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- PDB-2w9j: The crystal structure of SRP14 from the Schizosaccharomyces pombe... -

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Basic information

Entry
Database: PDB / ID: 2w9j
TitleThe crystal structure of SRP14 from the Schizosaccharomyces pombe signal recognition particle
ComponentsSIGNAL RECOGNITION PARTICLE SUBUNIT SRP14
KeywordsSIGNALING PROTEIN / SCHIZOSACCHAROMYCES POMBE / RADIATION-INDUCED PHASING / RNA-BINDING / RIBONUCLEOPROTEIN / SIGNAL RECOGNITION PARTICLE / ARSENIC / ALU-DOMAIN / CACODYLATE
Function / homology
Function and homology information


Neutrophil degranulation / SRP-dependent cotranslational protein targeting to membrane / SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition / signal recognition particle, endoplasmic reticulum targeting / endoplasmic reticulum signal peptide binding / protein targeting to ER / 7S RNA binding / nucleolus / nucleus
Similarity search - Function
Signal recognition particle alu RNA binding heterodimer, srp9/1 / Signal recognition particle, SRP14 subunit / Signal recognition particle, SRP9/SRP14 subunit / Signal recognition particle 14kD protein / Signal recognition particle alu RNA binding heterodimer, srp9/1 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Signal recognition particle subunit srp14
Similarity search - Component
Biological speciesSCHIZOSACCHAROMYCES POMBE (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.6 Å
AuthorsBrooks, M.A. / Ravelli, R.B.G. / McCarthy, A.A. / Strub, K. / Cusack, S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2009
Title: Structure of Srp14 from the Schizosaccharomyces Pombe Signal Recognition Particle.
Authors: Brooks, M.A. / Ravelli, R.B.G. / Mccarthy, A.A. / Strub, K. / Cusack, S.
History
DepositionJan 25, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SIGNAL RECOGNITION PARTICLE SUBUNIT SRP14
B: SIGNAL RECOGNITION PARTICLE SUBUNIT SRP14


Theoretical massNumber of molelcules
Total (without water)20,5692
Polymers20,5692
Non-polymers00
Water724
1
A: SIGNAL RECOGNITION PARTICLE SUBUNIT SRP14


Theoretical massNumber of molelcules
Total (without water)10,2841
Polymers10,2841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: SIGNAL RECOGNITION PARTICLE SUBUNIT SRP14


Theoretical massNumber of molelcules
Total (without water)10,2841
Polymers10,2841
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)57.040, 57.040, 86.370
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.489, -0.87, -0.058), (-0.498, 0.225, 0.838), (-0.716, 0.439, -0.543)
Vector: -30.24111, 0.70896, -28.87677)

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Components

#1: Protein SIGNAL RECOGNITION PARTICLE SUBUNIT SRP14 / SIGNAL RECOGNITION PARTICLE 14 KDA PROTEIN HOMOLOG / SRP14 FROM SCHIZOSACCHAROMYCES POMBE SIGNAL ...SIGNAL RECOGNITION PARTICLE 14 KDA PROTEIN HOMOLOG / SRP14 FROM SCHIZOSACCHAROMYCES POMBE SIGNAL RECOGNITION PARTICLE


Mass: 10284.420 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-91
Source method: isolated from a genetically manipulated source
Details: CYSTEINES 33 AND 78 REACTED WITH CACODYLATE, YIELDING CACODYLATED CYSTEINE ADDUCT (CAS)
Source: (gene. exp.) SCHIZOSACCHAROMYCES POMBE (fission yeast)
Strain: NCYC 1354
Description: NATIONAL COLLECTION OF YEAST CULTURES, NORWICH, UK
Plasmid: PST39 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(AI) / References: UniProt: Q9P372
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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 Å3/Da / Density % sol: 37 % / Description: PHASES WERE COMBINED FROM RIP AND SAD
Crystal growDetails: 50MM CACODYLIC ACID, PH 6.5, 22% POLY-ETHYLENE GLYCOL 4000, 50MM SODIUM ACETATE

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONESRF ID14-410.93927
SYNCHROTRONESRF ID23-120.97835
Detector
TypeIDDetectorDateDetails
ADSC CCD1CCDMar 19, 2004TOROIDAL FOCUSING MIRROR
2
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE SILICON (111) CRYSTALSINGLE WAVELENGTHMx-ray1
2Mx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.939271
20.978351
ReflectionResolution: 2.6→5 Å / Num. obs: 5174 / % possible obs: 97.4 % / Observed criterion σ(I): -3 / Redundancy: 5.8 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 16
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 6.17 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 5 / % possible all: 95.5

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Processing

Software
NameVersionClassification
REFMAC5.4.0065refinement
XDSdata reduction
XSCALEdata scaling
SHELXphasing
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2.6→32.62 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.897 / SU B: 37.967 / SU ML: 0.349 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 1.612 / ESU R Free: 0.367
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.281 236 4.6 %RANDOM
Rwork0.238 ---
obs0.24 4924 97.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.08 Å2
Baniso -1Baniso -2Baniso -3
1-3.59 Å21.8 Å20 Å2
2--3.59 Å20 Å2
3----5.39 Å2
Refinement stepCycle: LAST / Resolution: 2.6→32.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1181 0 0 4 1185
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221192
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2431.9971601
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1445148
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.50426.1747
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.68115215
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.42152
X-RAY DIFFRACTIONr_chiral_restr0.0690.2196
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02836
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5111.5754
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.04421206
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.813438
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.124.5395
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.67 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.316 12
Rwork0.313 339
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.8955-0.07770.76165.5434-0.56558.72130.2790.27950.1293-0.1532-0.0173-0.3135-0.5633-0.4149-0.2617-0.00110.1491-0.0190.17250.1024-0.0801-17.06822.6055-21.4486
25.9361-0.0792-1.21195.2136-0.6719.5623-0.21620.1717-0.08690.22410.10250.2060.0043-0.47790.1137-0.0994-0.014-0.0751-0.17270.0325-0.0806-12.8146-8.4328-2.2298
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 83
2X-RAY DIFFRACTION2B1 - 84

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