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- PDB-5eoh: Crystal structure of murine neuroglobin at 270 MPa pressure -

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Basic information

Entry
Database: PDB / ID: 5eoh
TitleCrystal structure of murine neuroglobin at 270 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: 1.9 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 10, 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)17,3473
Polymers16,6351
Non-polymers7132
Water1,45981
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1290 Å2
ΔGint-33 kcal/mol
Surface area7590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.560, 87.560, 113.636
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-380-

HOH

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Components

#1: Protein Neuroglobin


Mass: 16634.871 Da / Num. of mol.: 1 / Mutation: C55S 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.: 81 / 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: 2.52 Å3/Da / Density % sol: 51.19 %
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: SOLEIL / Beamline: CRISTAL / Wavelength: 0.454 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 2, 2012
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.454 Å / Relative weight: 1
ReflectionResolution: 1.9→45.47 Å / Num. all: 13380 / Num. obs: 13380 / % possible obs: 99.8 % / Redundancy: 4.7 % / Rpim(I) all: 0.049 / Rrim(I) all: 0.106 / Rsym value: 0.093 / Net I/av σ(I): 5.5 / Net I/σ(I): 10.3 / Num. measured all: 62535
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
1.9-24.70.4731.6898619080.2440.4733.399.7
2-2.124.70.3362.2870718360.1740.3364.5100
2.12-2.274.70.223.3824117440.1130.226.6100
2.27-2.454.70.1724757316070.0890.1728100
2.45-2.694.70.1245.7691414700.0630.12410.5100
2.69-34.70.0987639513670.050.09812.699.9
3-3.474.70.0758.4549111800.0390.07516.199.8
3.47-4.254.60.05810.3467010160.030.05820.199.7
4.25-6.014.50.05410.936137960.0290.05421.399.4
6.01-45.474.30.0548.419454560.0320.05420.898.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å45.47 Å
Translation2.5 Å45.47 Å
Phasing dmMethod: Solvent flattening and Histogram matching

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
SCALA3.3.20data scaling
PHASER2.3.0phasing
DM6.2phasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4O4T

4o4t


Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.938 / WRfactor Rfree: 0.2223 / WRfactor Rwork: 0.1677 / FOM work R set: 0.8553 / SU B: 3.431 / SU ML: 0.099 / SU R Cruickshank DPI: 0.1384 / SU Rfree: 0.1386 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.138 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2214 662 5 %RANDOM
Rwork0.1686 ---
obs0.1711 12703 99.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 101.27 Å2 / Biso mean: 31.738 Å2 / Biso min: 11.91 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20.04 Å20 Å2
2--0.09 Å20 Å2
3----0.29 Å2
Refinement stepCycle: final / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1172 0 48 81 1301
Biso mean--22.25 38.11 -
Num. residues----148
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0191281
X-RAY DIFFRACTIONr_bond_other_d0.0030.021207
X-RAY DIFFRACTIONr_angle_refined_deg2.012.0281748
X-RAY DIFFRACTIONr_angle_other_deg1.97532777
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7785147
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.26222.10557
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.35115219
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.8461514
X-RAY DIFFRACTIONr_chiral_restr0.1420.2187
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211416
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02308
X-RAY DIFFRACTIONr_mcbond_it3.3372.834591
X-RAY DIFFRACTIONr_mcbond_other3.3372.825590
X-RAY DIFFRACTIONr_mcangle_it4.9754.219737
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.236 48 -
Rwork0.241 910 -
all-958 -
obs--99.38 %

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