Regulation of HMOX1 expression and activity / arachidonic acid omega-hydroxylase activity / Iron uptake and transport / response to 3-methylcholanthrene / Heme degradation / Cytoprotection by HMOX1 / negative regulation of mast cell degranulation / response to arachidonic acid / heme metabolic process / phospholipase D activity ...Regulation of HMOX1 expression and activity / arachidonic acid omega-hydroxylase activity / Iron uptake and transport / response to 3-methylcholanthrene / Heme degradation / Cytoprotection by HMOX1 / negative regulation of mast cell degranulation / response to arachidonic acid / heme metabolic process / phospholipase D activity / heme oxygenase (biliverdin-producing) / cellular response to cisplatin / heme oxidation / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / heme oxygenase (decyclizing) activity / wound healing involved in inflammatory response / negative regulation of muscle cell apoptotic process / positive regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / negative regulation of mast cell cytokine production / heme catabolic process / cellular response to arsenic-containing substance / cellular response to nutrient / negative regulation of epithelial cell apoptotic process / positive regulation of epithelial cell apoptotic process / erythrocyte homeostasis / epithelial cell apoptotic process / positive regulation of cell migration involved in sprouting angiogenesis / small GTPase-mediated signal transduction / negative regulation of macroautophagy / negative regulation of vascular associated smooth muscle cell proliferation / positive regulation of macroautophagy / phospholipid metabolic process / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / cellular response to cadmium ion / caveola / liver regeneration / macroautophagy / negative regulation of smooth muscle cell proliferation / positive regulation of smooth muscle cell proliferation / response to nicotine / response to hydrogen peroxide / regulation of blood pressure / multicellular organismal-level iron ion homeostasis / response to estrogen / positive regulation of angiogenesis / intrinsic apoptotic signaling pathway in response to DNA damage / cellular response to heat / cellular response to hypoxia / angiogenesis / intracellular iron ion homeostasis / response to oxidative stress / negative regulation of neuron apoptotic process / response to hypoxia / intracellular signal transduction / response to xenobiotic stimulus / negative regulation of cell population proliferation / 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 / identical protein binding / nucleus / metal ion binding Similarity search - Function
Resolution: 2.15→30 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.947 / SU B: 8.734 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.169 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.20855
861
5.1 %
RANDOM
Rwork
0.16245
-
-
-
obs
0.16467
16139
99.99 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parameters
Biso mean: 33.27 Å2
Baniso -1
Baniso -2
Baniso -3
1-
2.03 Å2
1.02 Å2
0 Å2
2-
-
2.03 Å2
0 Å2
3-
-
-
-3.05 Å2
Refinement step
Cycle: LAST / Resolution: 2.15→30 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1723
0
51
135
1909
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.025
0.022
1830
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
1.916
2.033
2491
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.815
5
211
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
36.17
24
90
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
15.434
15
307
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
15.908
15
11
X-RAY DIFFRACTION
r_chiral_restr
0.144
0.2
259
X-RAY DIFFRACTION
r_gen_planes_refined
0.011
0.021
1410
X-RAY DIFFRACTION
r_gen_planes_other
X-RAY DIFFRACTION
r_nbd_refined
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
X-RAY DIFFRACTION
r_symmetry_hbond_other
X-RAY DIFFRACTION
r_symmetry_metal_ion_refined
X-RAY DIFFRACTION
r_symmetry_metal_ion_other
X-RAY DIFFRACTION
r_mcbond_it
1.156
1.5
1062
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
2
2
1709
X-RAY DIFFRACTION
r_scbond_it
3.506
3
768
X-RAY DIFFRACTION
r_scangle_it
5.326
4.5
782
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 2.15→2.206 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.228
56
-
Rwork
0.186
1169
-
obs
-
-
99.84 %
Refinement TLS params.
Method: refined / Refine-ID: X-RAY DIFFRACTION
ID
L11 (°2)
L12 (°2)
L13 (°2)
L22 (°2)
L23 (°2)
L33 (°2)
S11 (Å °)
S12 (Å °)
S13 (Å °)
S21 (Å °)
S22 (Å °)
S23 (Å °)
S31 (Å °)
S32 (Å °)
S33 (Å °)
T11 (Å2)
T12 (Å2)
T13 (Å2)
T22 (Å2)
T23 (Å2)
T33 (Å2)
Origin x (Å)
Origin y (Å)
Origin z (Å)
1
0.484
-0.0774
-0.2762
0.6719
0.4986
1.9801
-0.013
-0.0043
-0.0003
0.0143
0.0085
-0.0088
0.0852
0.0067
0.0045
0.0039
0.001
0.0008
0.0066
0.0037
0.0024
-7.3219
-35.8456
-164.6782
2
1.4152
0.4774
-1.3414
6.1556
1.8383
5.6994
-0.0217
0.1796
-0.0068
-0.1255
-0.1234
-0.0985
-0.2451
-0.1595
0.1451
0.0164
-0.0045
-0.0087
0.0325
0.0044
0.0115
-2.2948
-27.3544
-168.6443
3
12.3828
-13.4153
-2.9232
51.0992
-8.5886
4.4718
-0.5444
-0.0521
0.1926
0.148
0.6771
0.0054
0.2657
-0.1904
-0.1326
0.0391
0.0034
0.0079
0.0232
0.0162
0.1046
-3.426
-32.92
-169.6492
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
11 - 222
2
X-RAY DIFFRACTION
2
A
300
3
X-RAY DIFFRACTION
3
A
2002
+
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