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- PDB-6m0a: The heme-bound structure of the chloroplast protein At3g03890 -

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Basic information

Entry
Database: PDB / ID: 6m0a
TitleThe heme-bound structure of the chloroplast protein At3g03890
ComponentsAT3G03890 protein
KeywordsPLANT PROTEIN / heme binding protein
Function / homology
Function and homology information


tetrapyrrole biosynthetic process / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen / heme catabolic process / chloroplast / oxidoreductase activity / heme binding / protein homodimerization activity / metal ion binding
Similarity search - Function
Domain of unknown function DUF2470 / Domain of unknown function (DUF2470) / Haem oxygenase HugZ-like superfamily / Pyridoxamine 5'-phosphate oxidase, putative / Pyridoxamine 5'-phosphate oxidase / FMN-binding split barrel
Similarity search - Domain/homology
AZIDE ION / PROTOPORPHYRIN IX CONTAINING FE / Non-canonical heme oxygenase HOZ, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsWang, J. / Liu, L.
Funding support China, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2017YFA0503703 China
National Natural Science Foundation of China (NSFC)31370759 China
CitationJournal: Biochem.J. / Year: 2020
Title: The Arabidopsis locus AT3G03890 encodes a dimeric beta-barrel protein implicated in heme degradation.
Authors: Wang, J. / Guo, Q. / Li, X. / Wang, X. / Liu, L.
History
DepositionFeb 20, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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: AT3G03890 protein
B: AT3G03890 protein
C: AT3G03890 protein
D: AT3G03890 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,49212
Polymers127,8574
Non-polymers2,6348
Water4,900272
1
A: AT3G03890 protein
B: AT3G03890 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,2466
Polymers63,9292
Non-polymers1,3174
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5350 Å2
ΔGint-55 kcal/mol
Surface area24160 Å2
MethodPISA
2
C: AT3G03890 protein
D: AT3G03890 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,2466
Polymers63,9292
Non-polymers1,3174
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5510 Å2
ΔGint-56 kcal/mol
Surface area23780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.346, 79.936, 80.105
Angle α, β, γ (deg.)99.950, 109.410, 104.050
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 69 through 70 and (name N...
21(chain B and ((resid 69 through 70 and (name N...
31(chain C and ((resid 69 through 70 and (name N...
41(chain D and (resid 69 through 95 or resid 97...

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
11LYSLYSLEULEU(chain A and ((resid 69 through 70 and (name N...AA69 - 7040 - 41
12ASPASPHOHHOH(chain A and ((resid 69 through 70 and (name N...AA - M66 - 50137
13ASPASPHOHHOH(chain A and ((resid 69 through 70 and (name N...AA - M66 - 50137
21LYSLYSLEULEU(chain B and ((resid 69 through 70 and (name N...BB69 - 7040 - 41
22THRTHRHOHHOH(chain B and ((resid 69 through 70 and (name N...BB - N65 - 50136
23THRTHRHOHHOH(chain B and ((resid 69 through 70 and (name N...BB - N65 - 50136
31LYSLYSLEULEU(chain C and ((resid 69 through 70 and (name N...CC69 - 7040 - 41
32THRTHRHOHHOH(chain C and ((resid 69 through 70 and (name N...CC - O65 - 50136
33THRTHRHOHHOH(chain C and ((resid 69 through 70 and (name N...CC - O65 - 50136
41LYSLYSILEILE(chain D and (resid 69 through 95 or resid 97...DD69 - 9540 - 66
42GLYGLYGLYGLY(chain D and (resid 69 through 95 or resid 97...DD97 - 21268 - 183
43VALVALALAALA(chain D and (resid 69 through 95 or resid 97...DD213 - 214184 - 185
44VALVALHOHHOH(chain D and (resid 69 through 95 or resid 97...DD - P67 - 50138
45THRTHRTHRTHR(chain D and (resid 69 through 95 or resid 97...DD215186

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Components

#1: Protein
AT3G03890 protein / FMN binding protein


Mass: 31964.373 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At3g03890, F20H23.6, F20H23_6 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8LDU1
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-AZI / AZIDE ION


Mass: 42.020 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: N3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 272 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.66 Å3/Da / Density % sol: 53.71 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.2 M ammonium acetate, 0.1 M trisodium citrate, 25% (w/v) PEG 4,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 3, 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: 60833 / % possible obs: 78.3 % / Redundancy: 3.5 % / CC1/2: 0.99 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.047 / Net I/σ(I): 14.2
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.574 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 5279 / CC1/2: 0.764 / Rpim(I) all: 0.345

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4N7R

4n7r


Resolution: 2.2→32.844 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 25.5
RfactorNum. reflection% reflection
Rfree0.2329 2993 4.94 %
Rwork0.192 --
obs0.194 60639 90.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 127.06 Å2 / Biso mean: 56.9764 Å2 / Biso min: 24.16 Å2
Refinement stepCycle: final / Resolution: 2.2→32.844 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7748 0 184 272 8204
Biso mean--59.92 49.66 -
Num. residues----1016
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098124
X-RAY DIFFRACTIONf_angle_d0.9711054
X-RAY DIFFRACTIONf_chiral_restr0.0561236
X-RAY DIFFRACTIONf_plane_restr0.0051412
X-RAY DIFFRACTIONf_dihedral_angle_d16.4142955
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4658X-RAY DIFFRACTION10.708TORSIONAL
12B4658X-RAY DIFFRACTION10.708TORSIONAL
13C4658X-RAY DIFFRACTION10.708TORSIONAL
14D4658X-RAY DIFFRACTION10.708TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2-2.23610.28931090.2471218271
2.2361-2.27460.28981220.243256286
2.2746-2.3160.31581390.2392279593
2.316-2.36050.30671520.227287494
2.3605-2.40870.26761600.2208285095
2.4087-2.4610.28711330.2143286495
2.461-2.51820.28251630.2167288594
2.5182-2.58120.27131510.2169281994
2.5812-2.6510.26491620.205279093
2.651-2.72890.2471320.2156279092
2.7289-2.8170.30051300.2163267889
2.817-2.91760.30341360.2061248182
2.9176-3.03430.25121660.215289296
3.0343-3.17230.29721780.2164285795
3.1723-3.33940.23831360.2057288094
3.3394-3.54840.26371370.1999280393
3.5484-3.8220.23081130.1924278091
3.822-4.20590.18851500.1817249884
4.2059-4.81290.18011710.1517273792
4.8129-6.05750.19421400.1706289895
6.0575-32.8440.20031130.1727273190

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