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- PDB-2wbm: Crystal structure of mthSBDS, the homologue of the Shwachman-Bodi... -

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Basic information

Entry
Database: PDB / ID: 2wbm
TitleCrystal structure of mthSBDS, the homologue of the Shwachman-Bodian- Diamond syndrome protein in the euriarchaeon Methanothermobacter thermautotrophicus
ComponentsRIBOSOME MATURATION PROTEIN SDO1 HOMOLOG
KeywordsRNA BINDING PROTEIN / SHWACHMAN-BODIAN-DIAMOND SYNDROME PROTEIN / RIBOSOME BINDING / CONFORMATIONAL FLEXIBILITY / RNA-BINDING PROTEIN
Function / homology
Function and homology information


cytosolic ribosome assembly
Similarity search - Function
SBDS protein C-terminal domain, subdomain 1 / Hypothetical 12.0 Kda Protein In Nam8-gar1 Intergenic Region; Chain: A; / Ribosome maturation protein SBDS, N-terminal domain / Ribosome maturation protein Sdo1/SBDS / Ribosome maturation protein SBDS, conserved site / Ribosome maturation protein SDO1/SBDS, central domain / Ribosome maturation protein Sdo1/SBDS, central domain superfamily / SBDS protein, domain II / Uncharacterized protein family UPF0023 signature. / Ribosome maturation protein SDO1/SBDS, N-terminal ...SBDS protein C-terminal domain, subdomain 1 / Hypothetical 12.0 Kda Protein In Nam8-gar1 Intergenic Region; Chain: A; / Ribosome maturation protein SBDS, N-terminal domain / Ribosome maturation protein Sdo1/SBDS / Ribosome maturation protein SBDS, conserved site / Ribosome maturation protein SDO1/SBDS, central domain / Ribosome maturation protein Sdo1/SBDS, central domain superfamily / SBDS protein, domain II / Uncharacterized protein family UPF0023 signature. / Ribosome maturation protein SDO1/SBDS, N-terminal / Ribosome maturation protein SBDS, N-terminal domain superfamily / Ribosome maturation protein Sdo1/SBDS-like / Shwachman-Bodian-Diamond syndrome (SBDS) protein / Alpha-Beta Plaits - #240 / EF-G domain III/V-like / Arc Repressor Mutant, subunit A / Alpha-Beta Plaits / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Ribosome maturation protein SDO1 homolog
Similarity search - Component
Biological speciesMETHANOTHERMOBACTER THERMAUTOTROPHICUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsNg, C.L. / Isupov, M.N. / Lebedev, A.A. / Ortiz-Lombardia, M. / Antson, A.A.
CitationJournal: Bmc Struct.Biol. / Year: 2009
Title: Conformational Flexibility and Molecular Interactions of an Archaeal Homologue of the Shwachman-Bodian-Diamond Syndrome Protein.
Authors: Ng, C.L. / Waterman, D.G. / Koonin, E.V. / Walters, A.D. / Chong, J.P. / Isupov, M.N. / Lebedev, A.A. / Bunka, D.H. / Stockley, P.G. / Ortiz-Lombardia, M. / Antson, A.A.
History
DepositionMar 2, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 2, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Mar 7, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.3Mar 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RIBOSOME MATURATION PROTEIN SDO1 HOMOLOG
B: RIBOSOME MATURATION PROTEIN SDO1 HOMOLOG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,63112
Polymers56,7552
Non-polymers87610
Water7,404411
1
A: RIBOSOME MATURATION PROTEIN SDO1 HOMOLOG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7465
Polymers28,3771
Non-polymers3684
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: RIBOSOME MATURATION PROTEIN SDO1 HOMOLOG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8857
Polymers28,3771
Non-polymers5086
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)68.300, 72.108, 146.829
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221

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Components

#1: Protein RIBOSOME MATURATION PROTEIN SDO1 HOMOLOG / MTHSBDS


Mass: 28377.365 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) METHANOTHERMOBACTER THERMAUTOTROPHICUS (archaea)
Strain: DELTA H / Plasmid: PYCL02 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: O26781
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 411 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSEQUENCE INCLUDES AN N-TERMINAL FUSION TAG SEQUENCE. THE R175M MUTATION WAS INTRODUCED DURING THE ...SEQUENCE INCLUDES AN N-TERMINAL FUSION TAG SEQUENCE. THE R175M MUTATION WAS INTRODUCED DURING THE PCR AMPLIFICATION OF THE GENE FROM THE GENOMIC DNA OF M. THERMAUTOTROPHICUS.

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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: 3.2 Å3/Da / Density % sol: 61.6 % / Description: NONE
Crystal growMethod: vapor diffusion / pH: 6
Details: PROTEIN AT 22.5 MG/ML IN 25 MM TRIS (PH 7.5) AND 0.1 M NACL, WAS CRYSTALLIZED BY THE VAPOUR DIFFUSION METHOD AGAINST A RESERVOIR COMPOSED OF 0.9 M LITHIUM SULPHATE, 0.5 M AMMONIUM SULPHATE ...Details: PROTEIN AT 22.5 MG/ML IN 25 MM TRIS (PH 7.5) AND 0.1 M NACL, WAS CRYSTALLIZED BY THE VAPOUR DIFFUSION METHOD AGAINST A RESERVOIR COMPOSED OF 0.9 M LITHIUM SULPHATE, 0.5 M AMMONIUM SULPHATE AND 0.1 M SODIUM CITRATE (PH 5.6)

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.0081
DetectorType: MARRESEARCH / Detector: CCD / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0081 Å / Relative weight: 1
ReflectionResolution: 1.75→27 Å / Num. obs: 72559 / % possible obs: 98.4 % / Observed criterion σ(I): 1.7 / Redundancy: 3.9 % / Biso Wilson estimate: 25 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 20.3
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 3 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 1.7 / % possible all: 82.8

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Processing

Software
NameVersionClassification
REFMAC5.5.0074refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1P9Q

1p9q


Resolution: 1.75→26.98 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.951 / SU B: 5.288 / SU ML: 0.074 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES ARE RESIDUAL ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.214 1457 2 %RANDOM
Rwork0.191 ---
obs0.191 71100 98.4 %-
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: 37.1 Å2
Baniso -1Baniso -2Baniso -3
1-2.36 Å2-0 Å2-0 Å2
2---1.34 Å20 Å2
3----1.02 Å2
Refinement stepCycle: LAST / Resolution: 1.75→26.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3655 0 52 411 4118
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223885
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1731.9825266
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2945501
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.08324.309188
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.92815742
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1751538
X-RAY DIFFRACTIONr_chiral_restr0.0850.2594
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212912
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_it1.4461.52369
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.3123877
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.89231516
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.3134.51368
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: 1.75→1.8 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 78 -
Rwork0.325 4498 -
obs--85.29 %
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)
13.269-1.05331.04428.006-0.05325.4079-0.01420.06890.1671-0.25040.1014-0.1582-0.54830.1879-0.08720.0759-0.04070.02010.0422-0.00770.014532.814214.552973.1414
20.77821.2589-0.732710.9286-3.66152.7823-0.02940.10870.0926-0.54490.0583-0.0684-0.099-0.0424-0.02890.17530.0347-0.01340.1032-0.0220.057724.814330.72650.0415
33.6923-0.7690.18976.9230.8833.2390.18550.0325-0.0963-0.3202-0.07360.37560.1108-0.2511-0.11190.0308-0.0143-0.02480.06350.01340.061517.67656.98557.4103
46.1374-1.60740.68535.55381.300413.62280.13760.0813-0.67430.0921-0.11130.89931.54070.3254-0.02630.17910.05270.02260.30440.05820.550364.0536-12.833467.8526
56.6150.33543.14644.16770.5064.7324-0.1835-0.24410.2444-0.02760.0379-0.4101-0.38070.31680.14560.0402-0.0035-0.01650.1661-0.02520.057347.49769.562152.195
61.0195-0.4664-0.84291.28411.65126.2545-0.0421-0.02790.0376-0.07930.052-0.19120.06290.2637-0.00990.0579-0.00460.00520.06450.00410.049640.73241.57125.1482
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 88
2X-RAY DIFFRACTION2A89 - 162
3X-RAY DIFFRACTION3A163 - 232
4X-RAY DIFFRACTION4B1 - 88
5X-RAY DIFFRACTION5B89 - 162
6X-RAY DIFFRACTION6B163 - 232

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