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- PDB-3ptj: Structural and functional Analysis of Arabidopsis thaliana thylak... -

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Basic information

Entry
Database: PDB / ID: 3ptj
TitleStructural and functional Analysis of Arabidopsis thaliana thylakoid lumen protein AtTLP18.3
ComponentsUPF0603 protein At1g54780, chloroplastic
KeywordsHYDROLASE / TAP domain / Rossmann fold / Acid Phosphatase / Arabidopsis thaliana thylakoid lumen
Function / homology
Function and homology information


photosystem II repair / thylakoid lumen / chloroplast thylakoid / acid phosphatase activity / thylakoid / chloroplast thylakoid membrane / chloroplast / mRNA binding / nucleus
Similarity search - Function
Diaminopimelate Epimerase; Chain A, domain 1 - #50 / TPM domain / TPM domain / Diaminopimelate Epimerase; Chain A, domain 1 / Roll / Alpha Beta
Similarity search - Domain/homology
UPF0603 protein At1g54780, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsWu, H.Y. / Liu, M.S. / Lin, T.P. / Cheng, Y.S.
CitationJournal: Plant Physiol. / Year: 2011
Title: Structural and functional assays of AtTLP18.3 identify its novel acid phosphatase activity in thylakoid lumen
Authors: Wu, H.Y. / Liu, M.S. / Lin, T.P. / Cheng, Y.S.
History
DepositionDec 3, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 26, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2012Group: Database references
Revision 1.2Nov 12, 2014Group: Structure summary
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UPF0603 protein At1g54780, chloroplastic


Theoretical massNumber of molelcules
Total (without water)16,7801
Polymers16,7801
Non-polymers00
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.977, 49.839, 76.672
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein UPF0603 protein At1g54780, chloroplastic / AtTLP18.3 / Thylakoid lumen 18.3 kDa protein


Mass: 16779.549 Da / Num. of mol.: 1 / Fragment: Phosphatase domain, UNP residues 84-235 / Mutation: L128M, I159M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Strain: cv. Columbia / Gene: At1g54780, T22H22.19 / Plasmid: pGEX6P1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9ZVL6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.67 Å3/Da / Density % sol: 54.01 %
Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS
Crystal growTemperature: 296 K / Method: vapor diffusion / pH: 6
Details: 0.2M Sodium acetate trihydrate, 0.1M Sodium cacodylate, 25-30% (w/v) Polyethylene glycol 4000, 2mM TCEP , pH 6.0, VAPOR DIFFUSION, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.97884 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 21, 2008 / Details: MIRRORS
RadiationMonochromator: Si (111) Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97884 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 11594 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.9 % / Biso Wilson estimate: 33.5 Å2 / Rmerge(I) obs: 0.046 / Rsym value: 0.046 / Net I/σ(I): 30.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym value% possible all
2.6-2.6910.20.05538.45670.06299.6
2.69-2.810.20.0638.25840.06299.8
2.8-2.9310.20.05739.15790.05699.3
2.93-3.0810.10.04840.55600.04999.5
3.08-3.2810.20.04445.25820.04399.1
3.28-3.539.90.04541.55690.04298.1
3.53-3.889.70.04836.45790.04398.1
3.88-4.449.40.04929.95700.04595.8
4.44-5.599.20.04426.55860.04495.1
5.59-309.40.04922.96210.04994.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.6→30 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: SF file contains Friedel pairs
RfactorNum. reflection% reflectionSelection details
Rfree0.269 552 -RANDOM
Rwork0.199 ---
all-10699 --
obs-10497 98.1 %-
Solvent computationBsol: 36.14 Å2
Displacement parametersBiso mean: 32.44 Å2
Baniso -1Baniso -2Baniso -3
1-0.843 Å20 Å20 Å2
2---8.148 Å20 Å2
3---7.305 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1174 0 0 67 1241
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_torsion_deg22.5
X-RAY DIFFRACTIONc_torsion_impr_deg1.17
X-RAY DIFFRACTIONc_mcbond_it1.4291.5
X-RAY DIFFRACTIONc_scbond_it2.3512
X-RAY DIFFRACTIONc_mcangle_it2.3822
X-RAY DIFFRACTIONc_scangle_it3.4732.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRfactor Rfree errorNum. reflection obs% reflection obs (%)
2.6-2.720.304740.2110.035130798.4
2.72-2.860.369520.2210.051135398.8
2.86-3.040.323780.2240.037130799.5
3.04-3.270.234680.1940.028133599.2
3.27-3.60.236790.1770.027131197.9
3.6-4.120.293650.1810.036131898.2
4.12-5.190.21750.1830.024126795.6
5.19-300.308610.2340.039129997.1
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4glycerol.paramglycerol.top

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