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- PDB-1v5h: Crystal Structure of Human Cytoglobin (Ferric Form) -

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Basic information

Entry
Database: PDB / ID: 1v5h
TitleCrystal Structure of Human Cytoglobin (Ferric Form)
ComponentsCytoglobin
KeywordsOXYGEN STORAGE/TRANSPORT / globin / heme / oxygen transport / oxygen storage / ligand binding / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics / OXYGEN STORAGE-TRANSPORT COMPLEX
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
PROTOPORPHYRIN IX CONTAINING FE / Cytoglobin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsSugimoto, H. / Makino, M. / Sawai, H. / Kawada, N. / Yoshizato, K. / Shiro, Y. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Citation
Journal: J.Mol.Biol. / Year: 2004
Title: Structural basis of human cytoglobin for ligand binding.
Authors: Sugimoto, H. / Makino, M. / Sawai, H. / Kawada, N. / Yoshizato, K. / Shiro, Y.
#1: Journal: Biochemistry / Year: 2003
Title: Characterization of the heme environmental structure of cytoglobin, a fourth globin in humans
Authors: Sawai, H. / Kawada, N. / Yoshizato, K. / Nakajima, H. / Aono, S. / Shiro, Y.
History
DepositionNov 23, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 8, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: 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.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_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

Downloads & links

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Assembly

Deposited unit
A: Cytoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3322
Polymers21,7161
Non-polymers6161
Water54030
1
A: Cytoglobin
hetero molecules

A: Cytoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6654
Polymers43,4322
Non-polymers1,2332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_764-x+2,-x+y+1,-z-1/31
Unit cell
Length a, b, c (Å)74.401, 74.401, 59.634
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
DetailsThe second part of the dimeric assembly is generated by the two fold axis: 2-X, Y-X+1, -1/3-Z

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Components

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


Mass: 21715.893 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CYGB, STAP / Plasmid: pET-15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.69 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9.2
Details: Sodium Citrate, CHES, pH 9.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1.0, 1.7409, 1.7394, 1.7364, 1.7432
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 13, 2003
RadiationMonochromator: Si / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.74091
31.73941
41.73641
51.74321
ReflectionResolution: 2.4→20 Å / Num. all: 7348 / Num. obs: 7348 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 63.3 Å2 / Rsym value: 0.06
Reflection shellResolution: 2.4→2.49 Å / Num. unique all: 579 / Rsym value: 0.289 / % possible all: 76.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.4→20 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 761175.43 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.25 384 5.2 %RANDOM
Rwork0.248 ---
obs0.248 7331 95.8 %-
all-7331 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 62.5286 Å2 / ksol: 0.329863 e/Å3
Displacement parametersBiso mean: 71.3 Å2
Baniso -1Baniso -2Baniso -3
1-6.31 Å24.67 Å20 Å2
2--11.63 Å20 Å2
3----17.95 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.4 Å0.46 Å
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1220 0 43 30 1293
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
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_deg2.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.32
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.057 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.409 52 5.5 %
Rwork0.372 896 -
obs--76.6 %

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