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- PDB-1q1f: Crystal structure of murine neuroglobin -

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Basic information

Entry
Database: PDB / ID: 1q1f
TitleCrystal structure of murine neuroglobin
ComponentsNeuroglobin
KeywordsOXYGEN STORAGE/TRANSPORT / globin fold / heme protein / neuroglobin / OXYGEN STORAGE-TRANSPORT COMPLEX
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
PROTOPORPHYRIN IX CONTAINING FE / Neuroglobin
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsVallone, B. / Nienhaus, K. / Matthes, K. / Brunori, M. / Nienhaus, G.U.
CitationJournal: Proteins / Year: 2004
Title: The structure of murine neuroglobin: Novel pathways for ligand migration and binding.
Authors: Vallone, B. / Nienhaus, K. / Brunori, M. / Nienhaus, G.U.
History
DepositionJul 19, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: 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
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)17,6412
Polymers17,0241
Non-polymers6161
Water2,000111
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.973, 86.973, 110.815
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Neuroglobin


Mass: 17024.295 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 / Plasmid: PET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLys / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 2.37 Å3/Da / Density % sol: 48.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1 M Na acetate, 2M Na formate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.2, 1.7
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 12, 2003
RadiationMonochromator: Si(111)and Si(220) followed by a toroidally focussing mirror
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.21
21.71
ReflectionResolution: 1.5→40 Å / Num. all: 26718 / Num. obs: 26076 / % possible obs: 99.5 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 10.8 % / Biso Wilson estimate: 20.84 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.057 / Net I/σ(I): 35
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 7 % / Rmerge(I) obs: 0.536 / Mean I/σ(I) obs: 2.79 / Num. unique all: 2563 / Rsym value: 0.533 / % possible all: 100

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Processing

Software
NameVersionClassification
DENZOdata reduction
TRUNCATEdata reduction
SOLVEphasing
REFMACrefinement
CCP4(TRUNCATE)data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.5→20 Å / Isotropic thermal model: anisotropic / σ(F): 2 / σ(I): 2 / Stereochemistry target values: from Refmac / Details: model built by resolve after phasing with solve
RfactorNum. reflection% reflectionSelection details
Rfree0.2075 1321 -RANDOM
Rwork0.184 ---
all0.216 25971 --
obs0.21 24647 94.9 %-
Displacement parametersBiso mean: 40.9 Å2
Refine analyzeLuzzati coordinate error obs: 0.202 Å
Refinement stepCycle: LAST / Resolution: 1.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1221 0 86 111 1418
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_other_d0.015
X-RAY DIFFRACTIONr_angle_other_deg0.037
X-RAY DIFFRACTIONr_gen_planes_other0.045
LS refinement shellResolution: 1.5→20 Å
RfactorNum. reflection% reflection
Rfree0.207 1321 -
Rwork0.184 --
obs-25971 99.9 %

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