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- PDB-1twr: Crystal structures of ferrous and ferrous-NO forms of verdoheme i... -

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Basic information

Entry
Database: PDB / ID: 1twr
TitleCrystal structures of ferrous and ferrous-NO forms of verdoheme in a complex with human heme oxygenase-1: catalytic implications for heme cleavage
ComponentsHeme oxygenase 1
KeywordsOXIDOREDUCTASE / heme oxygenase-1 / heme degredation
Function / homology
Function and homology information


Regulation of HMOX1 expression and activity / heme oxygenase (biliverdin-producing) / heme oxidation / low-density lipoprotein particle clearance / smooth muscle hyperplasia / negative regulation of leukocyte migration / 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 / smooth muscle hyperplasia / negative regulation of leukocyte migration / 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 / epithelial cell apoptotic process / negative regulation of ferroptosis / erythrocyte homeostasis / Heme degradation / positive regulation of cell migration involved in sprouting angiogenesis / NFE2L2 regulating anti-oxidant/detoxification enzymes / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / negative regulation of macroautophagy / cellular response to cadmium ion / positive regulation of macroautophagy / The NLRP3 inflammasome / 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 / response to nicotine / positive regulation of smooth muscle cell proliferation / macroautophagy / negative regulation of smooth muscle cell proliferation / Heme signaling / Iron uptake and transport / Cytoprotection by HMOX1 / response to hydrogen peroxide / multicellular organismal-level iron ion homeostasis / positive regulation of angiogenesis / cellular response to heat / Interleukin-4 and Interleukin-13 signaling / angiogenesis / response to oxidative stress / mitochondrial outer membrane / intracellular iron ion homeostasis / positive regulation of canonical NF-kappaB signal transduction / intracellular signal transduction / 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 / 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
NITRIC OXIDE / IRON-OCTAETHYLPORPHYRIN / Heme oxygenase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLad, L. / Ortiz de Montellano, P.R. / Poulos, T.L.
CitationJournal: J.Inorg.Biochem. / Year: 2004
Title: Crystal structures of ferrous and ferrous-NO forms of verdoheme in a complex with human heme oxygenase-1: catalytic implications for heme cleavage.
Authors: Lad, L. / Ortiz de Montellano, P.R. / Poulos, T.L.
History
DepositionJul 1, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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

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Assembly

Deposited unit
A: Heme oxygenase 1
B: Heme oxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9526
Polymers53,7972
Non-polymers1,1554
Water3,477193
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.038, 54.258, 70.249
Angle α, β, γ (deg.)90.00, 98.12, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Heme oxygenase 1 / HO-1


Mass: 26898.615 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HMOX1, HO1, HO / Plasmid: pCWORI / Production host: Escherichia coli (E. coli) / Strain (production host): dh5alpha
References: UniProt: P09601, heme oxygenase (biliverdin-producing)
#2: Chemical ChemComp-VER / IRON-OCTAETHYLPORPHYRIN / VERDOHEME


Mass: 547.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C30H27FeN4O3
#3: Chemical ChemComp-NO / NITRIC OXIDE / Nitrogen monoxide


Mass: 30.006 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / Source method: isolated from a natural source / Formula: H2O

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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 Å3/Da / Density % sol: 23 %
Crystal growTemperature: 301 K / Method: liquid diffusion / pH: 8
Details: NH4SO4, Hepes, NaCl, pH 8.0, LIQUID DIFFUSION, temperature 301K

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Data collection

DiffractionMean temperature: 119 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 64321 / Num. obs: 59654 / % possible obs: 93.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8.1 % / Rmerge(I) obs: 0.097 / Rsym value: 0.025 / Net I/σ(I): 10.3
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.082 / Mean I/σ(I) obs: 2 / Num. unique all: 5476 / Rsym value: 0.25 / % possible all: 94.3

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1qq8

1qq8
PDB Unreleased entry


Highest resolution: 2.1 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
all0.276 64321 -
obs0.241 59654 93.1 %
Rfree-5476 -
Refinement stepCycle: LAST / Highest resolution: 2.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3490 0 80 193 3763
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.007
X-RAY DIFFRACTIONc_bond_d1.1
LS refinement shellResolution: 2.1→2.18 Å
RfactorNum. reflection% reflection
Rfree0.3361 248 -
Rwork0.2979 --
obs-4404 9.62 %

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