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- PDB-4o4z: MURINE NEUROGLOBIN UNDER 30 BAR PRESSURE NITROUS Oxide -

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Basic information

Entry
Database: PDB / ID: 4o4z
TitleMURINE NEUROGLOBIN UNDER 30 BAR PRESSURE NITROUS Oxide
ComponentsNeuroglobin
KeywordsOXYGEN STORAGE/TRANSPORT PROTEIN / Globin / OXYGEN STORAGE-TRANSPORT PROTEIN complex
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 hydrogen peroxide / neuron projection development / cellular response to hypoxia ...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 hydrogen peroxide / neuron projection development / cellular response to hypoxia / perikaryon / response to hypoxia / mitochondrial matrix / heme binding / negative regulation of apoptotic process / 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 / NITROUS OXIDE / Neuroglobin
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsColloc'h, N. / Prange, T. / Vallone, B.
CitationJournal: 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.
History
DepositionDec 19, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 24, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 17, 2014Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)18,2398
Polymers17,3071
Non-polymers9337
Water1,11762
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.275, 89.275, 114.765
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-352-

HOH

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Components

#1: Protein Neuroglobin


Mass: 17306.572 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 / Production host: Escherichia coli (E. coli) / 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-N2O / NITROUS OXIDE / NITROGEN OXIDE


Mass: 44.013 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: N2O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 52.42 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.6M ammonium sulphate, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 22, 2009 / Details: mirrors
RadiationMonochromator: Si 111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 19567 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4 / Redundancy: 7.3 % / Biso Wilson estimate: 22.1 Å2 / Rsym value: 0.041 / Net I/σ(I): 26.1
Reflection shellResolution: 1.7→1.74 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 6.4 / Num. unique all: 2835 / Rsym value: 0.298 / % possible all: 99.9

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Processing

Software
NameClassification
MxCuBEdata collection
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GKT

3gkt


Resolution: 1.7→20 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.603 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.18768 1001 5.1 %RANDOM
Rwork0.17231 ---
obs0.17303 18566 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.564 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20.04 Å20 Å2
2--0.09 Å20 Å2
3----0.13 Å2
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1172 0 63 62 1297
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0191286
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg3.0222.0281748
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.045149
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.71721.96456
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.18315215
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9321514
X-RAY DIFFRACTIONr_chiral_restr0.0910.2184
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021969
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.234 83 -
Rwork0.226 1273 -
obs--99.85 %

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