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- PDB-5mjc: metNeuroglobin under oxygen at 50 bar -

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Basic information

Entry
Database: PDB / ID: 5mjc
TitlemetNeuroglobin under oxygen at 50 bar
ComponentsNeuroglobin
KeywordsTRANSPORT PROTEIN / oxygen complex storage cavity
Function / homology
Function and homology information


Intracellular oxygen transport / positive regulation of catalytic activity / GDP-dissociation inhibitor activity / nitrite reductase activity / Oxidoreductases; Acting on other nitrogenous compounds as donors / oxygen transport / oxygen carrier activity / oxygen binding / cellular response to hydrogen peroxide / neuron projection development ...Intracellular oxygen transport / positive regulation of catalytic activity / GDP-dissociation inhibitor activity / nitrite reductase activity / Oxidoreductases; Acting on other nitrogenous compounds as donors / oxygen transport / oxygen carrier activity / oxygen binding / cellular response to hydrogen peroxide / neuron projection development / cellular response to hypoxia / response to hypoxia / perikaryon / mitochondrial matrix / heme binding / negative regulation of apoptotic process / metal ion binding / cytosol
Similarity search - Function
: / Globin/Protoglobin / Globins / Globin-like / Globin / Globin / Globin domain profile. / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
1,4-DIETHYLENE DIOXIDE / PROTOPORPHYRIN IX CONTAINING FE / OXYGEN MOLECULE / Neuroglobin
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.62 Å
AuthorsPrange, T. / Colloc'h, N. / Carpentier, P. / Vallone, B.
Citation
Journal: Iucrj / Year: 2019
Title: Ligand pathways in neuroglobin revealed by low-temperature photodissociation and docking experiments.
Authors: Ardiccioni, C. / Arcovito, A. / Della Longa, S. / van der Linden, P. / Bourgeois, D. / Weik, M. / Montemiglio, L.C. / Savino, C. / Avella, G. / Exertier, C. / Carpentier, P. / Prange, T. / ...Authors: Ardiccioni, C. / Arcovito, A. / Della Longa, S. / van der Linden, P. / Bourgeois, D. / Weik, M. / Montemiglio, L.C. / Savino, C. / Avella, G. / Exertier, C. / Carpentier, P. / Prange, T. / Brunori, M. / Colloc'h, N. / Vallone, B.
#1: Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2005
Title: Neuroglobin, nitric oxide, and oxygen: functional pathways and conformational changes.
Authors: Brunori, M. / Giuffre, A. / Nienhaus, K. / Nienhaus, G.U. / Scandurra, F.M. / Vallone, B.
History
DepositionNov 30, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.title / _citation_author.name
Revision 1.2Jul 10, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: audit_author / citation ...audit_author / citation / citation_author / pdbx_database_proc / pdbx_struct_special_symmetry
Item: _audit_author.identifier_ORCID / _citation.country ..._audit_author.identifier_ORCID / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.title / _citation.year
Revision 1.3Oct 16, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.4Jan 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
Revision 1.5Aug 26, 2026Group: Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature ...pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_atom_coordination / pdbx_nonpoly_atom_coordination_sphere / pdbx_nonpoly_atom_coordination_sphere_order
Description: Metalloprotein remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Neuroglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5566
Polymers16,6351
Non-polymers9215
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-29 kcal/mol
Surface area7640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.351, 87.351, 112.650
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-310-

HOH

21A-318-

HOH

31A-372-

HOH

41A-378-

HOH

51A-413-

HOH

61A-425-

HOH

71A-429-

HOH

81A-431-

HOH

91A-441-

HOH

101A-443-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Neuroglobin


Mass: 16634.871 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ngb / Plasmid: PET14B / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): PLYSS / References: UniProt: Q9ER97

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Non-polymers , 5 types, 149 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-DIO / 1,4-DIETHYLENE DIOXIDE


Mass: 88.105 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H8O2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.49 Å3/Da / Density % sol: 50.56 % / Description: DEEP RED CUBES
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.6M AMMONIUM SULPHATE, 0.1M MES, PH 6.5, 10% DIOXANE, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.8859 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 20, 2016 / Details: BENT MIRROR
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8859 Å / Relative weight: 1
ReflectionResolution: 1.55→59.66 Å / Num. obs: 20818 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4 / Redundancy: 7.3 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 21.4
Reflection shellResolution: 1.55→1.7 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.281 / Mean I/σ(I) obs: 4.3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4O4T

4o4t


Resolution: 1.62→62.8 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.623 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.09 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.20705 1071 5.2 %RANDOM
Rwork0.16826 ---
obs0.1702 19661 98.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.663 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å2-0.03 Å20 Å2
2---0.06 Å20 Å2
3---0.21 Å2
Refinement stepCycle: 1 / Resolution: 1.62→62.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1172 0 62 144 1378
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0191340
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.092.0741838
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2075149
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.81721.60756
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.06415215
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9461515
X-RAY DIFFRACTIONr_chiral_restr0.1810.2188
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.0211016
X-RAY DIFFRACTIONr_gen_planes_other
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_it3.6332.497593
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.0043.727740
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.7842.779746
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined8.7921.7012404
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.623→1.665 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.232 69 -
Rwork0.227 1121 -
obs--77.17 %

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