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- PDB-2ged: Signal Recognition Particle Receptor Beta-Subunit in nucleotide-f... -

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Basic information

Entry
Database: PDB / ID: 2ged
TitleSignal Recognition Particle Receptor Beta-Subunit in nucleotide-free dimerized form
ComponentsSignal recognition particle receptor beta subunit
KeywordsPROTEIN TRANSPORT / SIGNALING PROTEIN / G protein / signal recognition particle / proline isomerization / circular permutation
Function / homology
Function and homology information


signal recognition particle receptor complex / SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition / signal recognition particle binding / protein targeting to ER / endoplasmic reticulum membrane / GTP binding / identical protein binding / membrane
Similarity search - Function
Signal recognition particle receptor, beta subunit / Signal recognition particle receptor beta subunit / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Signal recognition particle receptor subunit beta
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSchmidt, D. / Schwartz, T.U.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2006
Title: Homodimerization of the G protein SR{beta} in the nucleotide-free state involves proline cis/trans isomerization in the switch II region.
Authors: Schwartz, T.U. / Schmidt, D. / Brohawn, S.G. / Blobel, G.
#1: Journal: Protein Sci. / Year: 2004
Title: Circular permutation as a tool to reduce surface entropy triggers crystallization of the signal recognition particle receptor beta subunit.
Authors: Schwartz, T.U. / Walczak, R. / Blobel, G.
History
DepositionMar 19, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.4Aug 30, 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
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). THE BIOLOGICAL UNIT HAS NOT BEEN CONFIRMED YET AS OCCURRING IN VIVO. IT IS VERY LIKELY A DIMER BUT NOT CERTAIN. SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S).
Remark 999SEQUENCE THIS PROTEIN IS A RECOMBINANT PROTEIN. THE COORDINATE NUMBERING IS BASED ON NATURAL ...SEQUENCE THIS PROTEIN IS A RECOMBINANT PROTEIN. THE COORDINATE NUMBERING IS BASED ON NATURAL PROTEIN NUMBERING. N-TERMINUS RESIDUES 210-244 ARE LINKED TO RESIDUES 36-183 WITH GGGSGGG LINKER. RESIDUES 184-209 WERE DELETED. THE GGGSGGG LINKER IS NOT OBSERVED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Signal recognition particle receptor beta subunit
B: Signal recognition particle receptor beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7998
Polymers42,2222
Non-polymers5766
Water5,260292
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4530 Å2
ΔGint-123 kcal/mol
Surface area16870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.996, 74.996, 158.475
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Detailsthe asymmetric unit contains the homodimerized protein. no further symmetry operation is needed to build the biological assembly.

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Components

#1: Protein Signal recognition particle receptor beta subunit / SR-beta


Mass: 21111.119 Da / Num. of mol.: 2 / Mutation: deletion residues 184-209
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SRP102 / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P36057
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 292 / 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: 2.99 Å3/Da / Density % sol: 58.91 %
Crystal growTemperature: 277 K / Method: microbatch under paraffin oil / pH: 5.5
Details: 1.3M ammonium sulfate, 50mM Bis/Tris/HCl, 0.5mM GDP, 5mM magnesium chloride, 5mM Hepes, 125mM sodium chloride, 2.5mM DTT, 0.25mM EDTA, pH 5.5, MICROBATCH UNDER PARAFFIN OIL, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9A / Wavelength: 1.00944 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 16, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00944 Å / Relative weight: 1
ReflectionResolution: 2→33.8 Å / Num. all: 33853 / Num. obs: 33373 / % possible obs: 98.6 % / Observed criterion σ(F): 1 / Redundancy: 5.6 % / Biso Wilson estimate: 49.4 Å2 / Rsym value: 0.074 / Net I/σ(I): 24.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
BEASTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NRJ chain B

1nrj


Resolution: 2.2→25 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.932 / SU B: 5.804 / SU ML: 0.146 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.212 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23941 2527 9.9 %RANDOM
Rwork0.18264 ---
all0.223 25288 --
obs0.18832 22942 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 38.144 Å2
Baniso -1Baniso -2Baniso -3
1-1.76 Å20.88 Å20 Å2
2--1.76 Å20 Å2
3----2.64 Å2
Refinement stepCycle: LAST / Resolution: 2.2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2591 0 30 294 2915
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0222657
X-RAY DIFFRACTIONr_bond_other_d0.0010.021802
X-RAY DIFFRACTIONr_angle_refined_deg1.8941.9893594
X-RAY DIFFRACTIONr_angle_other_deg1.08634421
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7295327
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.85124.369103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.00415482
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.281514
X-RAY DIFFRACTIONr_chiral_restr0.1250.2425
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022843
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02507
X-RAY DIFFRACTIONr_nbd_refined0.2280.2564
X-RAY DIFFRACTIONr_nbd_other0.1980.21728
X-RAY DIFFRACTIONr_nbtor_refined0.1810.21290
X-RAY DIFFRACTIONr_nbtor_other0.0920.21327
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2140.2224
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1470.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.180.237
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.120.25
X-RAY DIFFRACTIONr_mcbond_it1.6411.51852
X-RAY DIFFRACTIONr_mcbond_other0.2991.5668
X-RAY DIFFRACTIONr_mcangle_it2.33122688
X-RAY DIFFRACTIONr_scbond_it3.30131095
X-RAY DIFFRACTIONr_scangle_it4.8154.5906
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 203 -
Rwork0.257 1641 -
obs--99.73 %

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