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- PDB-5eyj: Crystal structure of murine neuroglobin mutant V101F at 240 MPa p... -

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Basic information

Entry
Database: PDB / ID: 5eyj
TitleCrystal structure of murine neuroglobin mutant V101F at 240 MPa pressure
ComponentsNeuroglobin
KeywordsTRANSPORT PROTEIN / GLOBIN / OXYGEN STORAGE-TRANSPORTER / HPMX
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 hydrogen peroxide / neuron projection development / cellular response to hypoxia ...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 hydrogen peroxide / neuron projection development / cellular response to hypoxia / perikaryon / response to hypoxia / mitochondrial matrix / heme binding / negative regulation of apoptotic process / metal ion binding / cytosol
Similarity search - Function
: / Globin/Protoglobin / Globins / Globin domain profile. / Globin-like / Globin / Globin / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Neuroglobin
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsColloc'h, N. / Girard, E. / Vallone, B. / Prange, T.
CitationJournal: Sci Rep / Year: 2017
Title: Determinants of neuroglobin plasticity highlighted by joint coarse-grained simulations and high pressure crystallography.
Authors: Colloc'h, N. / Sacquin-Mora, S. / Avella, G. / Dhaussy, A.C. / Prange, T. / Vallone, B. / Girard, E.
History
DepositionNov 25, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 19, 2016Provider: repository / Type: Initial release
Revision 1.1May 31, 2017Group: Database references
Revision 1.2Nov 29, 2017Group: Database references / Category: pdbx_database_related / Item: _pdbx_database_related.db_id
Revision 1.3Jul 28, 2021Group: Structure summary / Category: struct_keywords / Item: _struct_keywords.text
Revision 1.4Jan 10, 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)17,3953
Polymers16,6831
Non-polymers7132
Water91951
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint-35 kcal/mol
Surface area7840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.199, 87.199, 113.904
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Neuroglobin


Mass: 16682.914 Da / Num. of mol.: 1 / Mutation: C55S C120S V101F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ngb / Plasmid: PET3A / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 2.5 Å3/Da / Density % sol: 50.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 1.6 M ammonium sulfate, 0.1 M MES, 10 % dioxane

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID09 / Wavelength: 0.4104 Å
DetectorType: MAR555 FLAT PANEL / Detector: IMAGE PLATE / Date: Jul 12, 2013
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.4104 Å / Relative weight: 1
ReflectionResolution: 2.4→62.94 Å / Num. all: 6714 / Num. obs: 6714 / % possible obs: 100 % / Redundancy: 5 % / Biso Wilson estimate: 32.1 Å2 / Rpim(I) all: 0.089 / Rrim(I) all: 0.205 / Rsym value: 0.183 / Net I/av σ(I): 3.026 / Net I/σ(I): 4.9 / Num. measured all: 33463
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.4-2.535.10.7810.949079660.3660.7811.8100
2.53-2.685.10.5911.245949070.2810.5912.4100
2.68-2.8750.4961.443428620.2410.4962.8100
2.87-3.15.10.3431.940327950.1680.3433.8100
3.1-3.3950.2232.737497440.1070.2234.8100
3.39-3.7950.1613.633836820.0790.1616.8100
3.79-4.3850.1264.729665970.0610.1268.3100
4.38-5.374.90.1124.825015140.0550.1128.6100
5.37-7.594.80.15.319444060.050.17.7100
7.59-45.4714.30.076.410452410.0380.0711.699.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.4 Å28.64 Å
Translation2.4 Å28.64 Å
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 8103
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
5.89-10038.80.557501
4.6-5.8949.70.682504
4.01-4.642.60.728501
3.62-4.0144.20.715506
3.36-3.6243.10.715501
3.15-3.3647.20.68502
2.99-3.1549.40.635508
2.86-2.9951.80.648501
2.74-2.8653.80.616509
2.65-2.7458.40.579507
2.56-2.6558.20.594504
2.49-2.5656.70.57508
2.42-2.4961.10.556519
2.36-2.4259.60.515506
2.3-2.3662.50.505509
2.25-2.362.10.46517

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
SCALA3.3.22data scaling
PHASER2.5.7phasing
DM6.2phasing
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4O4T

4o4t


Resolution: 2.4→20 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.894 / WRfactor Rfree: 0.2243 / WRfactor Rwork: 0.1251 / FOM work R set: 0.7877 / SU B: 10.113 / SU ML: 0.224 / SU R Cruickshank DPI: 0.4407 / SU Rfree: 0.3 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.441 / ESU R Free: 0.3 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2603 297 4.7 %RANDOM
Rwork0.1437 ---
obs0.149 6028 94.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 147.61 Å2 / Biso mean: 38.765 Å2 / Biso min: 12 Å2
Baniso -1Baniso -2Baniso -3
1-0.51 Å20.25 Å20 Å2
2--0.51 Å20 Å2
3----1.65 Å2
Refinement stepCycle: final / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1176 0 48 51 1275
Biso mean--26.6 36.19 -
Num. residues----148
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0330.0191277
X-RAY DIFFRACTIONr_bond_other_d0.0030.021203
X-RAY DIFFRACTIONr_angle_refined_deg2.9222.0251743
X-RAY DIFFRACTIONr_angle_other_deg1.88832761
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2315147
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.42921.78656
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.30615214
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5821514
X-RAY DIFFRACTIONr_chiral_restr0.2020.2186
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0211415
X-RAY DIFFRACTIONr_gen_planes_other0.010.02313
X-RAY DIFFRACTIONr_mcbond_it5.6033.441591
X-RAY DIFFRACTIONr_mcbond_other5.5883.427590
X-RAY DIFFRACTIONr_mcangle_it8.415.129737
LS refinement shellResolution: 2.4→2.461 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.433 23 -
Rwork0.235 390 -
all-413 -
obs--86.22 %

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