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- PDB-5vrt: Nonheme Iron Replacement in a Biosynthetic Nitric Oxide Reductase... -

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Basic information

Entry
Database: PDB / ID: 5vrt
TitleNonheme Iron Replacement in a Biosynthetic Nitric Oxide Reductase Model Performing O2 Reduction to Water: Co-bound FeBMb
ComponentsMyoglobin
KeywordsOXYGEN TRANSPORT / oxygen / reduction / biosynthetic / myoglobin
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 domain 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 speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.995 Å
AuthorsReed, J. / Shi, Y. / Zhu, Q. / Chakraborty, S. / Mirs, E.N. / Petrik, I.D. / Bhagi-Damodaran, A. / Ross, M. / Moenne-Loccoz, P. / Zhang, Y. / Lu, Y.
CitationJournal: J. Am. Chem. Soc. / Year: 2017
Title: Manganese and Cobalt in the Nonheme-Metal-Binding Site of a Biosynthetic Model of Heme-Copper Oxidase Superfamily Confer Oxidase Activity through Redox-Inactive Mechanism.
Authors: Reed, J.H. / Shi, Y. / Zhu, Q. / Chakraborty, S. / Mirts, E.N. / Petrik, I.D. / Bhagi-Damodaran, A. / Ross, M. / Moenne-Loccoz, P. / Zhang, Y. / Lu, Y.
History
DepositionMay 11, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: 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 20, 2019Group: Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
Revision 1.3Oct 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
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9563
Polymers17,2811
Non-polymers6752
Water70339
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.657, 47.328, 76.056
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: 17280.896 Da / Num. of mol.: 1 / Mutation: H29L, H43F, and E68V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physeter catodon (sperm whale) / Gene: MB / Production host: Escherichia coli (E. coli) / References: UniProt: P02185
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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 Å3/Da / Density % sol: 38.58 %
Crystal growTemperature: 277 K / Method: vapor diffusion
Details: 1.5 mM protein solution in 20 mM potassium phosphate pH 7 mixed 1:1 with well buffer (0.2 M sodium acetate trihydrate, 0.1 M sodium 2-(N-morpholino)ethansulfonate (MES) pH 6.5 and 30% w/v PEG 10,000)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.2 Å
DetectorType: RAYONIX MX325HE / Detector: CCD / Date: Jun 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2 Å / Relative weight: 1
ReflectionResolution: 1.995→50 Å / Num. obs: 14401 / % possible obs: 99.3 % / Redundancy: 4.2 % / CC1/2: 0.703 / Net I/σ(I): 19.36

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3K9Z

3k9z


Resolution: 1.995→35.164 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2391 704 4.89 %
Rwork0.1891 --
obs0.1915 14401 76.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.995→35.164 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1207 0 44 39 1290
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051286
X-RAY DIFFRACTIONf_angle_d1.3771737
X-RAY DIFFRACTIONf_dihedral_angle_d19.303469
X-RAY DIFFRACTIONf_chiral_restr0.024180
X-RAY DIFFRACTIONf_plane_restr0.003214
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9954-2.14940.2267850.2191430X-RAY DIFFRACTION41
2.1494-2.36570.27511090.19592228X-RAY DIFFRACTION62
2.3657-2.70790.26851410.19652952X-RAY DIFFRACTION82
2.7079-3.41120.26411900.20723512X-RAY DIFFRACTION98
3.4112-35.16940.21241790.17253575X-RAY DIFFRACTION100

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