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- PDB-8wb2: Heme-bound Arabidopsis thaliana temperature-induced lipocalin -

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Basic information

Entry
Database: PDB / ID: 8wb2
TitleHeme-bound Arabidopsis thaliana temperature-induced lipocalin
ComponentsTemperature-induced lipocalin-1
KeywordsPLANT PROTEIN / heme / Arabidopsis thaliana / lipocalin
Function / homology
Function and homology information


response to paraquat / response to freezing / positive regulation of response to salt stress / heat acclimation / seed maturation / positive regulation of response to oxidative stress / chloroplast membrane / response to high light intensity / hyperosmotic salinity response / intracellular chloride ion homeostasis ...response to paraquat / response to freezing / positive regulation of response to salt stress / heat acclimation / seed maturation / positive regulation of response to oxidative stress / chloroplast membrane / response to high light intensity / hyperosmotic salinity response / intracellular chloride ion homeostasis / nutrient reservoir activity / response to water deprivation / plasmodesma / plant-type vacuole / intracellular sodium ion homeostasis / chloroplast envelope / plastid / response to light stimulus / response to cold / lipid metabolic process / cytoplasmic side of plasma membrane / cellular response to hypoxia / response to heat / Golgi apparatus / endoplasmic reticulum / mitochondrion / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Lipocalin, bacterial / : / Lipocalin-like domain / Lipocalin, ApoD type / Lipocalin family conserved site / Lipocalin/cytosolic fatty-acid binding domain / Calycin / Lipocalin signature.
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Temperature-induced lipocalin-1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsDong, C. / Liu, L.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32000444 China
National Natural Science Foundation of China (NSFC)32201041 China
CitationJournal: Biochim Biophys Acta Gen Subj / Year: 2023
Title: Crystallographic and functional studies of a plant temperature-induced lipocalin.
Authors: Dong, C.S. / Zhang, W.L. / Wang, X.Y. / Wang, X. / Wang, J. / Wang, M. / Fang, Y. / Liu, L.
History
DepositionSep 8, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 27, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 3, 2024Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Temperature-induced lipocalin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3052
Polymers23,6891
Non-polymers6161
Water2,504139
1
A: Temperature-induced lipocalin-1
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)145,83112
Polymers142,1326
Non-polymers3,6996
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
crystal symmetry operation10_545y+2/3,x-2/3,-z+1/31
crystal symmetry operation11_445x-y-1/3,-y-2/3,-z+1/31
crystal symmetry operation12_555-x+2/3,-x+y+1/3,-z+1/31
Buried area20870 Å2
ΔGint-228 kcal/mol
Surface area45680 Å2
MethodPISA
2
A: Temperature-induced lipocalin-1
hetero molecules

A: Temperature-induced lipocalin-1
hetero molecules

A: Temperature-induced lipocalin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,9156
Polymers71,0663
Non-polymers1,8493
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area8850 Å2
ΔGint-95 kcal/mol
Surface area24430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.685, 75.685, 208.238
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-463-

HOH

21A-496-

HOH

31A-502-

HOH

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Components

#1: Protein Temperature-induced lipocalin-1 / AtTIL1


Mass: 23688.615 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: TIL, At5g58070, K21L19.6 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9FGT8
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2.42 Å3/Da / Density % sol: 49.23 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: Tris-HCl, PEG4000, lithium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 17, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 18556 / % possible obs: 99.9 % / Redundancy: 18.9 % / CC1/2: 0.993 / CC star: 0.998 / Rmerge(I) obs: 0.069 / Rrim(I) all: 0.071 / Net I/σ(I): 42.4
Reflection shellResolution: 1.9→1.97 Å / Mean I/σ(I) obs: 2.25 / Num. unique obs: 1811 / CC1/2: 0.844 / Rpim(I) all: 0.374 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→27.09 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1953 940 5.09 %
Rwork0.1738 --
obs0.1749 18472 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→27.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1500 0 0 139 1639
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071565
X-RAY DIFFRACTIONf_angle_d0.862148
X-RAY DIFFRACTIONf_dihedral_angle_d17.14571
X-RAY DIFFRACTIONf_chiral_restr0.056215
X-RAY DIFFRACTIONf_plane_restr0.006271
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-20.2871230.26142478X-RAY DIFFRACTION100
2-2.130.27261410.21472437X-RAY DIFFRACTION100
2.13-2.290.2351390.19912486X-RAY DIFFRACTION100
2.29-2.520.2891470.20232464X-RAY DIFFRACTION100
2.52-2.880.24021160.20122515X-RAY DIFFRACTION100
2.88-3.630.20821310.18182539X-RAY DIFFRACTION100
3.63-27.090.1511430.14672613X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 16.5203 Å / Origin y: -23.258 Å / Origin z: 15.8159 Å
111213212223313233
T0.3683 Å2-0.0033 Å20.0283 Å2-0.4046 Å2-0.0217 Å2--0.3546 Å2
L1.9826 °20.0462 °20.8296 °2-1.1677 °20.1916 °2--1.5654 °2
S-0.018 Å °-0.2521 Å °0.0602 Å °0.0111 Å °-0.0439 Å °0.1747 Å °-0.0721 Å °-0.2643 Å °0.0626 Å °
Refinement TLS groupSelection details: all

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