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- PDB-2v94: Crystal structure of P. abyssi RPS24 -

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Basic information

Entry
Database: PDB / ID: 2v94
TitleCrystal structure of P. abyssi RPS24
Components30S RIBOSOMAL PROTEIN S24E
KeywordsRIBOSOMAL PROTEIN / RIBONUCLEOPROTEIN
Function / homology
Function and homology information


structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex
Similarity search - Function
RRM (RNA recognition motif) domain / Ribosomal S24e conserved site / Ribosomal protein S24e signature. / Ribosomal protein S24e / Ribosomal protein S24e / Ribosomal protein L23/L15e core domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Small ribosomal subunit protein eS24
Similarity search - Component
Biological speciesPYROCOCCUS ABYSSI (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsLegrand, P. / Pinaud, N. / Gleizes, P.E. / Fribourg, S.
CitationJournal: Hum.Mol.Genet. / Year: 2008
Title: Mutation of Ribosomal Protein Rps24 in Diamond- Blackfan Anemia Results in a Ribosome Biogenesis Disorder.
Authors: Choesmel, V. / Fribourg, S. / Aguissa-Toure, A.H. / Pinaud, N. / Legrand, P. / Gazda, H.T. / Gleizes, P.E.
History
DepositionAug 21, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 30S RIBOSOMAL PROTEIN S24E
B: 30S RIBOSOMAL PROTEIN S24E


Theoretical massNumber of molelcules
Total (without water)26,0532
Polymers26,0532
Non-polymers00
Water1,72996
1
A: 30S RIBOSOMAL PROTEIN S24E


Theoretical massNumber of molelcules
Total (without water)13,0261
Polymers13,0261
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: 30S RIBOSOMAL PROTEIN S24E


Theoretical massNumber of molelcules
Total (without water)13,0261
Polymers13,0261
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)66.810, 85.630, 42.110
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Refine code: 3

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUVALVALAA2 - 810 - 16
21GLUGLUVALVALBB2 - 810 - 16
12ARGARGILEILEAA16 - 2324 - 31
22ARGARGILEILEBB16 - 2324 - 31
13PROPROLYSLYSAA31 - 3739 - 45
23PROPROLYSLYSBB31 - 3739 - 45
14LEULEUTYRTYRAA46 - 5554 - 63
24LEULEUTYRTYRBB46 - 5554 - 63
15GLYGLYTYRTYRAA67 - 7375 - 81
25GLYGLYTYRTYRBB67 - 7375 - 81
16ARGARGLEULEUAA77 - 7985 - 87
26ARGARGLEULEUBB77 - 7985 - 87
17ILEILEPROPROAA81 - 8389 - 91
27ILEILEPROPROBB81 - 8389 - 91
18TYRTYRLEULEUAA85 - 8793 - 95
28TYRTYRLEULEUBB85 - 8793 - 95

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Components

#1: Protein 30S RIBOSOMAL PROTEIN S24E / RPS24


Mass: 13026.407 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PYROCOCCUS ABYSSI (archaea) / Plasmid: PET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA / References: UniProt: Q9UY20
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.04 Å3/Da / Density % sol: 60 % / Description: NONE
Crystal growpH: 4.2 / Details: 100MM NA ACETATE 40% PEG 400 185MM MGCL2, pH 4.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9793
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 5, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 13468 / % possible obs: 97.5 % / Observed criterion σ(I): 2 / Redundancy: 5.3 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.3
Reflection shellResolution: 1.9→2.02 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 4.8 / % possible all: 91.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.9→27.39 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.92 / SU B: 8.878 / SU ML: 0.13 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.163 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.266 1001 5.1 %RANDOM
Rwork0.221 ---
obs0.224 18584 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 29.52 Å2
Baniso -1Baniso -2Baniso -3
1--3.19 Å20 Å20 Å2
2---1.46 Å20 Å2
3---4.65 Å2
Refinement stepCycle: LAST / Resolution: 1.9→27.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1600 0 0 96 1696
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0221637
X-RAY DIFFRACTIONr_bond_other_d0.0020.021185
X-RAY DIFFRACTIONr_angle_refined_deg1.7222.0022200
X-RAY DIFFRACTIONr_angle_other_deg0.90432885
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5055188
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.13723.46775
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.02315322
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.871510
X-RAY DIFFRACTIONr_chiral_restr0.0940.2230
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021747
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02335
X-RAY DIFFRACTIONr_nbd_refined0.220.2319
X-RAY DIFFRACTIONr_nbd_other0.2080.21164
X-RAY DIFFRACTIONr_nbtor_refined0.1940.2798
X-RAY DIFFRACTIONr_nbtor_other0.0890.2882
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.284
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2420.224
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3070.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.270.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3971.51138
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.52321545
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.9073803
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.6744.5655
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
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
284tight positional0.160.3
442loose positional0.391.6
284tight thermal0.170.3
442loose thermal0.932.3
LS refinement shellResolution: 1.9→1.98 Å / Total num. of bins used: 12 /
RfactorNum. reflection
Rfree0.341 117
Rwork0.262 2159
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)
14.9655-1.1058-0.05143.637-0.61271.3450.0833-0.3320.11130.2331-0.0203-0.1473-0.08440.0855-0.063-0.06440.0044-0.0013-0.0995-0.0084-0.204147.25467.911934.0201
25.4224-1.35091.13743.1361-1.14841.9112-0.02330.2486-0.129-0.1683-0.1311-0.12520.1520.33640.1544-0.1111-0.01030.0054-0.10260.0475-0.095150.055323.452616.2133
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-3 - 93
2X-RAY DIFFRACTION2B1 - 94

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