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- PDB-5btq: Crystal structure of human heme oxygenase 1 H25R with biliverdin bound -

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Basic information

Entry
Database: PDB / ID: 5btq
TitleCrystal structure of human heme oxygenase 1 H25R with biliverdin bound
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 / smooth muscle hyperplasia / heme oxygenase (decyclizing) activity / 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 / smooth muscle hyperplasia / heme oxygenase (decyclizing) activity / 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 / erythrocyte homeostasis / NFE2L2 regulating anti-oxidant/detoxification enzymes / 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 / Purinergic signaling in leishmaniasis infection / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / 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
BILIVERDINE IX ALPHA / Heme oxygenase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 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
DepositionJun 3, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 8, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2016Group: Database references
Revision 1.2Sep 14, 2016Group: Database references
Revision 1.3Feb 19, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9245
Polymers54,6622
Non-polymers1,2613
Water3,117173
1
A: Heme oxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0103
Polymers27,3311
Non-polymers6792
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Heme oxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9142
Polymers27,3311
Non-polymers5831
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4740 Å2
ΔGint-37 kcal/mol
Surface area19180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.700, 54.740, 72.510
Angle α, β, γ (deg.)90.00, 99.37, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: THR / End label comp-ID: THR / Refine code: _ / Auth seq-ID: 11 - 222 / Label seq-ID: 15 - 226

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Heme oxygenase 1 / HO-1


Mass: 27331.133 Da / Num. of mol.: 2 / Fragment: UNP residues 1-233 / Mutation: H29R
Source method: isolated from a genetically manipulated source
Details: Mutation H25R / Source: (gene. exp.) Homo sapiens (human) / Gene: HMOX1, HO, HO1 / Plasmid: pET28 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: P09601, heme oxygenase (biliverdin-producing)
#2: Chemical ChemComp-BLA / BILIVERDINE IX ALPHA


Mass: 582.646 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C33H34N4O6
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 2.21 Å3/Da / Density % sol: 44.35 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 100mM HEPES 2.1M Ammonium sulfate 0.9% 1,6-hexanediol

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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: Nov 4, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.08→43.5 Å / Num. obs: 26949 / % possible obs: 93.3 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 14.4
Reflection shellResolution: 2.08→2.19 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.407 / Mean I/σ(I) obs: 3.5 / % possible all: 75.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1N45

1n45


Resolution: 2.08→43.5 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.924 / SU B: 5.444 / SU ML: 0.143 / Cross valid method: THROUGHOUT / ESU R: 0.237 / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22818 1399 5.2 %RANDOM
Rwork0.18269 ---
obs0.18503 25550 93.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.208 Å2
Baniso -1Baniso -2Baniso -3
1-1 Å20 Å2-1.3 Å2
2---1.44 Å20 Å2
3---0.82 Å2
Refinement stepCycle: 1 / Resolution: 2.08→43.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3493 0 91 173 3757
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0193675
X-RAY DIFFRACTIONr_bond_other_d0.0050.023510
X-RAY DIFFRACTIONr_angle_refined_deg1.9061.9944977
X-RAY DIFFRACTIONr_angle_other_deg1.12338053
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0225428
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.11223.846182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.24215641
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9321528
X-RAY DIFFRACTIONr_chiral_restr0.0860.2524
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214135
X-RAY DIFFRACTIONr_gen_planes_other0.010.02885
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_it1.972.7211712
X-RAY DIFFRACTIONr_mcbond_other1.9652.7191711
X-RAY DIFFRACTIONr_mcangle_it2.9594.0682137
X-RAY DIFFRACTIONr_mcangle_other2.964.072138
X-RAY DIFFRACTIONr_scbond_it2.7963.1881963
X-RAY DIFFRACTIONr_scbond_other2.7923.1841960
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4894.6192833
X-RAY DIFFRACTIONr_long_range_B_refined6.03523.0224435
X-RAY DIFFRACTIONr_long_range_B_other5.98922.9974371
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 12947 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.08→2.134 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 71 -
Rwork0.249 1385 -
obs--68.61 %

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