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- PDB-5nw6: Crystal structure of murine neuroglobin under 50 bar krypton pressure -

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Basic information

Entry
Database: PDB / ID: 5nw6
TitleCrystal structure of murine neuroglobin under 50 bar krypton pressure
ComponentsNeuroglobin
KeywordsOXYGEN TRANSPORT / globin / oxygen transporter
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: 1.7 Å
AuthorsColloc'h, N. / Prange, T.
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 5, 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 1.2Feb 21, 2018Group: Structure summary / Category: audit_author / struct / Item: _audit_author.name / _struct.title
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 / 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)17,5996
Polymers16,6351
Non-polymers9645
Water1,36976
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-39 kcal/mol
Surface area8000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.126, 89.126, 115.265
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 / Mutation: C155S C120S
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) / 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.: 3 / Source method: obtained synthetically / Formula: Kr
#5: 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: 2.65 Å3/Da / Density % sol: 53.55 %
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: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 23, 2012 / Details: mirrors
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.7→64.134 Å / Num. obs: 19585 / % possible obs: 99.9 % / Redundancy: 7.1 % / Biso Wilson estimate: 23.4 Å2 / Rpim(I) all: 0.017 / Rrim(I) all: 0.046 / Rsym value: 0.043 / Net I/av σ(I): 11 / Net I/σ(I): 21.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRpim(I) allRrim(I) allRsym value% possible all
1.7-1.797.30.3662.10.1460.3950.366100
1.79-1.97.30.2253.40.090.2420.225100
1.9-2.037.30.1355.50.0540.1460.135100
2.03-2.197.20.0838.80.0330.090.083100
2.19-2.47.20.05712.50.0230.0610.057100
2.4-2.697.20.04913.10.020.0530.049100
2.69-3.17.10.069.70.0240.0650.06100
3.1-3.86.80.03914.80.0160.0420.039100
3.8-5.386.60.0229.60.0080.0220.02100
5.38-26.0296.70.01927.40.0080.0210.01997.6

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
REFMAC5.8.0135refinement
PDB_EXTRACT3.22data extraction
MOSFLMdata reduction
REFMAC5.8.0135phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Q1F

1q1f


Resolution: 1.7→20 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.641 / SU ML: 0.055 / SU R Cruickshank DPI: 0.0846 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.085 / ESU R Free: 0.083
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1806 1001 5.1 %RANDOM
Rwork0.1551 ---
obs0.1564 18573 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 110.2 Å2 / Biso mean: 31.654 Å2 / Biso min: 12.51 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20.03 Å20 Å2
2--0.05 Å20 Å2
3----0.16 Å2
Refinement stepCycle: final / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1172 0 51 76 1299
Biso mean--22.16 43.26 -
Num. residues----148
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0191274
X-RAY DIFFRACTIONr_bond_other_d0.0020.021190
X-RAY DIFFRACTIONr_angle_refined_deg1.5582.0251738
X-RAY DIFFRACTIONr_angle_other_deg2.32232740
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5415147
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.5421.96456
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.89215216
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8631514
X-RAY DIFFRACTIONr_chiral_restr0.1060.2185
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211412
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02308
LS refinement shellResolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.195 69 -
Rwork0.186 1368 -
all-1437 -
obs--100 %

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