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- PDB-4ak9: Structure of chloroplast FtsY from Physcomitrella patens -

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Basic information

Entry
Database: PDB / ID: 4ak9
TitleStructure of chloroplast FtsY from Physcomitrella patens
ComponentsCPFTSY
KeywordsPROTEIN TRANSPORT / CHLOROPLAST BIOGENESIS / SIMIBI GTPASE
Function / homology
Function and homology information


SRP-dependent cotranslational protein targeting to membrane / GTP binding / membrane
Similarity search - Function
SRP54, nucleotide-binding domain / Signal-recognition particle receptor FtsY / SRP/SRP receptor, N-terminal / SRP54-type proteins GTP-binding domain signature. / Signal recognition particle SRP54, helical bundle / Signal recognition particle SRP54, N-terminal domain superfamily / SRP54-type protein, helical bundle domain / SRP54-type protein, helical bundle domain / Signal recognition particle, SRP54 subunit, GTPase domain / SRP54-type protein, GTPase domain ...SRP54, nucleotide-binding domain / Signal-recognition particle receptor FtsY / SRP/SRP receptor, N-terminal / SRP54-type proteins GTP-binding domain signature. / Signal recognition particle SRP54, helical bundle / Signal recognition particle SRP54, N-terminal domain superfamily / SRP54-type protein, helical bundle domain / SRP54-type protein, helical bundle domain / Signal recognition particle, SRP54 subunit, GTPase domain / SRP54-type protein, GTPase domain / SRP54-type protein, GTPase domain / Four Helix Bundle (Hemerythrin (Met), subunit A) / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Up-down Bundle / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesPHYSCOMITRELLA PATENS (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsTrager, C. / Schunemann, D. / Hofmann, E.
CitationJournal: Plant Cell / Year: 2012
Title: Evolution from the Prokaryotic to the Higher Plant Chloroplast Signal Recognition Particle: The Signal Recognition Particle RNA is Conserved in Plastids of a Wide Range of Photosynthetic Organisms.
Authors: Trager, C. / Rosenblad, M.A. / Ziehe, D. / Garcia-Petit, C. / Schrader, L. / Kock, K. / Vera Richter, C. / Klinkert, B. / Narberhaus, F. / Herrmann, C. / Hofmann, E. / Aronsson, H. / Schunemann, D.
History
DepositionFeb 22, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 16, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2013Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CPFTSY
B: CPFTSY


Theoretical massNumber of molelcules
Total (without water)69,1212
Polymers69,1212
Non-polymers00
Water8,737485
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2090 Å2
ΔGint-4.2 kcal/mol
Surface area24680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.580, 123.460, 75.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-2117-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 80:101 OR RESSEQ 110:138 OR RESSEQ...
211CHAIN B AND (RESSEQ 80:101 OR RESSEQ 110:138 OR RESSEQ...

NCS oper:
IDCodeMatrixVector
1given(-0.991158, -0.130699, 0.022884), (-0.130586, 0.991417, 0.006374), (-0.023521, 0.003329, -0.999718)0.91759, 0.16267, -39.8886
2given(-0.991158, -0.130699, 0.022884), (-0.130586, 0.991417, 0.006374), (-0.023521, 0.003329, -0.999718)0.91759, 0.16267, -39.8886
3given(-0.991158, -0.130699, 0.022884), (-0.130586, 0.991417, 0.006374), (-0.023521, 0.003329, -0.999718)0.91759, 0.16267, -39.8886
4given(-0.991158, -0.130699, 0.022884), (-0.130586, 0.991417, 0.006374), (-0.023521, 0.003329, -0.999718)0.91759, 0.16267, -39.8886
5given(-0.991158, -0.130699, 0.022884), (-0.130586, 0.991417, 0.006374), (-0.023521, 0.003329, -0.999718)0.91759, 0.16267, -39.8886
6given(-0.991158, -0.130699, 0.022884), (-0.130586, 0.991417, 0.006374), (-0.023521, 0.003329, -0.999718)0.91759, 0.16267, -39.8886
7given(-0.991158, -0.130699, 0.022884), (-0.130586, 0.991417, 0.006374), (-0.023521, 0.003329, -0.999718)0.91759, 0.16267, -39.8886
8given(-0.991158, -0.130699, 0.022884), (-0.130586, 0.991417, 0.006374), (-0.023521, 0.003329, -0.999718)0.91759, 0.16267, -39.8886
9given(-0.991158, -0.130699, 0.022884), (-0.130586, 0.991417, 0.006374), (-0.023521, 0.003329, -0.999718)0.91759, 0.16267, -39.8886

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Components

#1: Protein CPFTSY


Mass: 34560.488 Da / Num. of mol.: 2 / Fragment: RESIDUES 80-383
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PHYSCOMITRELLA PATENS (plant) / Plasmid: PET-DUET-1-PP-CPFTSYD1-79 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA PLYSS / References: UniProt: A9SNI6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 485 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsPREDICTED TRANSIT PEPTIDE (1-56) AND 23 ADDITIONAL RESIDUES WERE REMOVED FROM THE N-TERMINUS

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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: 2.3 Å3/Da / Density % sol: 47 % / Description: NONE
Crystal growpH: 6.6
Details: 0.2M SODIUM NITRATE, 0.1M BIS-TRIS PROPANE PH6.5, 20% PEG3350, pH 6.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 27, 2011 / Details: MIRRORS
RadiationMonochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→47.7 Å / Num. obs: 58928 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 21.4 % / Biso Wilson estimate: 36 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 15.89
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 26.62 % / Rmerge(I) obs: 0.94 / Mean I/σ(I) obs: 4.28 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2OG2

2og2


Resolution: 1.8→47.672 Å / SU ML: 0.19 / σ(F): 2 / Phase error: 27.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2468 2981 5.1 %
Rwork0.2153 --
obs0.217 58921 99.98 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 26.733 Å2 / ksol: 0.304 e/Å3
Displacement parametersBiso mean: 33 Å2
Baniso -1Baniso -2Baniso -3
1-0.7631 Å20 Å20 Å2
2--0.5453 Å20 Å2
3----1.3084 Å2
Refinement stepCycle: LAST / Resolution: 1.8→47.672 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4547 0 0 485 5032
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114598
X-RAY DIFFRACTIONf_angle_d1.256213
X-RAY DIFFRACTIONf_dihedral_angle_d14.9681710
X-RAY DIFFRACTIONf_chiral_restr0.089754
X-RAY DIFFRACTIONf_plane_restr0.005798
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2081X-RAY DIFFRACTIONPOSITIONAL
12B2081X-RAY DIFFRACTIONPOSITIONAL0.104
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.8295000.3042788X-RAY DIFFRACTION100
1.8295-1.8611000.28362707X-RAY DIFFRACTION100
1.8611-1.89490.31513660.26822415X-RAY DIFFRACTION100
1.8949-1.9313000.25872804X-RAY DIFFRACTION100
1.9313-1.97080.31612360.25772508X-RAY DIFFRACTION100
1.9708-2.01360.26211130.262655X-RAY DIFFRACTION100
2.0136-2.0605000.27072799X-RAY DIFFRACTION100
2.0605-2.1120.30683040.26152465X-RAY DIFFRACTION100
2.112-2.1691000.24812773X-RAY DIFFRACTION100
2.1691-2.23290.27552890.24222494X-RAY DIFFRACTION100
2.2329-2.3050.25762680.22722521X-RAY DIFFRACTION100
2.305-2.3874000.21842776X-RAY DIFFRACTION100
2.3874-2.4830.27662260.23092577X-RAY DIFFRACTION100
2.483-2.5960.26542040.22742604X-RAY DIFFRACTION100
2.596-2.7328000.22962796X-RAY DIFFRACTION100
2.7328-2.9040.2841790.23572639X-RAY DIFFRACTION100
2.904-3.12820.28131500.21752673X-RAY DIFFRACTION100
3.1282-3.44290.22951440.20682682X-RAY DIFFRACTION100
3.4429-3.94090.20062010.18822661X-RAY DIFFRACTION100
3.9409-4.96430.20791370.16562741X-RAY DIFFRACTION100
4.9643-47.6890.21511640.19982862X-RAY DIFFRACTION100

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