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- PDB-4wd4: Crystal structure of human HO1 H25R -

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Basic information

Entry
Database: PDB / ID: 4wd4
TitleCrystal structure of human HO1 H25R
ComponentsHeme oxygenase 1
KeywordsOXIDOREDUCTASE / 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) / heme oxidation / low-density lipoprotein particle clearance / negative regulation of leukocyte migration / heme oxygenase (decyclizing) activity / smooth muscle hyperplasia / wound healing involved in inflammatory response / cellular response to cisplatin / positive regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis ...Regulation of HMOX1 expression and activity / heme oxygenase (biliverdin-producing) / heme oxidation / low-density lipoprotein particle clearance / negative regulation of leukocyte migration / heme oxygenase (decyclizing) activity / smooth muscle hyperplasia / wound healing involved in inflammatory response / cellular response to cisplatin / positive regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / cellular response to arsenic-containing substance / heme catabolic process / positive regulation of epithelial cell apoptotic process / endothelial cell proliferation / positive regulation of cell migration involved in sprouting angiogenesis / epithelial cell apoptotic process / Heme degradation / NFE2L2 regulating anti-oxidant/detoxification enzymes / erythrocyte homeostasis / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / negative regulation of ferroptosis / negative regulation of macroautophagy / cellular response to cadmium ion / The NLRP3 inflammasome / positive regulation of macroautophagy / regulation of angiogenesis / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / Purinergic signaling in leishmaniasis infection / positive regulation of chemokine production / negative regulation of cytokine production involved in inflammatory response / positive regulation of smooth muscle cell proliferation / response to nicotine / macroautophagy / negative regulation of smooth muscle cell proliferation / response to hydrogen peroxide / Iron uptake and transport / Heme signaling / Cytoprotection by HMOX1 / multicellular organismal-level iron ion homeostasis / positive regulation of angiogenesis / cellular response to heat / response to oxidative stress / angiogenesis / Interleukin-4 and Interleukin-13 signaling / intracellular iron ion homeostasis / mitochondrial outer membrane / positive regulation of canonical NF-kappaB signal transduction / intracellular signal transduction / heme binding / regulation of transcription by RNA polymerase II / endoplasmic reticulum membrane / perinuclear region of cytoplasm / structural molecule activity / enzyme binding / endoplasmic reticulum / protein homodimerization activity / extracellular space / nucleoplasm / metal ion binding / identical protein binding / nucleus / membrane / cytosol
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 FE / Heme oxygenase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsCaaveiro, J.M.M. / Morante, K. / Sigala, P. / Tsumoto, K.
CitationJournal: 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
DepositionSep 6, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2016Group: Database references
Revision 1.2Sep 14, 2016Group: Database references
Revision 1.3Jan 29, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,11510
Polymers133,1724
Non-polymers2,9436
Water41423
1
A: Heme oxygenase 1
B: Heme oxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,0575
Polymers66,5862
Non-polymers1,4713
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4560 Å2
ΔGint-35 kcal/mol
Surface area19150 Å2
MethodPISA
2
C: Heme oxygenase 1
D: Heme oxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,0575
Polymers66,5862
Non-polymers1,4713
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4530 Å2
ΔGint-33 kcal/mol
Surface area19260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.080, 54.410, 122.280
Angle α, β, γ (deg.)90.00, 99.09, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

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

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Heme oxygenase 1 / HO-1


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 / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.83 Å3/Da / Density % sol: 32.69 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 28, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.95→74.1 Å / Num. obs: 20111 / % possible obs: 97.4 % / Redundancy: 6.6 % / Net I/σ(I): 8.7
Reflection shellResolution: 2.95→3.11 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 2 / % possible all: 92.4

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Processing

SoftwareName: REFMAC / Version: 5.8.0073 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1N45

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
RfactorNum. reflection% reflectionSelection details
Rfree0.25859 1052 5.2 %RANDOM
Rwork0.20326 ---
obs0.20608 19055 97.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.051 Å2
Baniso -1Baniso -2Baniso -3
1--0.94 Å20 Å2-1.16 Å2
2---2.74 Å20 Å2
3---3.85 Å2
Refinement stepCycle: 1 / Resolution: 2.95→70.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6984 0 202 23 7209
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0197377
X-RAY DIFFRACTIONr_bond_other_d0.0040.027047
X-RAY DIFFRACTIONr_angle_refined_deg1.3882.00310025
X-RAY DIFFRACTIONr_angle_other_deg1.075316172
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6885852
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.1223.778360
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.634151277
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8121556
X-RAY DIFFRACTIONr_chiral_restr0.0780.21060
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0218284
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021780
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_it2.5564.7493420
X-RAY DIFFRACTIONr_mcbond_other2.5514.7483419
X-RAY DIFFRACTIONr_mcangle_it4.2667.1154268
X-RAY DIFFRACTIONr_mcangle_other4.2667.1164269
X-RAY DIFFRACTIONr_scbond_it2.8515.2073957
X-RAY DIFFRACTIONr_scbond_other2.8515.2073957
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9327.75758
X-RAY DIFFRACTIONr_long_range_B_refined7.538.8078713
X-RAY DIFFRACTIONr_long_range_B_other7.538.8098714
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)
11A132130.09
12B132130.09
21A133640.09
22C133640.09
31A134010.09
32D134010.09
41B134320.09
42C134320.09
51B132500.08
52D132500.08
61C132780.09
62D132780.09
LS refinement shellResolution: 2.95→3.027 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 94 -
Rwork0.33 1271 -
obs--89.63 %

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