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- PDB-6bmg: Structure of Recombinant Dwarf Sperm Whale Myoglobin (Oxy) -

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Basic information

Entry
Database: PDB / ID: 6bmg
TitleStructure of Recombinant Dwarf Sperm Whale Myoglobin (Oxy)
ComponentsMyoglobin
KeywordsOXYGEN STORAGE / myoglobin / oxygen storage-transport complex / globin
Function / homology
Function and homology information


Oxidoreductases; Acting on other nitrogenous compounds as donors / nitrite reductase activity / sarcoplasm / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / removal of superoxide radicals / oxygen carrier activity / peroxidase activity / oxygen binding / heme binding / extracellular exosome / metal ion binding
Similarity search - Function
Myoglobin / Globins / Globin-like / Globin / Globin / Globin domain profile. / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / : / PROTOPORPHYRIN IX CONTAINING FE / OXYGEN MOLECULE / Myoglobin
Similarity search - Component
Biological speciesKogia sima (dwarf sperm whale)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.88 Å
AuthorsSamuel, P.P. / Miller, M.D. / Xu, W. / Alvarado, S. / Phillips Jr., G.N. / Olson, J.S.
Funding support United States, 2items
OrganizationGrant numberCountry
Robert A. Welch FoundationC-0612 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM115261 United States
Citation
Journal: To Be Published
Title: Structure of Recombinant Dwarf Sperm Whale Myoglobin (Oxy)
Authors: Samuel, P.P. / Miller, M.D. / Xu, W. / Alvarado, S. / Phillips Jr., G.N. / Olson, J.S.
#1: Journal: J. Biol. Chem. / Year: 2015
Title: Apoglobin Stability Is the Major Factor Governing both Cell-free and in Vivo Expression of Holomyoglobin.
Authors: Samuel, P.P. / Smith, L.P. / Phillips, G.N. / Olson, J.S.
#2: Journal: J. Biol. Chem. / Year: 2000
Title: The stabilities of mammalian apomyoglobins vary over a 600-fold range and can be enhanced by comparative mutagenesis.
Authors: Scott, E.E. / Paster, E.V. / Olson, J.S.
History
DepositionNov 14, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 29, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 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 / struct_ncs_dom_lim
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_alt_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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _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_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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.ptnr1_symmetry / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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)37,41821
Polymers34,8082
Non-polymers2,61019
Water5,909328
1
A: Myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,08115
Polymers17,4041
Non-polymers1,67714
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3376
Polymers17,4041
Non-polymers9325
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.995, 85.995, 109.010
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-363-

HOH

21A-369-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 0 through 17 or resid 19...
21(chain B and (resid 0 through 17 or resid 19...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETVALVAL(chain A and (resid 0 through 17 or resid 19...AA0 - 171 - 18
12ALAALATHRTHR(chain A and (resid 0 through 17 or resid 19...AA19 - 3920 - 40
13LYSLYSASPASP(chain A and (resid 0 through 17 or resid 19...AA42 - 4443 - 45
14PHEPHEILEILE(chain A and (resid 0 through 17 or resid 19...AA46 - 10147 - 102
15TYRTYRILEILE(chain A and (resid 0 through 17 or resid 19...AA103 - 111104 - 112
16HISHISALAALA(chain A and (resid 0 through 17 or resid 19...AA113 - 121114 - 122
17PHEPHEALAALA(chain A and (resid 0 through 17 or resid 19...AA123 - 127124 - 128
18GLYGLYTYRTYR(chain A and (resid 0 through 17 or resid 19...AA129 - 151130 - 152
19GLYGLYGLYGLY(chain A and (resid 0 through 17 or resid 19...AA153154
21METMETVALVAL(chain B and (resid 0 through 17 or resid 19...BB0 - 171 - 18
22ALAALATHRTHR(chain B and (resid 0 through 17 or resid 19...BB19 - 3920 - 40
23LYSLYSASPASP(chain B and (resid 0 through 17 or resid 19...BB42 - 4443 - 45
24PHEPHEILEILE(chain B and (resid 0 through 17 or resid 19...BB46 - 10147 - 102
25TYRTYRILEILE(chain B and (resid 0 through 17 or resid 19...BB103 - 111104 - 112
26HISHISALAALA(chain B and (resid 0 through 17 or resid 19...BB113 - 121114 - 122
27PHEPHEALAALA(chain B and (resid 0 through 17 or resid 19...BB123 - 127124 - 128
28GLYGLYTYRTYR(chain B and (resid 0 through 17 or resid 19...BB129 - 151130 - 152
29GLYGLYGLYGLY(chain B and (resid 0 through 17 or resid 19...BB153154

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Myoglobin


Mass: 17404.219 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kogia sima (dwarf sperm whale) / Gene: MB / Plasmid: pVP80K / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P02184

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Non-polymers , 5 types, 347 molecules

#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-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O2
#4: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cd
#5: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 328 / Source method: isolated from a natural source / Formula: H2O

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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: 2.89 Å3/Da / Density % sol: 57.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M sodium HEPES, pH 7.5, 1 M sodium acetate, 0.05 M cadmium sulfate 8/3-hydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 16, 2016 / Details: Adjustable focus K-B pair
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.88→29.29 Å / Num. obs: 33947 / % possible obs: 99.9 % / Redundancy: 6.4 % / Biso Wilson estimate: 28.85 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.042 / Rrim(I) all: 0.107 / Net I/σ(I): 14.5 / Num. measured all: 218789 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.88-1.926.51.39621620.5570.591.518100
9.02-29.295.60.0253700.9990.0110.02797.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XDSdata scaling
Aimless0.5.32data scaling
PHASERphasing
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2MBW

2mbw


Resolution: 1.88→29.286 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.48
RfactorNum. reflection% reflectionSelection details
Rfree0.1903 1693 5.03 %Random
Rwork0.1541 ---
obs0.1558 33885 99.74 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.88→29.286 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2456 0 126 328 2910
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0172680
X-RAY DIFFRACTIONf_angle_d1.2993616
X-RAY DIFFRACTIONf_dihedral_angle_d12.0741552
X-RAY DIFFRACTIONf_chiral_restr0.063371
X-RAY DIFFRACTIONf_plane_restr0.008453
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1738X-RAY DIFFRACTION3.912TORSIONAL
12B1738X-RAY DIFFRACTION3.912TORSIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.88-1.90810.36321380.32922641X-RAY DIFFRACTION100
1.9081-1.93790.28231350.30022620X-RAY DIFFRACTION100
1.9379-1.96960.28241360.27522601X-RAY DIFFRACTION100
1.9696-2.00360.29131400.25342641X-RAY DIFFRACTION100
2.0036-2.040.25791390.24652604X-RAY DIFFRACTION100
2.04-2.07920.26621420.23032601X-RAY DIFFRACTION100
2.0792-2.12170.22731390.20352630X-RAY DIFFRACTION100
2.1217-2.16780.261400.18792657X-RAY DIFFRACTION100
2.1678-2.21820.22271350.18532573X-RAY DIFFRACTION100
2.2182-2.27370.1831390.16252625X-RAY DIFFRACTION99
2.2737-2.33510.18261440.15292589X-RAY DIFFRACTION100
2.3351-2.40380.17511370.14452634X-RAY DIFFRACTION100
2.4038-2.48130.17151410.14042616X-RAY DIFFRACTION100
2.4813-2.570.17621400.13862607X-RAY DIFFRACTION100
2.57-2.67280.17831290.14022641X-RAY DIFFRACTION100
2.6728-2.79440.15991390.13972617X-RAY DIFFRACTION100
2.7944-2.94160.19821380.15242605X-RAY DIFFRACTION100
2.9416-3.12570.19561400.15132605X-RAY DIFFRACTION99
3.1257-3.36670.20371380.14462615X-RAY DIFFRACTION100
3.3667-3.70490.15631400.13142624X-RAY DIFFRACTION100
3.7049-4.23960.1461380.11732605X-RAY DIFFRACTION100
4.2396-5.33620.1811380.11892626X-RAY DIFFRACTION100
5.3362-29.28960.17441400.14822612X-RAY DIFFRACTION100
Refinement TLS params.

S33: 0 Å ° / 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 °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.7443-0.14650.34041.05490.15070.95940.0469-0.0887-0.04080.06410.01130.03440.1424-0.06850.25590.01060.00930.24290.00970.23979.073325.990210.0646
20.49130.1843-0.04791.08310.46510.9732-0.01730.02910.0311-0.19940.1038-0.0852-0.19250.11170.2871-0.02550.01220.26770.00370.271717.170552.9099-6.069
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 153 or resid 201 or resid 202)
2X-RAY DIFFRACTION2chain 'B' and (resid 0 through 153 or resid 201 or resid 202)

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