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- PDB-5mjd: metNgb under oxygen at 80 bar -

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Basic information

Entry
Database: PDB / ID: 5mjd
TitlemetNgb under oxygen at 80 bar
ComponentsNeuroglobin
KeywordsTRANSPORT PROTEIN / oxygen complex storage cavity
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 / Globins / Globin-like / Globin / Globin / Globin domain profile. / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / OXYGEN MOLECULE / Neuroglobin
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.7 Å
AuthorsPrange, T. / Colloc'h, N. / Carpentier, P.
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 / Structure summary / Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.journal_abbrev ..._audit_author.name / _citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jul 10, 2019Group: Data collection / Database references / Structure summary
Category: audit_author / citation ...audit_author / citation / citation_author / pdbx_database_proc
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 1.3Sep 11, 2019Group: Data collection / Database references / Category: citation / Item: _citation.pdbx_database_id_DOI / _citation.title
Revision 1.4Oct 9, 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_PubMed / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.5Jan 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)17,3794
Polymers16,6351
Non-polymers7453
Water2,306128
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-35 kcal/mol
Surface area7840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.819, 87.819, 113.522
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-316-

HOH

21A-427-

HOH

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Components

#1: Protein Neuroglobin


Mass: 16634.871 Da / Num. of mol.: 1 / Mutation: S-C
Source method: isolated from a genetically manipulated source
Details: contains in the storage site a dioxygen molecule / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ngb / Plasmid: pET24B / 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-OXY / OXYGEN MOLECULE


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


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.4 Å3/Da / Density % sol: 48.77 % / Description: DEEP RED CUBES
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.6M AMMONIUM SULPHATE, 0.1M MES,PH6.5, 10%(V/V) DIOXANE

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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: 1.7→45.49 Å / Num. all: 102328 / Num. obs: 17697 / % possible obs: 95.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4 / Redundancy: 5.8 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 16
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.475 / Mean I/σ(I) obs: 3.2 / Num. measured obs: 14539 / Num. unique all: 2592 / % possible all: 93.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1OJ6

1oj6


Resolution: 1.7→20 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.924 / SU B: 2.172 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24172 830 4.7 %RANDOM
Rwork0.17888 ---
obs0.18153 16853 94.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.873 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20.05 Å2-0 Å2
2--0.11 Å2-0 Å2
3----0.36 Å2
Refinement stepCycle: 1 / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1172 0 50 128 1350
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0191280
X-RAY DIFFRACTIONr_bond_other_d0.0020.021194
X-RAY DIFFRACTIONr_angle_refined_deg1.7792.0271748
X-RAY DIFFRACTIONr_angle_other_deg2.01332746
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3925149
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.11721.96456
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.21615215
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9681514
X-RAY DIFFRACTIONr_chiral_restr0.1160.2186
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211427
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02309
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_it2.7022.996596
X-RAY DIFFRACTIONr_mcbond_other2.6932.987595
X-RAY DIFFRACTIONr_mcangle_it4.1144.473745
X-RAY DIFFRACTIONr_mcangle_other4.1114.485746
X-RAY DIFFRACTIONr_scbond_it3.2743.352684
X-RAY DIFFRACTIONr_scbond_other3.2783.36677
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.2914.862997
X-RAY DIFFRACTIONr_long_range_B_refined7.35225.0761640
X-RAY DIFFRACTIONr_long_range_B_other7.21324.4761578
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.703→1.747 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 75 -
Rwork0.224 1226 -
obs--95.17 %

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