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- PDB-5o1k: Crystal structure of murine neuroglobin mutant V140W under 20 bar... -

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Basic information

Entry
Database: PDB / ID: 5o1k
TitleCrystal structure of murine neuroglobin mutant V140W under 20 bar xenon pressure
ComponentsNeuroglobin
KeywordsTRANSPORT PROTEIN / 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
1,4-DIETHYLENE DIOXIDE / PROTOPORPHYRIN IX CONTAINING FE / XENON / Neuroglobin
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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 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 / pdbx_database_related
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _pdbx_database_related.db_id
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

Downloads & links

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Assembly

Deposited unit
A: Neuroglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,31010
Polymers16,7221
Non-polymers1,5889
Water93752
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2450 Å2
ΔGint-37 kcal/mol
Surface area8010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.257, 89.257, 115.416
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-220-

DIO

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Neuroglobin


Mass: 16721.949 Da / Num. of mol.: 1 / Mutation: C55S C120S V140W
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

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Non-polymers , 5 types, 61 molecules

#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-XE / XENON


Mass: 131.293 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Xe
#5: Chemical ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE


Mass: 88.105 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 53.51 % / 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: BM16 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 20, 2011 / 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: 2.048→23.121 Å / Num. obs: 11323 / % possible obs: 99.6 % / Redundancy: 7.4 % / Biso Wilson estimate: 28.01 Å2 / Rpim(I) all: 0.034 / Rrim(I) all: 0.092 / Rsym value: 0.077 / Net I/av σ(I): 8.2 / Net I/σ(I): 14.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRpim(I) allRrim(I) allRsym value% possible all
2.05-2.167.30.75810.3230.8820.75897.9
2.16-2.297.50.4661.70.1950.5370.466100
2.29-2.457.50.3112.50.130.3590.311100
2.45-2.647.50.19440.0820.2260.194100
2.64-2.97.50.1295.90.0540.150.129100
2.9-3.247.50.0849.10.0360.0980.084100
3.24-3.747.40.05213.20.0220.0610.052100
3.74-4.587.30.03917.70.0170.0460.039100
4.58-6.487.20.03816.60.0180.0480.038100
6.48-23.1216.70.031160.0150.040.03198

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Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
REFMAC5.8.0135refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
REFMAC5.8.0135phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1q1f

1q1f


Resolution: 2.05→20 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.955 / SU B: 4.117 / SU ML: 0.111 / SU R Cruickshank DPI: 0.1551 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.155 / ESU R Free: 0.147
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2022 565 5 %RANDOM
Rwork0.1524 ---
obs0.1549 10750 99.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 122.88 Å2 / Biso mean: 43.341 Å2 / Biso min: 18.78 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20.05 Å20 Å2
2--0.1 Å20 Å2
3----0.34 Å2
Refinement stepCycle: final / Resolution: 2.05→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1179 0 60 52 1291
Biso mean--33.38 45.06 -
Num. residues----148
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0191287
X-RAY DIFFRACTIONr_bond_other_d0.0030.021196
X-RAY DIFFRACTIONr_angle_refined_deg2.0352.0221756
X-RAY DIFFRACTIONr_angle_other_deg1.55432750
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1075147
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.0822.06958
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.71415212
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9771514
X-RAY DIFFRACTIONr_chiral_restr0.1250.2184
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211426
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02314
LS refinement shellResolution: 2.048→2.101 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 41 -
Rwork0.256 750 -
all-791 -
obs--95.53 %

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