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- PDB-6h5z: Ferric murine neuroglobin F106A mutant -

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Basic information

Entry
Database: PDB / ID: 6h5z
TitleFerric murine neuroglobin F106A mutant
ComponentsNeuroglobin
KeywordsOXYGEN BINDING / heme protein / gas sensing
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
1,4-DIETHYLENE DIOXIDE / PROTOPORPHYRIN IX CONTAINING FE / Neuroglobin
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsExertier, C. / Vallone, B. / Savino, C. / Freda, I. / Montemiglio, L.C. / Cerutti, G. / Scaglione, A. / Parisi, G.
Funding support Italy, 1items
OrganizationGrant numberCountry
European Union637295 Italy
CitationJournal: Sci Rep / Year: 2019
Title: Proximal and distal control for ligand binding in neuroglobin: role of the CD loop and evidence for His64 gating.
Authors: Exertier, C. / Milazzo, L. / Freda, I. / Montemiglio, L.C. / Scaglione, A. / Cerutti, G. / Parisi, G. / Anselmi, M. / Smulevich, G. / Savino, C. / Vallone, B.
History
DepositionJul 25, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1454
Polymers16,3451
Non-polymers8013
Water1,22568
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-32 kcal/mol
Surface area7610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.733, 87.733, 113.625
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-341-

HOH

21A-356-

HOH

31A-361-

HOH

41A-364-

HOH

51A-368-

HOH

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Components

#1: Protein Neuroglobin


Mass: 16344.528 Da / Num. of mol.: 1 / Mutation: F106A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ngb / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: Q9ER97
#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-DIO / 1,4-DIETHYLENE DIOXIDE


Mass: 88.105 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 2.48 Å3/Da / Density % sol: 50.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.6 M ammonium sulfate, 0.1 M MES pH 6.5, 10% 1,4-dioxane

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 15824 / % possible obs: 99.9 % / Redundancy: 10.4 % / CC1/2: 1 / Net I/σ(I): 33.6
Reflection shellResolution: 1.8→1.91 Å / CC1/2: 0.872

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Q1F

1q1f


Resolution: 1.8→45.54 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.955 / SU B: 6.117 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.427 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20918 780 4.9 %RANDOM
Rwork0.15224 ---
obs0.15507 15044 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.499 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å2-0.15 Å20 Å2
2---0.15 Å20 Å2
3---0.47 Å2
Refinement stepCycle: 1 / Resolution: 1.8→45.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1194 0 11 68 1273
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0191619
X-RAY DIFFRACTIONr_bond_other_d0.0020.021530
X-RAY DIFFRACTIONr_angle_refined_deg1.972.0482287
X-RAY DIFFRACTIONr_angle_other_deg0.96233551
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0275220
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.18921.71176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.18715276
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1061520
X-RAY DIFFRACTIONr_chiral_restr0.1340.2240
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211903
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02429
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr4.76533147
X-RAY DIFFRACTIONr_sphericity_free32.578521
X-RAY DIFFRACTIONr_sphericity_bonded20.50953103
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.533 56 -
Rwork0.401 1095 -
obs--99.48 %

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