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- PDB-6ra6: Ferric murine neuroglobin Gly-loop44-47/F106A mutant -

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Basic information

Entry
Database: PDB / ID: 6ra6
TitleFerric murine neuroglobin Gly-loop44-47/F106A mutant
ComponentsNeuroglobin,Murine neuroglobin mutant,Neuroglobin
KeywordsOXYGEN BINDING / heme protein / globin / gas binding
Function / homology
Function and homology information


Intracellular oxygen transport / GDP-dissociation inhibitor activity / Oxidoreductases; Acting on other nitrogenous compounds as donors / nitrite reductase activity / oxygen transport / oxygen carrier activity / oxygen binding / cellular response to hypoxia / mitochondrial matrix / heme binding ...Intracellular oxygen transport / GDP-dissociation inhibitor activity / Oxidoreductases; Acting on other nitrogenous compounds as donors / nitrite reductase activity / oxygen transport / oxygen carrier activity / oxygen binding / cellular response to hypoxia / mitochondrial matrix / heme binding / metal ion binding / cytosol
Similarity search - Function
: / Globin/Protoglobin / Globin / Globin / Globin domain profile. / Globin-like superfamily
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / DI(HYDROXYETHYL)ETHER / Neuroglobin
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsExertier, C. / Freda, I. / Montemiglio, L.C. / Savino, C. / Vallone, B.
Funding support Italy, 1items
OrganizationGrant numberCountry
European Commission637295 Italy
CitationJournal: Febs J. / Year: 2020
Title: Lack of orientation selectivity of the heme insertion in murine neuroglobin revealed by resonance Raman spectroscopy.
Authors: Milazzo, L. / Exertier, C. / Becucci, M. / Freda, I. / Montemiglio, L.C. / Savino, C. / Vallone, B. / Smulevich, G.
History
DepositionApr 5, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 11, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Neuroglobin,Murine neuroglobin mutant,Neuroglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8029
Polymers16,4651
Non-polymers1,3378
Water1,17165
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2760 Å2
ΔGint-24 kcal/mol
Surface area8210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.587, 74.587, 77.091
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Neuroglobin,Murine neuroglobin mutant,Neuroglobin


Mass: 16464.723 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: For the segment SPEDSL, there was no electronic density, making it impossible to reconstruct.,For the segment SPEDSL, there was no electronic density, making it impossible to reconstruct. ...Details: For the segment SPEDSL, there was no electronic density, making it impossible to reconstruct.,For the segment SPEDSL, there was no electronic density, making it impossible to reconstruct.,For the segment SPEDSL, there was no electronic density, making it impossible to reconstruct.
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ngb / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q9ER97

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Non-polymers , 6 types, 73 molecules

#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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 3.91 Å3/Da / Density % sol: 68.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.8 M ammonium sulfate, 0.1 M Tris pH 8.5, 1% PEG1000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→37.32 Å / Num. obs: 10869 / % possible obs: 100 % / Redundancy: 11.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.114 / Rrim(I) all: 0.12 / Net I/σ(I): 17.35
Reflection shellResolution: 2.3→2.49 Å / Redundancy: 11.31 % / Mean I/σ(I) obs: 2.34 / Num. unique obs: 3693 / CC1/2: 0.81 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6H6I

6h6i


Resolution: 2.3→37.32 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.945 / SU B: 5.727 / SU ML: 0.136 / Cross valid method: THROUGHOUT / ESU R: 0.21 / ESU R Free: 0.185 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21855 534 4.7 %RANDOM
Rwork0.17057 ---
obs0.17298 10869 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 49.83 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20.09 Å20 Å2
2--0.18 Å2-0 Å2
3----0.58 Å2
Refinement stepCycle: LAST / Resolution: 2.3→37.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1115 0 89 65 1269
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0131416
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171318
X-RAY DIFFRACTIONr_angle_refined_deg1.6291.7541952
X-RAY DIFFRACTIONr_angle_other_deg1.2941.6323042
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8965168
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.29119.22177
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.88715228
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.8941516
X-RAY DIFFRACTIONr_chiral_restr0.0810.2159
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021582
X-RAY DIFFRACTIONr_gen_planes_other0.010.02350
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_it4.1644.861604
X-RAY DIFFRACTIONr_mcbond_other4.1114.842602
X-RAY DIFFRACTIONr_mcangle_it5.7347.226759
X-RAY DIFFRACTIONr_mcangle_other5.7317.239760
X-RAY DIFFRACTIONr_scbond_it4.9615.442808
X-RAY DIFFRACTIONr_scbond_other4.9585.446809
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.0517.8981177
X-RAY DIFFRACTIONr_long_range_B_refined9.98855.8741685
X-RAY DIFFRACTIONr_long_range_B_other9.99255.7871677
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 55 -
Rwork0.216 773 -
obs--100 %

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