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- PDB-6m09: The ligand-free structure of the chloroplast protein At3g03890 -

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Basic information

Entry
Database: PDB / ID: 6m09
TitleThe ligand-free structure of the chloroplast protein At3g03890
ComponentsAT3G03890 protein
KeywordsPLANT PROTEIN / heme binding protein
Function / homology
Function and homology information


heme catabolic process / chloroplast / heme binding / protein homodimerization activity / metal ion binding
Similarity search - Function
Pyridoxamine 5'-phosphate oxidase / Domain of unknown function DUF2470 / Domain of unknown function (DUF2470) / Haem oxygenase HugZ-like superfamily / Pyridoxamine 5'-phosphate oxidase / FMN-binding split barrel
Similarity search - Domain/homology
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.101 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


Theoretical massNumber of molelcules
Total (without water)127,8574
Polymers127,8574
Non-polymers00
Water10,233568
1
A: AT3G03890 protein
B: AT3G03890 protein


Theoretical massNumber of molelcules
Total (without water)63,9292
Polymers63,9292
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2760 Å2
ΔGint-12 kcal/mol
Surface area23250 Å2
MethodPISA
2
C: AT3G03890 protein
D: AT3G03890 protein


Theoretical massNumber of molelcules
Total (without water)63,9292
Polymers63,9292
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2710 Å2
ΔGint-12 kcal/mol
Surface area23380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.930, 79.964, 80.151
Angle α, β, γ (deg.)99.630, 109.800, 104.480
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 70 through 75 or (resid 76...
21(chain B and (resid 70 through 95 or resid 97...
31(chain C and (resid 70 through 75 or (resid 76...
41(chain D and (resid 70 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
11LEULEUGLUGLU(chain A and (resid 70 through 75 or (resid 76...AA70 - 7541 - 46
12GLUGLUALAALA(chain A and (resid 70 through 75 or (resid 76...AA76 - 7947 - 50
13LEULEUALAALA(chain A and (resid 70 through 75 or (resid 76...AA70 - 31741 - 288
14LEULEUALAALA(chain A and (resid 70 through 75 or (resid 76...AA70 - 31741 - 288
15LEULEUALAALA(chain A and (resid 70 through 75 or (resid 76...AA70 - 31741 - 288
16LEULEUALAALA(chain A and (resid 70 through 75 or (resid 76...AA70 - 31741 - 288
21LEULEUILEILE(chain B and (resid 70 through 95 or resid 97...BB70 - 9541 - 66
22GLYGLYGLYGLY(chain B and (resid 70 through 95 or resid 97...BB9768
23LEULEUTYRTYR(chain B and (resid 70 through 95 or resid 97...BB99 - 10670 - 77
24ASPASPASPASP(chain B and (resid 70 through 95 or resid 97...BB152123
25PHEPHELYSLYS(chain B and (resid 70 through 95 or resid 97...BB68 - 31939 - 290
26ASPASPASPASP(chain B and (resid 70 through 95 or resid 97...BB152123
27PHEPHELYSLYS(chain B and (resid 70 through 95 or resid 97...BB68 - 31939 - 290
28PHEPHELYSLYS(chain B and (resid 70 through 95 or resid 97...BB68 - 31939 - 290
29PHEPHELYSLYS(chain B and (resid 70 through 95 or resid 97...BB68 - 31939 - 290
210PHEPHELYSLYS(chain B and (resid 70 through 95 or resid 97...BB68 - 31939 - 290
31LEULEUGLUGLU(chain C and (resid 70 through 75 or (resid 76...CC70 - 7541 - 46
32GLUGLUALAALA(chain C and (resid 70 through 75 or (resid 76...CC76 - 7947 - 50
33LEULEUALAALA(chain C and (resid 70 through 75 or (resid 76...CC70 - 31741 - 288
34LEULEUALAALA(chain C and (resid 70 through 75 or (resid 76...CC70 - 31741 - 288
35LEULEUALAALA(chain C and (resid 70 through 75 or (resid 76...CC70 - 31741 - 288
36LEULEUALAALA(chain C and (resid 70 through 75 or (resid 76...CC70 - 31741 - 288
41LEULEUILEILE(chain D and (resid 70 through 95 or resid 97...DD70 - 9541 - 66
42GLYGLYGLYGLY(chain D and (resid 70 through 95 or resid 97...DD9768
43LEULEUTYRTYR(chain D and (resid 70 through 95 or resid 97...DD99 - 10670 - 77
44ALAALAARGARG(chain D and (resid 70 through 95 or resid 97...DD150 - 151121 - 122
45PHEPHESERSER(chain D and (resid 70 through 95 or resid 97...DD68 - 32039 - 291
46ASPASPASPASP(chain D and (resid 70 through 95 or resid 97...DD152123
47PHEPHESERSER(chain D and (resid 70 through 95 or resid 97...DD68 - 32039 - 291
48PHEPHESERSER(chain D and (resid 70 through 95 or resid 97...DD68 - 32039 - 291
49PHEPHESERSER(chain D and (resid 70 through 95 or resid 97...DD68 - 32039 - 291
410PHEPHESERSER(chain D and (resid 70 through 95 or resid 97...DD68 - 32039 - 291
411PHEPHESERSER(chain D and (resid 70 through 95 or resid 97...DD68 - 32039 - 291

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 568 / 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: 2.63 Å3/Da / Density % sol: 53.23 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.6 / Details: ammonium acetate, trisodium citrate, PEG 4000

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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: Nov 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 73700 / % possible obs: 97.2 % / Redundancy: 2 % / Biso Wilson estimate: 25.18 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.047 / Rrim(I) all: 0.066 / Net I/σ(I): 17.1
Reflection shellResolution: 2.1→2.18 Å / Rmerge(I) obs: 0.548 / Num. unique obs: 7308 / CC1/2: 0.577 / Rpim(I) all: 0.548 / Rrim(I) all: 0.775 / % possible all: 96.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXv1.12refinement
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4N7R

4n7r


Resolution: 2.101→37.763 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 25.49
RfactorNum. reflection% reflection
Rfree0.2395 3358 5.08 %
Rwork0.1996 --
obs0.2016 66069 87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 86.14 Å2 / Biso mean: 34.7165 Å2 / Biso min: 8.09 Å2
Refinement stepCycle: final / Resolution: 2.101→37.763 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7442 0 0 568 8010
Biso mean---33.52 -
Num. residues----997
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4269X-RAY DIFFRACTION10.052TORSIONAL
12B4269X-RAY DIFFRACTION10.052TORSIONAL
13C4269X-RAY DIFFRACTION10.052TORSIONAL
14D4269X-RAY DIFFRACTION10.052TORSIONAL
LS refinement shellResolution: 2.101→2.176 Å
RfactorNum. reflection% reflection
Rfree0.29 --
Rwork0.25 --
obs-4002 52.78 %

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