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- PDB-3pvh: Structural and Functional Analysis of Arabidopsis thaliana thylak... -

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Basic information

Entry
Database: PDB / ID: 3pvh
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 / FOURIER SYNTHESIS / Resolution: 1.6 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 7, 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 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UPF0603 protein At1g54780, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,42710
Polymers16,6501
Non-polymers7779
Water3,243180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.871, 49.890, 76.511
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: 16649.684 Da / Num. of mol.: 1 / Fragment: Phosphatase domain, UNP residues 84-235
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: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 2.69 Å3/Da / Density % sol: 54.21 %
Crystal growTemperature: 296 K / Method: vapor diffusion / pH: 6.5
Details: 0.2M Sodium acetate trihydrate, 0.1M Sodium cacodylate (pH 6.5), 25-30% (w/v) Polyethylene glycol 4000 , VAPOR DIFFUSION, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 26, 2008 / Details: mirrors
RadiationMonochromator: Si (111) Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. obs: 24243 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Redundancy: 14.2 % / Biso Wilson estimate: 28.5 Å2 / Rmerge(I) obs: 0.035 / Rsym value: 0.035 / Net I/σ(I): 58.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym value% possible all
1.6-1.6614.40.3168.723970.316100
1.66-1.7214.40.2311.924070.23100
1.72-1.814.40.16317.924060.163100
1.8-1.914.50.10827.223790.108100
1.9-2.0214.40.06643.724170.066100
2.02-2.1714.40.0554.824240.05100
2.17-2.3914.40.0465.224330.04100
2.39-2.7414.40.03277.924480.032100
2.74-3.4514.20.02884.224810.028100
3.45-3012.30.0315524510.03193.6

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 3PTJ

3ptj


Resolution: 1.6→23.44 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.23 2346 -RANDOM
Rwork0.195 ---
all-24317 --
obs-23609 97.1 %-
Solvent computationBsol: 73.0172 Å2
Displacement parametersBiso mean: 32.72 Å2
Baniso -1Baniso -2Baniso -3
1--2.067 Å20 Å20 Å2
2---3.039 Å20 Å2
3---5.106 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.6→23.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1174 0 49 180 1403
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.022
X-RAY DIFFRACTIONc_angle_deg2.2
X-RAY DIFFRACTIONc_torsion_deg21.6
X-RAY DIFFRACTIONc_torsion_impr_deg1.38
X-RAY DIFFRACTIONc_mcbond_it1.5051.5
X-RAY DIFFRACTIONc_scbond_it2.5282
X-RAY DIFFRACTIONc_mcangle_it2.3182
X-RAY DIFFRACTIONc_scangle_it3.7982.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRfactor Rfree errorNum. reflection obs% reflection obs (%)
1.6-1.670.2752830.2350.016277092.8
1.67-1.760.2672730.2210.016284095.3
1.76-1.870.2752750.2280.017292096.7
1.87-2.020.2412860.1940.014294798.3
2.02-2.220.2313310.2020.013299499.2
2.22-2.540.2353060.1950.013303599.3
2.54-3.20.2213040.1820.013305799.6
3.2-300.2152880.1930.013304694.8
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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