.2253039
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.653→1.696 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 128 -
Rwork0.241 2274 -
obs--94.27 %
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)
14.5704-3.41112.83387.1448-5.12226.9432-0.063-0.2179-0.12630.48570.16390.2637-0.19-0.3165-0.10090.0516-0.00230.02990.0612-0.01220.0431-0.3019-8.29783.7324
22.65680.9436-0.62121.6642-0.44492.4927-0.05650.0120.11620.0230.061-0.0179-0.1514-0.1514-0.00450.02470.0035-0.01230.01590.00310.02358.63311.4003-11.9962
30.5805-1.79370.68167.8137-4.72857.42430.04550.13570.0695-0.5033-0.038-0.05830.14130.078-0.00750.0904-0.0824-0.02760.13220.05190.02158.8825-1.8866-23.2411
40.49560.1995-0.15874.4269-3.03493.6664-0.02310.01750.0332-0.02860.0357-0.0158-0.0732-0.0319-0.01270.01620.0039-0.0050.0611-0.00870.04351.0913-6.2368-9.8584
51.61510.29620.76152.24030.71492.93410.00790.054-0.0564-0.06930.0192-0.05580.05440.0375-0.02710.04710.00410.00710.0420.00470.04713.5379-39.54957.4729
62.51311.03962.13522.16082.35065.6884-0.0550.06840.0369-0.1150.0386-0.0662-0.16460.23550.01640.0471-0.0060.01530.03450.00850.02147.4171-34.36811.7054
70.63310.0285-0.04691.0343-0.69371.6028-0.02120.0831-0.0655-0.0130.05020.00050.0667-0.0596-0.02910.03630.0004-0.00410.0187-0.01540.019-2.9876-41.56020.9471
81.79690.76790.12865.0931-1.69781.92450.0165-0.1618-0.0910.2526-0.0220.1170.1031-0.03960.00550.073-0.00650.02060.01620.00860.0137-3.7931-48.589617.4745
91.1342.378-2.31985.6816-5.82246.0908-0.05650.0790.0115-0.0070.024-0.0354-0.06160.03490.03250.0508-0.02480.01030.03610.00830.033-2.1979-29.1033-0.2366
105.2971.52671.74326.21540.0154.1403-0.09790.2343-0.1039-0.42310.1332-0.31080.04440.1365-0.03530.0738-0.00460.04530.038-0.02160.038510.9145-14.8026-16.6237
113.6751-2.1405-2.77433.88492.33874.51950.0095-0.13480.14170.16240.0446-0.069-0.12740.0246-0.05410.02530.002-0.00060.0095-0.00210.02298.4975-1.5362-3.1581
122.1626-1.2314-1.98044.77683.72766.3412-0.0161-0.0605-0.05520.09470.0803-0.2170.09510.1267-0.06420.035-0.0115-0.02730.02940.01890.053110.9253-14.2166-3.2646
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 21
2X-RAY DIFFRACTION2A22 - 40
3X-RAY DIFFRACTION3A41 - 49
4X-RAY DIFFRACTION4A50 - 86
5X-RAY DIFFRACTION5A87 - 121
6X-RAY DIFFRACTION6A122 - 153
7X-RAY DIFFRACTION7B1 - 39
8X-RAY DIFFRACTION8B40 - 65
9X-RAY DIFFRACTION9B66 - 88
10X-RAY DIFFRACTION10B89 - 102
11X-RAY DIFFRACTION11B103 - 121
12X-RAY DIFFRACTION12B122 - 153

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