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- PDB-5f0b: Crystal structure of murine neuroglobin mutant F106W at 280 MPa p... -

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Basic information

Entry
Database: PDB / ID: 5f0b
TitleCrystal structure of murine neuroglobin mutant F106W at 280 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 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 / Neuroglobin
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.146 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 27, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 19, 2016Provider: repository / Type: Initial release
Revision 1.1May 31, 2017Group: Database references
Revision 1.2Jul 28, 2021Group: Structure summary / Category: struct_keywords / Item: _struct_keywords.text
Revision 1.3Jan 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

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Assembly

Deposited unit
A: Neuroglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5163
Polymers16,8031
Non-polymers7132
Water1,31573
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-35 kcal/mol
Surface area7610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.212, 86.212, 114.459
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-370-

HOH

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Components

#1: Protein Neuroglobin


Mass: 16803.020 Da / Num. of mol.: 1 / Mutation: C55S F106W C120S
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.: 73 / 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: 2.45 Å3/Da / Density % sol: 49.89 %
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 / Details: mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.4104 Å / Relative weight: 1
ReflectionResolution: 2.146→45.421 Å / Num. all: 9151 / Num. obs: 9151 / % possible obs: 100 % / Redundancy: 8.8 % / Biso Wilson estimate: 30.74 Å2 / Rpim(I) all: 0.054 / Rrim(I) all: 0.161 / Rsym value: 0.151 / Net I/av σ(I): 4.062 / Net I/σ(I): 10.2 / Num. measured all: 80095
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
2.146-2.278.90.8630.81175013180.3060.8633.3100
2.27-2.490.6161.11119312480.2180.6164.2100
2.4-2.578.90.4341.51022211550.1540.4345.5100
2.57-2.788.90.292.3982611090.1030.297.3100
2.78-3.048.80.2063.3891510100.0730.2069.4100
3.04-3.48.90.1434.781379170.050.14313100
3.4-3.938.60.1066.371298300.0370.10617.8100
3.93-4.818.40.0897.158216940.0320.08921.4100
4.81-6.88.50.0857.545985440.030.08519100
6.8-45.4217.70.05710.125043260.0210.05725.199.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å43.11 Å
Translation2.5 Å43.11 Å
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 9150
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
5.84-10039.30.564506
4.56-5.8448.40.73509
3.98-4.5645.90.763501
3.6-3.98420.788503
3.33-3.644.90.778517
3.12-3.3346.90.755509
2.97-3.1251.70.731503
2.84-2.9747.20.715503
2.72-2.84490.689513
2.63-2.7255.30.686505
2.54-2.6354.30.672510
2.47-2.5452.40.704502
2.4-2.4750.50.683504
2.34-2.455.20.679502
2.29-2.3447.70.68513
2.24-2.2959.10.636507
2.19-2.2457.90.655504
2.15-2.1962.60.553539

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Processing

Software
NameVersionClassification
SCALA3.3.21data scaling
PHASER2.3.0phasing
DM6.5.015phasing
REFMAC5.8.0131refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4O4T

4o4t


Resolution: 2.146→20 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.932 / WRfactor Rfree: 0.2305 / WRfactor Rwork: 0.1632 / FOM work R set: 0.8024 / SU B: 6.277 / SU ML: 0.163 / SU R Cruickshank DPI: 0.2439 / SU Rfree: 0.2079 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.244 / ESU R Free: 0.208 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.238 424 4.8 %RANDOM
Rwork0.1706 ---
obs0.1741 8438 96.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 119.36 Å2 / Biso mean: 41.111 Å2 / Biso min: 13.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å2-0.03 Å2-0 Å2
2---0.06 Å2-0 Å2
3---0.18 Å2
Refinement stepCycle: final / Resolution: 2.146→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1175 0 48 73 1296
Biso mean--22.52 40.36 -
Num. residues----148
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0191283
X-RAY DIFFRACTIONr_bond_other_d0.0030.021213
X-RAY DIFFRACTIONr_angle_refined_deg2.4512.0261753
X-RAY DIFFRACTIONr_angle_other_deg2.03132787
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4545147
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.94321.96456
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.98315218
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6491514
X-RAY DIFFRACTIONr_chiral_restr0.1740.2188
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0211415
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02309
X-RAY DIFFRACTIONr_mcbond_it5.2853.742591
X-RAY DIFFRACTIONr_mcbond_other5.1973.734590
X-RAY DIFFRACTIONr_mcangle_it7.4225.567737
LS refinement shellResolution: 2.146→2.201 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.231 26 -
Rwork0.221 547 -
all-573 -
obs--89.67 %

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