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- PDB-3ag0: Crystal structure of carbonmonoxy human cytoglobin -

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Basic information

Entry
Database: PDB / ID: 3ag0
TitleCrystal structure of carbonmonoxy human cytoglobin
ComponentsCytoglobin
KeywordsOXYGEN TRANSPORT / Globins / Heme / Carbon Monoxide / Complex / Ligands / hexacoordination / bis-His / Disulfide bond / Iron / Metal-binding / Transport
Function / homology
Function and homology information


Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With NADH or NADPH as one donor, and incorporation of two atoms of oxygen into the other donor / fatty acid peroxidase activity / nitric oxide dioxygenase activity, heme protein as donor / negative regulation of hepatic stellate cell activation / Intracellular oxygen transport / nitric oxide catabolic process / negative regulation of collagen biosynthetic process / carbon monoxide binding / negative regulation of fibroblast migration / catalase activity ...Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With NADH or NADPH as one donor, and incorporation of two atoms of oxygen into the other donor / fatty acid peroxidase activity / nitric oxide dioxygenase activity, heme protein as donor / negative regulation of hepatic stellate cell activation / Intracellular oxygen transport / nitric oxide catabolic process / negative regulation of collagen biosynthetic process / carbon monoxide binding / negative regulation of fibroblast migration / catalase activity / superoxide dismutase / superoxide dismutase activity / fatty acid oxidation / nitrite reductase activity / Oxidoreductases; Acting on other nitrogenous compounds as donors / oxygen transport / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / eNOS activation / removal of superoxide radicals / oxygen carrier activity / oxygen binding / peroxidase activity / response to oxidative stress / oxidoreductase activity / response to hypoxia / neuron projection / iron ion binding / neuronal cell body / heme binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Globin, lamprey/hagfish type / 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 / Cytoglobin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsMakino, M. / Sawai, H. / Shiro, Y. / Sugimoto, H.
CitationJournal: Proteins / Year: 2011
Title: Crystal structure of the carbon monoxide complex of human cytoglobin
Authors: Makino, M. / Sawai, H. / Shiro, Y. / Sugimoto, H.
History
DepositionMar 17, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 12, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: database_2 / diffrn_source ...database_2 / diffrn_source / struct / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct.title / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2223
Polymers21,5781
Non-polymers6442
Water77543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.198, 43.977, 94.019
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cytoglobin / Histoglobin / HGb / Stellate cell activation-associated protein


Mass: 21577.744 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CYGB, STAP / Plasmid: pET15B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8WWM9
#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.: 43 / 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: 1.73 Å3/Da / Density % sol: 29.07 %
Crystal growTemperature: 293 K / Method: batch / pH: 8
Details: 20% PEG 3350, 20mM ammonium acetate, 5mM sodium dithionite, pH 8.0, batch, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 6, 2007 / Details: K-B mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionNumber: 34085 / Rmerge(I) obs: 0.104 / D res high: 2.6 Å / Num. obs: 4892 / % possible obs: 98.6
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)IDRmerge(I) obs
4.455.649898.610.059
3.884.455099910.06
3.533.8847998.610.08
3.283.5347999.210.109
3.083.285019910.158
2.933.0846497.310.224
2.82.9348610010.28
2.692.848096.410.36
2.62.6945610010.498
ReflectionResolution: 2.6→50 Å / Num. obs: 4892 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 36.121 Å2 / Rmerge F obs: 0.112 / Rmerge(I) obs: 0.104 / Rrim(I) all: 0.112 / Net I/σ(I): 16.31 / Num. measured all: 34085
Reflection shell
Resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.6-2.690.4280.4984.533274564560.54100
2.69-2.80.3180.365.734064984800.3996.4
2.8-2.930.2590.287.135284864860.3100
2.93-3.080.1970.2248.933294774640.2497.3
3.08-3.280.140.15811.935465065010.1799
3.28-3.530.0980.10915.634364834790.1299.2
3.53-3.880.0610.0821.133514864790.0998.6
3.88-4.450.0430.0626.234535145090.0699
4.45-5.60.0430.05927.233105054980.0698.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.84 Å47.01 Å
Translation2.84 Å47.01 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
CNS1.1refinement
PDB_EXTRACT3.1data extraction
BSSdata collection
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1V5H

1v5h


Resolution: 2.6→19.92 Å / Rfactor Rfree error: 0.016 / Data cutoff high absF: 1279585.97 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.248 246 5 %RANDOM
Rwork0.215 ---
obs0.215 4877 98.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.1626 Å2 / ksol: 0.33375 e/Å3
Displacement parametersBiso mean: 36.5 Å2
Baniso -1Baniso -2Baniso -3
1--7.04 Å20 Å20 Å2
2---2.08 Å20 Å2
3---9.12 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.6→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1264 0 45 43 1352
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.29
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.421.5
X-RAY DIFFRACTIONc_mcangle_it4.962
X-RAY DIFFRACTIONc_scbond_it5.042
X-RAY DIFFRACTIONc_scangle_it6.482.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.056 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.336 36 4.6 %
Rwork0.287 746 -
all-782 -
obs--98 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3hem.paramhem.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5cmo.paramcmo.top

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