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- PDB-4o1t: Crystal structure of murine neuroglobin mutant F106W -

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Basic information

Entry
Database: PDB / ID: 4o1t
TitleCrystal structure of murine neuroglobin mutant F106W
ComponentsNeuroglobin
KeywordsTRANSPORT PROTEIN / Globin / oxygen storage-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 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 / Neuroglobin
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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 16, 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_conn / 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_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _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)18,0583
Polymers17,3461
Non-polymers7132
Water2,864159
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.936, 87.936, 114.139
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-314-

HOH

21A-315-

HOH

31A-324-

HOH

41A-352-

HOH

51A-380-

HOH

61A-400-

HOH

71A-407-

HOH

81A-413-

HOH

91A-414-

HOH

101A-436-

HOH

111A-454-

HOH

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Components

#1: Protein Neuroglobin


Mass: 17345.607 Da / Num. of mol.: 1 / Mutation: C55S, F106W, 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / 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: 2.45 Å3/Da / Density % sol: 49.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.6M ammonium sulfate, 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: BESSY / Beamline: 14.1 / Wavelength: 0.86437 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 19, 2012
RadiationMonochromator: Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.86437 Å / Relative weight: 1
ReflectionResolution: 1.6→31.67 Å / Num. obs: 22607 / % possible obs: 99.97 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Biso Wilson estimate: 14.72 Å2
Reflection shellResolution: 1.6→1.657 Å / % possible all: 99.96

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Processing

Software
NameVersionClassificationNB
PHENIX1.7.1_743refinement
PDB_EXTRACT3.11data extraction
DNAdata collection
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→31.67 Å / Occupancy max: 1 / Occupancy min: 0.03 / FOM work R set: 0.8945 / SU ML: 0.39 / σ(F): 1.39 / Phase error: 17.4 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.195 2014 8.91 %RANDOM
Rwork0.1683 ---
obs0.1708 22607 99.97 %-
all-22608 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.16 Å2 / ksol: 0.355 e/Å3
Displacement parametersBiso max: 94.04 Å2 / Biso mean: 21.7715 Å2 / Biso min: 5.77 Å2
Baniso -1Baniso -2Baniso -3
1-0.5164 Å20 Å20 Å2
2--0.5164 Å20 Å2
3----1.0329 Å2
Refinement stepCycle: LAST / Resolution: 1.6→31.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1175 0 48 159 1382
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081519
X-RAY DIFFRACTIONf_angle_d1.0422124
X-RAY DIFFRACTIONf_chiral_restr0.067215
X-RAY DIFFRACTIONf_plane_restr0.005267
X-RAY DIFFRACTIONf_dihedral_angle_d16.891600
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.6-1.640.21451550.195714461601
1.64-1.68440.22011380.188314361574
1.6844-1.73390.21781400.177314581598
1.7339-1.78990.21611530.169214521605
1.7899-1.85390.17661420.164214461588
1.8539-1.92810.20461370.169414781615
1.9281-2.01580.21411410.174714401581
2.0158-2.12210.22291410.170914921633
2.1221-2.2550.19461400.166614741614
2.255-2.4290.20451370.165714671604
2.429-2.67340.19541440.166214831627
2.6734-3.05990.19261420.167214751617
3.0599-3.85410.17171400.151115021642
3.8541-31.68040.18591640.175315441708

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