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- PDB-3rrw: Crystal structure of the TL29 protein from Arabidopsis thaliana -

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Basic information

Entry
Database: PDB / ID: 3rrw
TitleCrystal structure of the TL29 protein from Arabidopsis thaliana
ComponentsThylakoid lumenal 29 kDa protein, chloroplastic
KeywordsPLANT PROTEIN / chloroplast thylakoid lumen
Function / homology
Function and homology information


thylakoid lumen / chloroplast thylakoid / thylakoid / chloroplast thylakoid lumen / Oxidoreductases / chloroplast thylakoid membrane / chloroplast / response to reactive oxygen species / hydrogen peroxide catabolic process / peroxidase activity ...thylakoid lumen / chloroplast thylakoid / thylakoid / chloroplast thylakoid lumen / Oxidoreductases / chloroplast thylakoid membrane / chloroplast / response to reactive oxygen species / hydrogen peroxide catabolic process / peroxidase activity / cellular response to oxidative stress / heme binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1620 / Class I peroxidase / Peroxidase; domain 1 - #10 / Peroxidase; domain 1 / Haem peroxidase / Peroxidase / Haem peroxidase superfamily / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PHOSPHATE ION / Thylakoid lumenal 29 kDa protein, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsLundberg, E. / Storm, P. / Schroder, W.P. / Funk, C.
CitationJournal: J.Struct.Biol. / Year: 2011
Title: Crystal structure of the TL29 protein from Arabidopsis thaliana: An APX homolog without peroxidase activity.
Authors: Lundberg, E. / Storm, P. / Schroder, W.P. / Funk, C.
History
DepositionMay 1, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2011Group: Database references
Revision 1.2Sep 21, 2011Group: Database references
Revision 1.3Nov 8, 2017Group: Data collection / Refinement description / Category: diffrn_source / software / Item: _diffrn_source.pdbx_synchrotron_site / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thylakoid lumenal 29 kDa protein, chloroplastic
B: Thylakoid lumenal 29 kDa protein, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,02611
Polymers59,2962
Non-polymers7319
Water77543
1
A: Thylakoid lumenal 29 kDa protein, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0626
Polymers29,6481
Non-polymers4145
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Thylakoid lumenal 29 kDa protein, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9645
Polymers29,6481
Non-polymers3164
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.350, 92.350, 143.460
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Thylakoid lumenal 29 kDa protein, chloroplastic / TL29 / AtAPx07 / P29 / Probable L-ascorbate peroxidase 4


Mass: 29647.926 Da / Num. of mol.: 2 / Fragment: Residues 83-349
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: TL29, APX4, At4g09010, F23J3.40 / Plasmid: pET-46 Ek/LIC / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 / References: UniProt: P82281
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 2.58 Å3/Da / Density % sol: 52.31 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: Reservoir solution: 16 % PEG 4000, 0.2M potassium phosphate, 10 % glycerol. Protein solution: 16 mM sodium phosphate, 0.1 M NaCl, 10 % glycerol, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 0.97926 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 6, 2009
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.5→48.28 Å / Num. all: 22173 / Num. obs: 22173 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.2 % / Rmerge(I) obs: 0.092
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.346 / Mean I/σ(I) obs: 4.3 / Num. unique all: 3160 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345data collection
PHENIXmodel building
REFMAC5.5.0072refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→46.17 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.901 / SU B: 21.384 / SU ML: 0.223 / Cross valid method: THROUGHOUT / ESU R Free: 0.306 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2755 1130 5.1 %RANDOM
Rwork0.22491 ---
all0.22753 20985 --
obs0.22753 20985 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.468 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å20 Å2
2---0.11 Å20 Å2
3---0.21 Å2
Refinement stepCycle: LAST / Resolution: 2.5→46.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3904 0 42 43 3989
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224001
X-RAY DIFFRACTIONr_angle_refined_deg1.3361.9795393
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6665505
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.36124.914175
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.99715710
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0081524
X-RAY DIFFRACTIONr_chiral_restr0.10.2596
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212978
X-RAY DIFFRACTIONr_mcbond_it0.7081.52510
X-RAY DIFFRACTIONr_mcangle_it1.33424012
X-RAY DIFFRACTIONr_scbond_it2.43431491
X-RAY DIFFRACTIONr_scangle_it3.8714.51381
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.38 84 -
Rwork0.323 1524 -
obs-1524 100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.7195-0.74150.36982.9737-1.93493.1-0.05-0.1309-0.04950.165-0.0174-0.0889-0.18720.26650.06750.0139-0.01770.00060.1431-0.020.057324.586187.537358.9641
23.7074-0.6989-0.08712.46690.37342.97050.02390.4225-0.3953-0.0253-0.00980.65270.3398-0.7271-0.01410.0484-0.0779-0.0020.23940.01880.242527.042450.019365.764
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 258
2X-RAY DIFFRACTION2B5 - 255

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