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- PDB-4o2g: Crystal structure of carbomonoxy murine neuroglobin mutant V140W -

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Basic information

Entry
Database: PDB / ID: 4o2g
TitleCrystal structure of carbomonoxy murine neuroglobin mutant V140W
ComponentsNeuroglobin
KeywordsTRANSPORT PROTEIN / Globin / OXYGEN STORAGE
Function / homology
Function and homology information


Intracellular oxygen transport / GDP-dissociation inhibitor activity / nitrite reductase activity / Oxidoreductases; Acting on other nitrogenous compounds as donors / 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 / nitrite reductase activity / Oxidoreductases; Acting on other nitrogenous compounds as donors / 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
CARBON MONOXIDE / PROTOPORPHYRIN IX CONTAINING FE / Neuroglobin
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsAvella, G. / Savino, C. / Vallone, B.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Engineering the internal cavity of neuroglobin demonstrates the role of the haem-sliding mechanism.
Authors: Avella, G. / Ardiccioni, C. / Scaglione, A. / Moschetti, T. / Rondinelli, C. / Montemiglio, L.C. / Savino, C. / Giuffre, A. / Brunori, M. / Vallone, B.
History
DepositionDec 17, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 18, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

Downloads & links

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Assembly

Deposited unit
A: Neuroglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0383
Polymers17,3941
Non-polymers6442
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.067, 85.067, 110.202
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: 17393.650 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 / 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-CMO / CARBON MONOXIDE


Mass: 28.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO

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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: 2.21 Å3/Da / Density % sol: 44.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.6M ammonium sulphate, 0.1M MES, 10% dioxane, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8732 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 8, 2011
RadiationMonochromator: Si-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8732 Å / Relative weight: 1
ReflectionResolution: 2.7→34.94 Å / Num. obs: 4286 / % possible obs: 97.9 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Biso Wilson estimate: 63.11 Å2
Reflection shellResolution: 2.7→2.795 Å / % possible all: 97.37

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Processing

Software
NameVersionClassificationNB
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
DNAdata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→34.935 Å / Occupancy max: 1 / Occupancy min: 0.36 / FOM work R set: 0.723 / SU ML: 0.41 / σ(F): 1.4 / Phase error: 33.26 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2695 428 9.99 %random
Rwork0.2077 ---
obs0.214 4285 97.85 %-
all-4286 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 121.76 Å2 / Biso mean: 62.8614 Å2 / Biso min: 20 Å2
Refinement stepCycle: LAST / Resolution: 2.7→34.935 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1167 0 45 0 1212
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111277
X-RAY DIFFRACTIONf_angle_d1.5331748
X-RAY DIFFRACTIONf_chiral_restr0.072184
X-RAY DIFFRACTIONf_plane_restr0.005218
X-RAY DIFFRACTIONf_dihedral_angle_d17.972470
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7-3.09070.321400.20871254139497
3.0907-3.89310.28161410.21321278141998
3.8931-34.93820.25311470.20481325147298

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