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- PDB-3dep: Structural basis for specific substrate recognition by the chloro... -

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Basic information

Entry
Database: PDB / ID: 3dep
TitleStructural basis for specific substrate recognition by the chloroplast signal recognition particle protein cpSRP43
Components
  • Signal recognition particle 43 kDa protein
  • YPGGSFDPLGLA
KeywordsPROTEIN TRANSPORT / MEMBRANE PROTEIN / Chloroplast SRP system / Signal recognition particle / signal sequence / ankyrin repeat / chromodomain / type I turn / substrate protein recognition / L18 region / LHCP / ANK repeat / Chloroplast / Coiled coil / Plastid / Ribonucleoprotein
Function / homology
Function and homology information


protein import into chloroplast thylakoid membrane / protein heterotrimerization / response to high light intensity / signal recognition particle, endoplasmic reticulum targeting / chloroplast envelope / chloroplast stroma / chloroplast thylakoid membrane / chloroplast / disordered domain specific binding / protein-macromolecule adaptor activity ...protein import into chloroplast thylakoid membrane / protein heterotrimerization / response to high light intensity / signal recognition particle, endoplasmic reticulum targeting / chloroplast envelope / chloroplast stroma / chloroplast thylakoid membrane / chloroplast / disordered domain specific binding / protein-macromolecule adaptor activity / protein domain specific binding / protein-containing complex / identical protein binding / metal ion binding / cytosol
Similarity search - Function
Signal recognition particle 43kDa protein / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. / Chromo/chromo shadow domain / Chromatin organization modifier domain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / Ankyrin repeat-containing domain / Chromo-like domain superfamily / Ankyrin repeat ...Signal recognition particle 43kDa protein / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. / Chromo/chromo shadow domain / Chromatin organization modifier domain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / Ankyrin repeat-containing domain / Chromo-like domain superfamily / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Signal recognition particle 43 kDa protein, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å
AuthorsHoldermann, I. / Stengel, K.F. / Wild, K. / Sinning, I.
CitationJournal: Science / Year: 2008
Title: Structural basis for specific substrate recognition by the chloroplast signal recognition particle protein cpSRP43.
Authors: Stengel, K.F. / Holdermann, I. / Cain, P. / Robinson, C. / Wild, K. / Sinning, I.
History
DepositionJun 10, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Signal recognition particle 43 kDa protein
B: YPGGSFDPLGLA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2713
Polymers21,2362
Non-polymers351
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1150 Å2
ΔGint-17 kcal/mol
Surface area10120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.473, 66.473, 219.703
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Signal recognition particle 43 kDa protein / Chromo protein SRP43 / CpSRP43


Mass: 20042.545 Da / Num. of mol.: 1 / Fragment: residues 85-267
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: CAO, At2g47450, T30B22.25 / Production host: Escherichia coli (E. coli) / References: UniProt: O22265
#2: Protein/peptide YPGGSFDPLGLA / LHCP L18 region


Mass: 1193.307 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic peptide
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 3.3 Å3/Da / Density % sol: 62.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 10, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2.7→35 Å / Num. all: 10129 / Num. obs: 8435 / % possible obs: 99.1 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.103 / Rsym value: 0.103 / Net I/σ(I): 3.6
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.451 / Mean I/σ(I) obs: 3.6 / Num. measured all: 8065 / Num. unique all: 1193 / Rsym value: 0.451 / % possible all: 99.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.25data scaling
PHASERphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 3DEO

3deo


Resolution: 2.7→35 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.903 / SU B: 14.793 / SU ML: 0.298 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.591 / ESU R Free: 0.355 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.298 397 4.7 %RANDOM
Rwork0.249 ---
obs0.252 8434 98.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 67.743 Å2
Baniso -1Baniso -2Baniso -3
1--3.3 Å2-1.65 Å20 Å2
2---3.3 Å20 Å2
3---4.95 Å2
Refinement stepCycle: LAST / Resolution: 2.7→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1492 0 1 8 1501
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221518
X-RAY DIFFRACTIONr_angle_refined_deg1.4521.9742058
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7875193
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.77924.28670
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.12815252
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7461512
X-RAY DIFFRACTIONr_chiral_restr0.1070.2229
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021162
X-RAY DIFFRACTIONr_nbd_refined0.2390.2705
X-RAY DIFFRACTIONr_nbtor_refined0.3140.21025
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2050.257
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1730.224
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0740.21
X-RAY DIFFRACTIONr_mcbond_it0.7761.5983
X-RAY DIFFRACTIONr_mcangle_it1.31421530
X-RAY DIFFRACTIONr_scbond_it1.5613610
X-RAY DIFFRACTIONr_scangle_it2.4934.5528
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.444 28 -
Rwork0.375 593 -
all-621 -
obs--99.36 %

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