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- PDB-5eqm: Crystal structure of murine neuroglobin at 310 MPa pressure -

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Basic information

Entry
Database: PDB / ID: 5eqm
TitleCrystal structure of murine neuroglobin at 310 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: 2.05 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 13, 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
Water1,27971
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint-34 kcal/mol
Surface area7560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.372, 87.372, 113.284
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-378-

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.: 71 / 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: 50.82 %
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: 2.05→45.345 Å / Num. all: 10340 / Num. obs: 10340 / % possible obs: 97.6 % / Redundancy: 5 % / Rpim(I) all: 0.057 / Rrim(I) all: 0.126 / Rsym value: 0.112 / Net I/av σ(I): 4.933 / Net I/σ(I): 9.8 / Num. measured all: 51538
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
2.05-2.1650.5411.3752515090.2680.5413.297.8
2.16-2.2950.3682709614070.1810.3684.698.1
2.29-2.4550.2882.5670313350.1420.2885.798.1
2.45-2.6550.23.6628612460.0990.27.698
2.65-2.950.1464.9573611440.0720.1469.597.7
2.9-3.2450.1094.4518110330.0560.10912.197.5
3.24-3.7450.0738.745859210.0370.07316.697.3
3.74-4.584.90.05810.838637840.0290.05819.797.3
4.58-6.484.90.068.529616100.0310.0619.596.8
6.48-45.3454.60.0517.616023510.0290.05121.395.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å31.46 Å
Translation2.5 Å31.46 Å
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 10338
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
5.71-10038.80.68506
4.5-5.7147.40.713501
3.92-4.5470.751512
3.56-3.9246.70.791501
3.3-3.5642.20.775515
3.1-3.349.20.751503
2.94-3.149.80.769511
2.81-2.9446.80.724501
2.7-2.8148.20.723502
2.61-2.752.30.697507
2.52-2.61500.743508
2.45-2.5246.70.725503
2.39-2.4549.50.733503
2.33-2.3947.30.74502
2.28-2.3348.60.738509
2.23-2.2849.30.693511
2.18-2.2347.40.708511
2.14-2.1853.30.689505
2.1-2.14550.681510
2.05-2.164.70.616717

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Processing

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

4o4t


Resolution: 2.05→20 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.914 / WRfactor Rfree: 0.228 / WRfactor Rwork: 0.1656 / FOM work R set: 0.8398 / SU B: 4.786 / SU ML: 0.13 / SU R Cruickshank DPI: 0.2046 / SU Rfree: 0.1886 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.205 / ESU R Free: 0.189 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2371 477 4.8 %RANDOM
Rwork0.1716 ---
obs0.1746 9463 93.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 115.32 Å2 / Biso mean: 33.088 Å2 / Biso min: 10.42 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å2-0.02 Å2-0 Å2
2---0.04 Å2-0 Å2
3---0.14 Å2
Refinement stepCycle: final / Resolution: 2.05→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1172 0 48 71 1291
Biso mean--22.09 35.91 -
Num. residues----148
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0191276
X-RAY DIFFRACTIONr_bond_other_d0.0030.021205
X-RAY DIFFRACTIONr_angle_refined_deg2.2192.0281742
X-RAY DIFFRACTIONr_angle_other_deg2.01432768
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7135147
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.82521.96456
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.98415216
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6281514
X-RAY DIFFRACTIONr_chiral_restr0.170.2187
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211412
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02308
X-RAY DIFFRACTIONr_mcbond_it3.932.994591
X-RAY DIFFRACTIONr_mcbond_other3.922.985590
X-RAY DIFFRACTIONr_mcangle_it5.7094.461737
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 35 -
Rwork0.224 643 -
all-678 -
obs--85.61 %

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