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- PDB-5eet: Crystal structure of murine neuroglobin at ambient pressure -

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Basic information

Entry
Database: PDB / ID: 5eet
TitleCrystal structure of murine neuroglobin at ambient 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 Å
AuthorsColloc'h, N. / Girard, E. / Vallone, B.
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
DepositionOct 23, 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
Water1,36976
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1310 Å2
ΔGint-34 kcal/mol
Surface area7700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.316, 88.316, 114.457
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: 16634.871 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ngb / Plasmid: PET3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / 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.: 76 / 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: 52.36 %
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
ReflectionRedundancy: 4 % / Number: 47048 / Rsym value: 0.104 / D res high: 2 Å / D res low: 45.821 Å / Num. obs: 11623 / % possible obs: 98.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsRsym valueRedundancy
6.3245.8210.0440.0443.8
4.476.3210.0510.0514
3.654.4710.0530.0534
3.163.6510.0720.0724
2.833.1610.1050.1054.1
2.582.8310.1420.1424.1
2.392.5810.1910.1914.1
2.242.3910.2570.2574.1
2.112.2410.3470.3474.1
22.1110.4790.4794.1
ReflectionResolution: 2→45.821 Å / Num. all: 11623 / Num. obs: 11623 / % possible obs: 98.7 % / Redundancy: 4 % / Rpim(I) all: 0.056 / Rrim(I) all: 0.119 / Rsym value: 0.104 / Net I/av σ(I): 5.818 / Net I/σ(I): 10.2 / Num. measured all: 47048
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
2-2.114.10.4791.5685416850.2560.4793.399.7
2.11-2.244.10.3472652716040.1860.3474.599.7
2.24-2.394.10.2572.6614315100.1370.2576.199.4
2.39-2.584.10.1913.5575014080.1020.1917.799.4
2.58-2.834.10.1424.7523712890.0760.1429.899
2.83-3.164.10.1056.4476111700.0550.10512.698.6
3.16-3.6540.0728.3411410270.040.07216.198.3
3.65-4.4740.05311.434718640.0290.05320.997.2
4.47-6.3240.05111.227426870.0290.05121.796.5
6.32-45.8213.80.04411.214493790.0250.04423.593.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å45.82 Å
Translation2.5 Å45.82 Å
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 11623
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
5.72-10037.20.702509
4.54-5.7250.10.778501
3.96-4.5444.80.789504
3.6-3.9645.20.823505
3.34-3.641.30.83502
3.14-3.3444.20.809504
2.98-3.1445.80.776508
2.85-2.9844.50.786511
2.74-2.8545.30.774505
2.64-2.7444.30.783514
2.56-2.6446.20.788504
2.49-2.5642.30.78510
2.42-2.4947.40.783503
2.36-2.42430.78508
2.31-2.3643.40.832515
2.25-2.3144.70.818516
2.21-2.2544.40.805527
2.16-2.2148.50.795555
2.12-2.1646.70.795524
2.08-2.1250.80.693594
2.04-2.0855.80.732562
2-2.0458.80.663742

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Processing

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

4o4t


Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.959 / WRfactor Rfree: 0.1758 / WRfactor Rwork: 0.1375 / FOM work R set: 0.8787 / SU B: 3.571 / SU ML: 0.096 / SU R Cruickshank DPI: 0.1425 / SU Rfree: 0.1288 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.142 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1805 552 4.8 %RANDOM
Rwork0.1431 ---
obs0.1449 11058 98.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 103.21 Å2 / Biso mean: 29.779 Å2 / Biso min: 9.64 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20.06 Å20 Å2
2--0.12 Å20 Å2
3----0.4 Å2
Refinement stepCycle: final / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1172 0 48 76 1296
Biso mean--20.14 38.88 -
Num. residues----148
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0191305
X-RAY DIFFRACTIONr_bond_other_d0.0020.021230
X-RAY DIFFRACTIONr_angle_refined_deg1.8792.0251774
X-RAY DIFFRACTIONr_angle_other_deg2.14432835
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0495147
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.75521.66760
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.93315229
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6971516
X-RAY DIFFRACTIONr_chiral_restr0.1310.2187
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211433
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02321
X-RAY DIFFRACTIONr_mcbond_it2.7732.609591
X-RAY DIFFRACTIONr_mcbond_other2.7732.599590
X-RAY DIFFRACTIONr_mcangle_it4.1923.89737
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 35 -
Rwork0.233 817 -
all-852 -
obs--99.42 %

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