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- PDB-1qzx: Crystal structure of the complete core of archaeal SRP and implic... -

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Basic information

Entry
Database: PDB / ID: 1qzx
TitleCrystal structure of the complete core of archaeal SRP and implications for inter-domain communication
ComponentsSignal recognition 54 kDa protein
KeywordsSIGNALING PROTEIN / Signal recognition particle / SRP / protein targeting / SRP54
Function / homology
Function and homology information


signal recognition particle / endoplasmic reticulum signal peptide binding / signal-recognition-particle GTPase / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane, translocation / GTPase activity / GTP binding / ATP hydrolysis activity / cytosol
Similarity search - Function
Signal recognition particle, SRP54 subunit, M-domain / SRP54, nucleotide-binding domain / SRP/SRP receptor, N-terminal / Signal recognition particle, SRP54 subunit / Signal recognition particle, SRP54 subunit, M-domain / Signal recognition particle, SRP54 subunit, M-domain superfamily / Signal peptide binding domain / Signal recognition particle SRP54, helical bundle / Signal recognition particle SRP54, N-terminal domain superfamily / SRP54-type protein, helical bundle domain ...Signal recognition particle, SRP54 subunit, M-domain / SRP54, nucleotide-binding domain / SRP/SRP receptor, N-terminal / Signal recognition particle, SRP54 subunit / Signal recognition particle, SRP54 subunit, M-domain / Signal recognition particle, SRP54 subunit, M-domain superfamily / Signal peptide binding domain / 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 / 434 Repressor (Amino-terminal 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Signal recognition particle 54 kDa protein
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4 Å
AuthorsRosendal, K.R. / Wild, K. / Montoya, G. / Sinning, I.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: Crystal structure of the complete core of archaeal signal recognition particle and implications for interdomain communication
Authors: Rosendal, K.R. / Wild, K. / Montoya, G. / Sinning, I.
History
DepositionSep 18, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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_ref_seq_dif / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_sheet.number_strands
Remark 650HELIX DETERMINED METHOD: Authors determined
Remark 700SHEET DETERMINED METHOD: Authors determined

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Signal recognition 54 kDa protein
B: Signal recognition 54 kDa protein


Theoretical massNumber of molelcules
Total (without water)98,9272
Polymers98,9272
Non-polymers00
Water00
1
A: Signal recognition 54 kDa protein


Theoretical massNumber of molelcules
Total (without water)49,4631
Polymers49,4631
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Signal recognition 54 kDa protein


Theoretical massNumber of molelcules
Total (without water)49,4631
Polymers49,4631
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)197.906, 197.906, 64.305
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein Signal recognition 54 kDa protein / SRP54


Mass: 49463.430 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: SRP54 / Plasmid: pET24d / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta pLysS / References: UniProt: Q97ZE7

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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: 3.18 Å3/Da / Density % sol: 61.34 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 8000, litium sulphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 291 K / Method: vapor diffusion, hanging drop
Details: Rosendal, K.R., (2004) Acta Crystallogr.,Sect.D, 60, 140.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
130 mg/mlprotein1drop
22-4 %PEG80001reservoir
31-1.2 M1reservoirLi2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.974 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 25, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.974 Å / Relative weight: 1
ReflectionResolution: 4→40 Å / Num. obs: 10545 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rsym value: 0.083 / Net I/σ(I): 4.8
Reflection shellResolution: 4→4.22 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 1.5 / Num. unique all: 1527 / Rsym value: 0.484 / % possible all: 99.2
Reflection
*PLUS
Highest resolution: 4 Å / Lowest resolution: 40 Å / Num. obs: 9576 / % possible obs: 89 % / Rmerge(I) obs: 0.083
Reflection shell
*PLUS
Lowest resolution: 4.21 Å / % possible obs: 97.9 % / Rmerge(I) obs: 0.484

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
BEASTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1J8M

1j8m


Resolution: 4→40 Å / Rfactor Rfree error: 0.02 / Data cutoff high absF: 4262703.03 / Data cutoff high rms absF: 4262703.03 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: The structure factor data associated with this file is from twinned crystal. To use structure factor data, this data will have to be detwinned.
RfactorNum. reflection% reflectionSelection details
Rfree0.3831 428 6.9 %RANDOM
Rwork0.3131 ---
all-10758 --
obs-9576 89 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.398666 e/Å3
Displacement parametersBiso mean: 101.1 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error1.02 Å1.17 Å
Luzzati d res low-5 Å
Luzzati sigma a-1.15 Å
Refinement stepCycle: LAST / Resolution: 4→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6698 0 0 0 6698
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.016
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_dihedral_angle_d22
X-RAY DIFFRACTIONc_improper_angle_d1.35
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkNum. reflection obs
4-4.180.403477.60.348416191098
4.18-4.40.4763530.3261115
4.4-4.680.4639470.32291134
4.68-5.040.4821590.31451135
5.04-5.540.4072610.32871128
5.54-6.340.3833490.33041146
6.34-7.980.3748500.32691161
7.98-400.3895620.3481231
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP
Refinement
*PLUS
Highest resolution: 4 Å / Lowest resolution: 40 Å / % reflection Rfree: 4 % / Rfactor Rfree: 0.383 / Rfactor Rwork: 0.313
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.93
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.35

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