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- PDB-5o17: Crystal structure of murine neuroglobin under 100 bar krypton -

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Basic information

Entry
Database: PDB / ID: 5o17
TitleCrystal structure of murine neuroglobin under 100 bar krypton
ComponentsNeuroglobin
KeywordsOXYGEN STORAGE / Globin / oxygen storage-transporter / transport protein
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 / KRYPTON / Neuroglobin
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsColloc'h, N. / Prange, T. / Vallone, B. / Carpentier, P.
CitationJournal: Biophys. J. / Year: 2017
Title: Mapping Hydrophobic Tunnels and Cavities in Neuroglobin with Noble Gas under Pressure.
Authors: Colloc'h, N. / Carpentier, P. / Montemiglio, L.C. / Vallone, B. / Prange, T.
History
DepositionMay 18, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / 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)17,6837
Polymers16,6351
Non-polymers1,0486
Water2,306128
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2040 Å2
ΔGint-39 kcal/mol
Surface area7910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.010, 88.010, 113.490
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-304-

HOH

21A-425-

HOH

31A-427-

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) / 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: Chemical
ChemComp-KR / KRYPTON


Mass: 83.798 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Kr
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.54 Å3/Da / Density % sol: 51.62 % / Mosaicity: 0 °
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: BM30A / Wavelength: 0.8556 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 22, 2016 / Details: mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8556 Å / Relative weight: 1
ReflectionResolution: 1.8→45.516 Å / Num. obs: 15227 / % possible obs: 96.6 % / Redundancy: 5.7 % / Biso Wilson estimate: 23.05 Å2 / Rpim(I) all: 0.029 / Rrim(I) all: 0.071 / Rsym value: 0.064 / Net I/av σ(I): 3.7 / Net I/σ(I): 19
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRpim(I) allRrim(I) allRsym value% possible all
1.8-1.95.50.4011.90.1850.4440.40197.9
1.9-2.015.70.2393.10.1080.2630.23998
2.01-2.155.70.1484.40.0670.1630.14897.7
2.15-2.335.70.0946.30.0430.1040.09497.1
2.33-2.555.70.0726.30.0320.0790.07296.9
2.55-2.855.80.0586.50.0260.0630.05896.2
2.85-3.295.80.0536.20.0230.0580.05395.7
3.29-4.035.70.0475.60.0210.0510.04794.8
4.03-5.75.60.0456.60.020.050.04593.8
5.7-45.5165.40.0515.60.0240.0570.05191.9

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Processing

Software
NameVersionClassification
SCALA3.3.9data scaling
REFMAC5.8.0135refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
REFMAC5.8.0135phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1q1f

1q1f


Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.932 / SU B: 2.598 / SU ML: 0.081 / SU R Cruickshank DPI: 0.1252 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.125 / ESU R Free: 0.126
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2199 757 5 %RANDOM
Rwork0.1725 ---
obs0.1749 14456 95.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 80.21 Å2 / Biso mean: 25.23 Å2 / Biso min: 6.33 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å2-0 Å2
2---0.01 Å2-0 Å2
3---0.03 Å2
Refinement stepCycle: final / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1172 0 52 128 1352
Biso mean--16.94 36.85 -
Num. residues----148
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0191270
X-RAY DIFFRACTIONr_bond_other_d0.0030.021190
X-RAY DIFFRACTIONr_angle_refined_deg1.8112.0261734
X-RAY DIFFRACTIONr_angle_other_deg2.62432737
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1445147
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.721.81855
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.11715213
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3181514
X-RAY DIFFRACTIONr_chiral_restr0.1150.2186
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211408
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02308
LS refinement shellResolution: 1.801→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 58 -
Rwork0.242 1050 -
all-1108 -
obs--97.36 %

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