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- PDB-1w92: The structure of carbomonoxy murine neuroglobin reveals a heme- s... -

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Basic information

Entry
Database: PDB / ID: 1w92
TitleThe structure of carbomonoxy murine neuroglobin reveals a heme- sliding mechanism for affinity regulation
ComponentsNEUROGLOBIN
KeywordsOXYGEN STORAGE/TRANSPORT / CARBOMONOXY NEUROGLOBIN / GLOBIN / HEME-SLIDING / OXYGEN STORAGE-TRANSPORT 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 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
CARBON MONOXIDE / PROTOPORPHYRIN IX CONTAINING FE / Neuroglobin
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsVallone, B. / Nienhaus, K. / Matthes, A. / Brunori, M. / Nienhaus, G.U.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2004
Title: The Structure of Carbonmonoxy Neuroglobin Reveals a Heme-Sliding Mechanism for Control of Ligand Affinity
Authors: Vallone, B. / Nienhaus, K. / Matthes, A. / Brunori, M. / Nienhaus, G.U.
#1: Journal: 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
DepositionOct 5, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 2, 2004Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2011Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Version format compliance
Revision 1.2May 22, 2019Group: Data collection / Other / Refinement description
Category: pdbx_database_proc / pdbx_database_status / refine
Item: _pdbx_database_status.recvd_author_approval / _refine.pdbx_ls_cross_valid_method
Revision 1.3Nov 27, 2019Group: Advisory / Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_conn_angle ...pdbx_database_status / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn
Item: _pdbx_database_status.status_code_sf
Revision 1.4Dec 13, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)17,6693
Polymers17,0241
Non-polymers6442
Water1,928107
1
A: NEUROGLOBIN
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)106,01318
Polymers102,1466
Non-polymers3,86712
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
crystal symmetry operation10_455y-1/3,x+1/3,-z+1/31
crystal symmetry operation11_565x-y+2/3,-y+4/3,-z+1/31
crystal symmetry operation12_555-x+2/3,-x+y+1/3,-z+1/31
MethodPQS
Unit cell
Length a, b, c (Å)88.373, 88.373, 110.983
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: YES
Source method: isolated from a genetically manipulated source
Details: CARBOMONOXY (CO) DERIVATIVE OF HEME FERROUS (FE2) NEUROGLOBIN
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Tissue: NERVE / Organ: BRAIN / Plasmid: PET3A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUES CYS 55 SER, CYS 120 SER FOR CHAIN A

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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: 2.35 Å3/Da / Density % sol: 47.16 %
Crystal growpH: 7.5 / Details: 0.1 M HEPES/NA PH 7.5 1.5 M LI SULPHATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 20, 2003
Details: TOROIDAL FOCUSSING MIRROR WITH A HORIZONTAL ACCEPTANCE OF 2.8 MRAD
RadiationMonochromator: DOUBLE-CRYSTAL MONOCHROMATOR (SI(111) AND SI(220) )
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→15 Å / Num. obs: 92704 / % possible obs: 94.8 % / Observed criterion σ(I): 2 / Redundancy: 2.5 % / Biso Wilson estimate: 22.8 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 20.8
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 2.39 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 2.94 / % possible all: 97.5

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1Q1F

1q1f


Resolution: 1.7→15 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22 903 0.1 %RANDOM
Rwork0.26 ---
obs0.26 882 97.5 %-
Displacement parametersBiso mean: 27.3 Å2
Refinement stepCycle: LAST / Resolution: 1.7→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1160 0 45 107 1312

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