+Open data
-Basic information
Entry | Database: PDB / ID: 4wd4 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of human HO1 H25R | ||||||
Components | Heme oxygenase 1 | ||||||
Keywords | OXIDOREDUCTASE / Heme oxygenase / Proximal histidine / Heme coordination / Site-directed mutagenesis / Biliverdin biosensor | ||||||
Function / homology | Function and homology information Regulation of HMOX1 expression and activity / heme oxygenase (biliverdin-producing) / low-density lipoprotein particle clearance / cellular response to cisplatin / heme oxidation / smooth muscle hyperplasia / heme oxygenase (decyclizing) activity / negative regulation of leukocyte migration / wound healing involved in inflammatory response / positive regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis ...Regulation of HMOX1 expression and activity / heme oxygenase (biliverdin-producing) / low-density lipoprotein particle clearance / cellular response to cisplatin / heme oxidation / smooth muscle hyperplasia / heme oxygenase (decyclizing) activity / negative regulation of leukocyte migration / wound healing involved in inflammatory response / positive regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / heme catabolic process / cellular response to arsenic-containing substance / positive regulation of epithelial cell apoptotic process / erythrocyte homeostasis / endothelial cell proliferation / epithelial cell apoptotic process / Heme degradation / NFE2L2 regulating anti-oxidant/detoxification enzymes / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / positive regulation of cell migration involved in sprouting angiogenesis / negative regulation of macroautophagy / The NLRP3 inflammasome / positive regulation of macroautophagy / regulation of angiogenesis / Purinergic signaling in leishmaniasis infection / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of chemokine production / cellular response to cadmium ion / macroautophagy / negative regulation of smooth muscle cell proliferation / Iron uptake and transport / positive regulation of smooth muscle cell proliferation / response to nicotine / Heme signaling / response to hydrogen peroxide / Cytoprotection by HMOX1 / multicellular organismal-level iron ion homeostasis / positive regulation of angiogenesis / cellular response to heat / cellular response to hypoxia / angiogenesis / Interleukin-4 and Interleukin-13 signaling / positive regulation of canonical NF-kappaB signal transduction / intracellular iron ion homeostasis / mitochondrial outer membrane / response to oxidative stress / intracellular signal transduction / heme binding / endoplasmic reticulum membrane / regulation of transcription by RNA polymerase II / structural molecule activity / perinuclear region of cytoplasm / enzyme binding / endoplasmic reticulum / protein homodimerization activity / extracellular space / nucleoplasm / identical protein binding / membrane / nucleus / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å | ||||||
Authors | Caaveiro, J.M.M. / Morante, K. / Sigala, P. / Tsumoto, K. | ||||||
Citation | Journal: Biochemistry / Year: 2016 Title: In-Cell Enzymology To Probe His-Heme Ligation in Heme Oxygenase Catalysis Authors: Sigala, P.A. / Morante, K. / Tsumoto, K. / Caaveiro, J.M. / Goldberg, D.E. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4wd4.cif.gz | 192.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4wd4.ent.gz | 152.7 KB | Display | PDB format |
PDBx/mmJSON format | 4wd4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4wd4_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4wd4_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 4wd4_validation.xml.gz | 34.1 KB | Display | |
Data in CIF | 4wd4_validation.cif.gz | 43.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wd/4wd4 ftp://data.pdbj.org/pub/pdb/validation_reports/wd/4wd4 | HTTPS FTP |
-Related structure data
Related structure data | 5btqC 1n45S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
2 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Unit cell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: HIS / End label comp-ID: HIS / Refine code: _ / Auth seq-ID: 10 - 223 / Label seq-ID: 14 - 227
NCS ensembles :
|
-Components
#1: Protein | Mass: 33293.074 Da / Num. of mol.: 4 / Mutation: H29R Source method: isolated from a genetically manipulated source Details: Mutation H25R First four residues do not belong to the sequence of HO1 (trombin cleavage site, and cloning artifact). Source: (gene. exp.) Homo sapiens (human) / Gene: HMOX1, HO, HO1 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 References: UniProt: P09601, heme oxygenase (biliverdin-producing) #2: Chemical | ChemComp-HEM / #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 1.83 Å3/Da / Density % sol: 32.69 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 100 mM HEPES, pH 7.4; 2.1 M (NH4)2SO4; 0.9% 1,6-hexane-diol; BIG_CHAP |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 28, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.95→74.1 Å / Num. obs: 20111 / % possible obs: 97.4 % / Redundancy: 6.6 % / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 2.95→3.11 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 2 / % possible all: 92.4 |
-Processing
Software | Name: REFMAC / Version: 5.8.0073 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1N45 Resolution: 2.95→70.1 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.885 / SU B: 22.227 / SU ML: 0.39 / Cross valid method: THROUGHOUT / ESU R Free: 0.482 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.051 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.95→70.1 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|