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- PDB-4mec: Crystal structure of RAT Heme oxygenase-1 in complex with ZN(II)-... -

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Basic information

Entry
Database: PDB / ID: 4mec
TitleCrystal structure of RAT Heme oxygenase-1 in complex with ZN(II)-Protoporphyrin IX
ComponentsHeme oxygenase 1HMOX1
KeywordsOXIDOREDUCTASE / All Alpha / Oxygenase / Heme Binding
Function / homology
Function and homology information


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 / heme metabolic process / response to arachidonic acid / 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 / heme metabolic process / response to arachidonic acid / 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 / erythrocyte homeostasis / positive regulation of epithelial cell apoptotic process / epithelial cell apoptotic process / negative regulation of macroautophagy / small GTPase-mediated signal transduction / positive regulation of cell migration involved in sprouting angiogenesis / 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 / response to nicotine / caveola / liver regeneration / negative regulation of smooth muscle cell proliferation / macroautophagy / positive regulation of smooth muscle cell proliferation / 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 / response to oxidative stress / intracellular iron ion homeostasis / 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 / perinuclear region of cytoplasm / structural molecule activity / enzyme binding / endoplasmic reticulum / protein homodimerization activity / identical protein binding / metal ion binding / nucleus
Similarity search - Function
Haem oxygenase conserved site / Heme oxygenase signature. / Haem oxygenase / Haem oxygenase-like / Heme oxygenase / Heme oxygenase-like / Heme Oxygenase; Chain A / Haem oxygenase-like, multi-helical / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING ZN / Heme oxygenase 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsSugishima, M.
CitationJournal: Biochemistry / Year: 2015
Title: Distal regulation of heme binding of heme oxygenase-1 mediated by conformational fluctuations
Authors: Harada, E. / Sugishima, M. / Harada, J. / Fukuyama, K. / Sugase, K.
History
DepositionAug 26, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 27, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2016Group: Database references
Revision 1.2Nov 8, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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: Heme oxygenase 1
B: Heme oxygenase 1
C: Heme oxygenase 1
D: Heme oxygenase 1
E: Heme oxygenase 1
F: Heme oxygenase 1
G: Heme oxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,21614
Polymers187,8347
Non-polymers4,3827
Water0
1
A: Heme oxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4592
Polymers26,8331
Non-polymers6261
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Heme oxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4592
Polymers26,8331
Non-polymers6261
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Heme oxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4592
Polymers26,8331
Non-polymers6261
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Heme oxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4592
Polymers26,8331
Non-polymers6261
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Heme oxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4592
Polymers26,8331
Non-polymers6261
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Heme oxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4592
Polymers26,8331
Non-polymers6261
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: Heme oxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4592
Polymers26,8331
Non-polymers6261
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.059, 73.167, 148.757
Angle α, β, γ (deg.)86.41, 87.62, 86.25
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16A
26G
17B
27C
18B
28D
19B
29E
110B
210F
111B
211G
112C
212D
113C
213E
114C
214F
115C
215G
116D
216E
117D
217F
118D
218G
119E
219F
120E
220G
121F
221G

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNTHRTHRAA11 - 22211 - 222
21GLNGLNTHRTHRBB11 - 22211 - 222
12GLNGLNTHRTHRAA11 - 22211 - 222
22GLNGLNTHRTHRCC11 - 22211 - 222
13SERSERTHRTHRAA10 - 22210 - 222
23SERSERTHRTHRDD10 - 22210 - 222
14SERSERGLUGLUAA10 - 22310 - 223
24SERSERGLUGLUEE10 - 22310 - 223
15ASPASPGLUGLUAA12 - 21212 - 212
25ASPASPGLUGLUFF12 - 21212 - 212
16ASPASPALAALAAA12 - 21912 - 219
26ASPASPALAALAGG12 - 21912 - 219
17GLNGLNTHRTHRBB11 - 22211 - 222
27GLNGLNTHRTHRCC11 - 22211 - 222
18GLNGLNTHRTHRBB11 - 22211 - 222
28GLNGLNTHRTHRDD11 - 22211 - 222
19GLNGLNTHRTHRBB11 - 22211 - 222
29GLNGLNTHRTHREE11 - 22211 - 222
110ASPASPGLUGLUBB12 - 21212 - 212
210ASPASPGLUGLUFF12 - 21212 - 212
111ASPASPALAALABB12 - 21912 - 219
211ASPASPALAALAGG12 - 21912 - 219
112GLNGLNTHRTHRCC11 - 22211 - 222
212GLNGLNTHRTHRDD11 - 22211 - 222
113GLNGLNGLUGLUCC11 - 22311 - 223
213GLNGLNGLUGLUEE11 - 22311 - 223
114ASPASPGLUGLUCC12 - 21212 - 212
214ASPASPGLUGLUFF12 - 21212 - 212
115ASPASPALAALACC12 - 21912 - 219
215ASPASPALAALAGG12 - 21912 - 219
116SERSERGLUGLUDD10 - 22310 - 223
216SERSERGLUGLUEE10 - 22310 - 223
117ASPASPGLUGLUDD12 - 21212 - 212
217ASPASPGLUGLUFF12 - 21212 - 212
118ASPASPALAALADD12 - 21912 - 219
218ASPASPALAALAGG12 - 21912 - 219
119ASPASPGLUGLUEE12 - 21212 - 212
219ASPASPGLUGLUFF12 - 21212 - 212
120ASPASPALAALAEE12 - 21912 - 219
220ASPASPALAALAGG12 - 21912 - 219
121ASPASPGLUGLUFF12 - 21212 - 212
221ASPASPGLUGLUGG12 - 21212 - 212

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21

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Components

#1: Protein
Heme oxygenase 1 / HMOX1 / HO-1 / HSP32


Mass: 26833.406 Da / Num. of mol.: 7 / Fragment: UNP residues 1-232
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Hmox1 / Plasmid: PET21A / Production host: Escherichia Coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P06762, heme oxygenase (biliverdin-producing)
#2: Chemical
ChemComp-ZNH / PROTOPORPHYRIN IX CONTAINING ZN


Mass: 626.051 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C34H32N4O4Zn

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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: 2.31 Å3/Da / Density % sol: 46.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 30% PEG 4000, 0.2M Sodium Acetate, 0.1M Tris-HCL, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1.2 / Wavelength: 1.2 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Apr 21, 2009
RadiationMonochromator: SI(111) DOUBLE MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.21
21.21
ReflectionResolution: 3.2→50 Å / Num. all: 27085 / Num. obs: 27085 / % possible obs: 97.8 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rsym value: 0.06 / Net I/σ(I): 14.4
Reflection shellResolution: 3.2→3.31 Å / Mean I/σ(I) obs: 2.7 / Rsym value: 0.27 / % possible all: 94

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DVE

1dve


Resolution: 3.2→38.94 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.913 / SU B: 81.531 / SU ML: 0.627 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.658 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.299 1347 5 %RANDOM
Rwork0.249 ---
all0.252 25650 --
obs0.252 25650 96.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 127.92 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å20.23 Å20.05 Å2
2---0.03 Å2-0.13 Å2
3---0.24 Å2
Refinement stepCycle: LAST / Resolution: 3.2→38.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11320 0 185 0 11505
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0211833
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8652.00216182
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.75751466
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.55124.044544
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.175151724
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.5521561
X-RAY DIFFRACTIONr_chiral_restr0.0540.21740
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0219266
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A2420.18
12B2420.18
21A2360.19
22C2360.19
31A2460.24
32D2460.24
41A2420.2
42E2420.2
51A1870.22
52F1870.22
61A1940.25
62G1940.25
71B2370.22
72C2370.22
81B2380.2
82D2380.2
91B2300.2
92E2300.2
101B1800.21
102F1800.21
111B1920.22
112G1920.22
121C2380.2
122D2380.2
131C2280.21
132E2280.21
141C1860.22
142F1860.22
151C1880.23
152G1880.23
161D2280.23
162E2280.23
171D1850.19
172F1850.19
181D1970.23
182G1970.23
191E1810.25
192F1810.25
201E1900.25
202G1900.25
211F1660.25
212G1660.25
LS refinement shellResolution: 3.19→3.28 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.434 98 -
Rwork0.318 1662 -
obs--85.19 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
13.10491.05110.71623.76721.66226.640.0080.23540.23-0.05110.16480.0246-0.2302-0.3633-0.17280.19490.25130.01110.3655-0.06480.8240.096-0.4540.323
25.2761.92221.3874.07941.07184.44270.0835-0.0245-0.66560.4013-0.06860.11520.2889-0.2078-0.01490.31870.30440.04020.398-0.00710.8338-20.626-27.00417
35.3468-0.52372.48212.12930.00116.38980.0953-0.2628-0.00840.4461-0.16450.2562-0.17840.03110.06920.54060.09330.1290.1097-0.11750.7505-29.726-52.7639.87
43.51941.42541.11843.77530.595212.03910.4089-0.10560.02691.22730.04840.12491.213-0.2481-0.45731.26320.13760.02970.0718-0.10320.4148-46.13-84.27356.432
52.78420.2211-1.15082.42362.986115.89190.4228-0.06260.2479-1.11410.03630.14571.1596-0.0248-0.4591.62930.1784-0.30460.1565-0.07620.3694-37.667-79.101103.433
66.31282.1435.10932.53651.651315.3038-0.1610.41830.01980.42920.1216-0.04920.55670.15960.03930.90820.1133-0.13280.1808-0.23230.3832-46.158-117.93877.868
72.4132-0.40093.83234.27834.504217.17950.23390.04630.0367-0.991-0.44160.17170.9690.20240.20761.08590.1658-0.0330.2655-0.12170.5636-31.568-111.321123.642
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 223
2X-RAY DIFFRACTION1A300
3X-RAY DIFFRACTION2B11 - 225
4X-RAY DIFFRACTION2B300
5X-RAY DIFFRACTION3C11 - 223
6X-RAY DIFFRACTION3C300
7X-RAY DIFFRACTION4D9 - 223
8X-RAY DIFFRACTION4D300
9X-RAY DIFFRACTION5E10 - 223
10X-RAY DIFFRACTION5E300
11X-RAY DIFFRACTION6F12 - 213
12X-RAY DIFFRACTION6F300
13X-RAY DIFFRACTION7G12 - 220
14X-RAY DIFFRACTION7G300

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