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- PDB-6r1q: murine Neuroglobin under 2 kBar of argon -

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Basic information

Entry
Database: PDB / ID: 6r1q
Titlemurine Neuroglobin under 2 kBar of argon
ComponentsNeuroglobin
KeywordsOXYGEN STORAGE / neuroglobin / argon / high pressure
Function / homology
Function and homology information


Intracellular oxygen transport / GDP-dissociation inhibitor activity / nitrite reductase activity / Oxidoreductases; Acting on other nitrogenous compounds as donors / oxygen transport / oxygen carrier activity / cellular response to hydrogen peroxide / oxygen binding / neuron projection development / cellular response to hypoxia ...Intracellular oxygen transport / GDP-dissociation inhibitor activity / nitrite reductase activity / Oxidoreductases; Acting on other nitrogenous compounds as donors / oxygen transport / oxygen carrier activity / cellular response to hydrogen peroxide / oxygen binding / neuron projection development / cellular response to hypoxia / perikaryon / response to hypoxia / mitochondrial matrix / apoptotic process / heme binding / negative regulation of apoptotic process / metal ion binding / cytosol
Similarity search - Function
Globin/Protoglobin / Globin family profile. / Globin / Globin / Globin-like superfamily
Similarity search - Domain/homology
ARGON / PROTOPORPHYRIN IX CONTAINING FE / Neuroglobin
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.95 Å
AuthorsPrange, T. / Colloc'h, N. / Carpentier, P. / Vallone, B.
Citation
Journal: To Be Published
Title: Argon-labelling protein crystals by high pressure cooling at 2000 Bar
Authors: Prange, T. / Colloc'h, N. / Carpentier, P. / van Linden, P.
#1: Journal: Journal of Applied Crystallography / Year: 2016
Title: Gas-sensitive biological crystals processed in pressurized oxygen and krypton atmospheres: deciphering gas channels in proteins using a novel `soak-and-freeze' methodology
Authors: Lafumat, B. / Mueller-Dieckmann, C. / Leonard, G. / Prange, T. / Giraud, T. / Dobias, F. / Royant, A. / van der Linden, P. / Carpentier, P.
History
DepositionMar 14, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 1, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,90217
Polymers16,6351
Non-polymers1,26716
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3380 Å2
ΔGint-47 kcal/mol
Surface area7820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.951, 87.951, 112.923
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-368-

HOH

21A-389-

HOH

31A-391-

HOH

41A-395-

HOH

51A-399-

HOH

61A-400-

HOH

71A-403-

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
Details: CYS 55 and CYS 120 mutated in SER residues / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ngb / Production host: Escherichia coli (E. coli) / References: UniProt: Q9ER97

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Non-polymers , 5 types, 119 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical
ChemComp-AR / ARGON / Argon


Mass: 39.948 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Ar
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.58 Å3/Da / Density % sol: 52.3 % / Description: Deep red cubes
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 6.5
Details: 1.6M AMMONIUM SULPHATE, 0.1M MES, PH 6.5, 10 % DIOXANE

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 1.771 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 27, 2018
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.771 Å / Relative weight: 1
ReflectionResolution: 1.8→45.35 Å / Num. obs: 15605 / % possible obs: 98.8 % / Redundancy: 16.3 % / Biso Wilson estimate: 31.8 Å2 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.019 / Net I/σ(I): 21.7
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.561 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 2089 / Rpim(I) all: 0.206 / % possible all: 92.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
SCALAdata scaling
FFTphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4o4T

4o4t


Resolution: 1.95→44.01 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.933 / SU B: 4.353 / SU ML: 0.125 / Cross valid method: THROUGHOUT / ESU R: 0.185 / ESU R Free: 0.178 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2585 633 5.1 %RANDOM
Rwork0.19353 ---
obs0.19674 11859 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 38.248 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.95→44.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1172 0 62 103 1337
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0131346
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171229
X-RAY DIFFRACTIONr_angle_refined_deg1.991.6981845
X-RAY DIFFRACTIONr_angle_other_deg1.7981.62838
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6415162
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.28819.675
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.37415222
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3421515
X-RAY DIFFRACTIONr_chiral_restr0.0880.2159
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021533
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02328
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_it4.2013.783633
X-RAY DIFFRACTIONr_mcbond_other4.2083.766631
X-RAY DIFFRACTIONr_mcangle_it5.8855.648797
X-RAY DIFFRACTIONr_mcangle_other5.8855.648797
X-RAY DIFFRACTIONr_scbond_it4.2554.145713
X-RAY DIFFRACTIONr_scbond_other4.2554.148711
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.3996.021047
X-RAY DIFFRACTIONr_long_range_B_refined9.03645.2531707
X-RAY DIFFRACTIONr_long_range_B_other9.07445.121694
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 58 -
Rwork0.253 859 -
obs--100 %

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