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- PDB-6eye: Crystal structure of murine neuroglobin under 150 bar krypton -

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Basic information

Entry
Database: PDB / ID: 6eye
TitleCrystal structure of murine neuroglobin under 150 bar krypton
ComponentsNeuroglobin
KeywordsOXYGEN TRANSPORT / ---- NGB KRYPTON 150 BAR
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 domain profile. / Globin-like / Globin / Globin / 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 / FOURIER SYNTHESIS / Resolution: 1.7 Å
AuthorsPrange, T. / Colloc'h, N. / Carpentier, P.
Citation
Journal: 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.
#1: Journal: Anesthesiology / Year: 2014
Title: Crystallographic Studies with Xenon and Nitrous Oxide Provide Evidence for Protein-dependent Processes in the Mechanisms of General Anesthesia
Authors: Abraini, J.H. / Marassio, G. / David, H.N. / Vallone, B. / Prange, T. / Colloc'h, N.
#2: Journal: J. of Applied Crystallogr. / Year: 2016
Title: Gas-sensitive biological crystals processed in pressurized oxygen and krypton atmospheres: deciphering gas channels in proteins using a novel "soak-and-freeze" methodology
Authors: Lafumat, B. / Mueller-Dieckmann, C. / Gordon, L. / Colloc'h, N. / Prange, T. / Giraud, T. / Dobias, F. / Royant, A. / van der Linden, P. / Carpentier, P.
History
DepositionNov 12, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 29, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2018Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.pdbx_database_id_DOI ..._audit_author.name / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation_author.name
Revision 1.2Sep 4, 2019Group: Data collection / Structure summary / Category: audit_author
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)19,27618
Polymers17,3071
Non-polymers1,97017
Water1,45981
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3720 Å2
ΔGint-42 kcal/mol
Surface area7620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.854, 87.854, 113.210
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-321-

HOH

21A-372-

HOH

31A-378-

HOH

41A-379-

HOH

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Components

#1: Protein Neuroglobin


Mass: 17306.572 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 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9ER97
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical
ChemComp-KR / KRYPTON


Mass: 83.798 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Kr
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 52.3 % / Description: Deep red prism
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 1.6M AMMONIUM SULPHATE, 0.1M MES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.8556 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 20, 2016
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8556 Å / Relative weight: 1
ReflectionResolution: 1.7→45.41 Å / Num. obs: 18730 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4 / Redundancy: 19.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.013 / Rrim(I) all: 0.045 / Net I/σ(I): 28.3
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.275 / Num. unique obs: 2672 / CC1/2: 0.893 / Rpim(I) all: 0.151 / Rrim(I) all: 0.318 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4O4T

4o4t


Resolution: 1.7→45.41 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.401 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.111 / ESU R Free: 0.121 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25394 866 4.6 %RANDOM
Rwork0.19373 ---
obs0.1962 17859 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 40.372 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.7→45.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1172 0 63 81 1316
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0191299
X-RAY DIFFRACTIONr_bond_other_d0.0030.021209
X-RAY DIFFRACTIONr_angle_refined_deg2.2412.0231786
X-RAY DIFFRACTIONr_angle_other_deg1.19532786
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6595160
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.59222.28157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.13915215
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9451513
X-RAY DIFFRACTIONr_chiral_restr0.1470.2192
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211467
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02316
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.9163.707605
X-RAY DIFFRACTIONr_mcbond_other3.9193.698604
X-RAY DIFFRACTIONr_mcangle_it5.2795.536758
X-RAY DIFFRACTIONr_mcangle_other5.2765.546759
X-RAY DIFFRACTIONr_scbond_it4.6564.173694
X-RAY DIFFRACTIONr_scbond_other4.6494.174688
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.0496.041015
X-RAY DIFFRACTIONr_long_range_B_refined9.28330.9461673
X-RAY DIFFRACTIONr_long_range_B_other9.25530.751641
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.743 Å
RfactorNum. reflection% reflection
Rfree0.279 72 -
Rwork0.239 1261 -
obs--98.16 %

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