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- PDB-7eqh: Crystal structure of Arabidopsis GUN2/HO1 in complex with heme -

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Basic information

Entry
Database: PDB / ID: 7eqh
TitleCrystal structure of Arabidopsis GUN2/HO1 in complex with heme
ComponentsHeme oxygenase 1, chloroplastic
KeywordsOXIDOREDUCTASE / Arabidopsis / GUN2 / heme oxygenase / heme metabolism / heme / biliverdin
Function / homology
Function and homology information


chloroplast-nucleus signaling pathway / regulation of meristem growth / phytochromobilin biosynthetic process / carotenoid biosynthetic process / flavonoid biosynthetic process / regulation of stomatal movement / heme oxygenase (biliverdin-producing) / heme oxidation / heme oxygenase (decyclizing) activity / cellular response to UV-C ...chloroplast-nucleus signaling pathway / regulation of meristem growth / phytochromobilin biosynthetic process / carotenoid biosynthetic process / flavonoid biosynthetic process / regulation of stomatal movement / heme oxygenase (biliverdin-producing) / heme oxidation / heme oxygenase (decyclizing) activity / cellular response to UV-C / photosynthesis / chloroplast / heme binding / metal ion binding
Similarity search - Function
Haem oxygenase (decyclizing), plant / Haem oxygenase / Haem oxygenase-like / Heme oxygenase / Haem oxygenase-like, multi-helical
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Heme oxygenase 1, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLi, X. / Wang, J. / Liu, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31800251 China
CitationJournal: Febs Open Bio / Year: 2022
Title: Enzymological and structural characterization of Arabidopsis thaliana heme oxygenase-1.
Authors: Wang, J. / Li, X. / Chang, J.W. / Ye, T. / Mao, Y. / Wang, X. / Liu, L.
History
DepositionMay 2, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 11, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)56,7104
Polymers55,4772
Non-polymers1,2332
Water2,972165
1
A: Heme oxygenase 1, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3552
Polymers27,7381
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-20 kcal/mol
Surface area10890 Å2
MethodPISA
2
B: Heme oxygenase 1, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3552
Polymers27,7381
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-21 kcal/mol
Surface area10770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.622, 84.759, 92.870
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 71 through 113 or resid 115...
21(chain B and (resid 71 through 88 or (resid 89...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERVALVAL(chain A and (resid 71 through 113 or resid 115...AA71 - 11325 - 67
12GLYGLYLEULEU(chain A and (resid 71 through 113 or resid 115...AA115 - 16069 - 114
13GLUGLUGLUGLU(chain A and (resid 71 through 113 or resid 115...AA161115
14SERSERSERSER(chain A and (resid 71 through 113 or resid 115...AA71 - 28225 - 236
15SERSERSERSER(chain A and (resid 71 through 113 or resid 115...AA71 - 28225 - 236
16SERSERSERSER(chain A and (resid 71 through 113 or resid 115...AA71 - 28225 - 236
17SERSERSERSER(chain A and (resid 71 through 113 or resid 115...AA71 - 28225 - 236
21SERSERLYSLYS(chain B and (resid 71 through 88 or (resid 89...BB71 - 8825 - 42
22ASPASPASPASP(chain B and (resid 71 through 88 or (resid 89...BB8943
23SERSERSERSER(chain B and (resid 71 through 88 or (resid 89...BB71 - 28225 - 236
24SERSERSERSER(chain B and (resid 71 through 88 or (resid 89...BB71 - 28225 - 236
25SERSERSERSER(chain B and (resid 71 through 88 or (resid 89...BB71 - 28225 - 236
26SERSERSERSER(chain B and (resid 71 through 88 or (resid 89...BB71 - 28225 - 236

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Components

#1: Protein Heme oxygenase 1, chloroplastic / AtHO1 / Protein GENOMES UNCOUPLED 2 / Protein REVERSAL OF THE DET PHENOTYPE 4


Mass: 27738.320 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: HO1, GUN2, HY1, HY6, TED4, At2g26670, F18A8.4 / Production host: Escherichia coli (E. coli)
References: UniProt: O48782, heme oxygenase (biliverdin-producing)
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.36 Å3/Da / Density % sol: 47.95 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion
Details: 0.17 M Ammonium acetate, 0.085 M Sodium acetate trihydrate pH 4.6, 25.5% w/v Polyethylene glycol 4000, 15% v/v Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 27162 / % possible obs: 99.8 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.058 / Rrim(I) all: 0.142 / Χ2: 0.893 / Net I/σ(I): 5.1 / Num. measured all: 197106
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. unique obsCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
2.2-2.287.426860.850.5870.973100
2.28-2.377.526800.9340.3540.7671000.910.977
2.37-2.487.626490.9570.2670.7851000.6880.739
2.48-2.617.626890.9670.2130.8591000.5460.587
2.61-2.777.526840.9780.1620.9691000.4130.444
2.77-2.997.527120.9870.1070.9191000.2730.294
2.99-3.297.427120.9910.0740.9411000.1840.199
3.29-3.76727230.9940.0541.07399.90.130.141
3.76-4.746.627700.9950.041.02599.80.090.099
4.74-506.628570.9950.030.62298.20.0680.075

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IW1

1iw1


Resolution: 2.2→34.75 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2498 1306 5.2 %
Rwork0.2077 23814 -
obs0.2098 25120 92.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 79.82 Å2 / Biso mean: 35.0677 Å2 / Biso min: 19.93 Å2
Refinement stepCycle: final / Resolution: 2.2→34.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3486 0 86 165 3737
Biso mean--30.86 37.4 -
Num. residues----424
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2096X-RAY DIFFRACTION7.682TORSIONAL
12B2096X-RAY DIFFRACTION7.682TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.290.3584870.29381803189063
2.29-2.390.35141190.26282245236480
2.39-2.520.2851410.2432581272291
2.52-2.680.2951580.23922787294598
2.68-2.890.25211830.221628042987100
2.89-3.180.23471580.217428683026100
3.18-3.630.24931500.20528623012100
3.63-4.580.21271610.17522882304399
4.58-34.750.23371490.18792982313197

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