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- PDB-2o5a: Crystal structure of Q9KD89 from Bacillus halodurans. Northeast S... -

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Basic information

Entry
Database: PDB / ID: 2o5a
TitleCrystal structure of Q9KD89 from Bacillus halodurans. Northeast Structural Genomics target BhR21
ComponentsBH1328 protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / bhr21 / NESG / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


negative regulation of ribosome biogenesis / cytosolic ribosome assembly / negative regulation of translation / cytoplasm
Similarity search - Function
Ribosomal silencing factor during starvation / Protein Iojap/ribosomal silencing factor RsfS / Beta Polymerase, domain 2 / Beta Polymerase; domain 2 / Nucleotidyltransferase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Ribosomal silencing factor RsfS
Similarity search - Component
Biological speciesBacillus halodurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å
AuthorsBenach, J. / Su, M. / Seetharaman, J. / Ho, C.H. / Janjua, H. / Cunningham, K. / Ma, L.-C. / Xiao, R. / Liu, J. / Baran, M.C. ...Benach, J. / Su, M. / Seetharaman, J. / Ho, C.H. / Janjua, H. / Cunningham, K. / Ma, L.-C. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of Q9KD89 from Bacillus halodurans. Northeast Structural Genomics target BhR21
Authors: Benach, J. / Su, M. / Seetharaman, J. / Ho, C.H. / Janjua, H. / Cunningham, K. / Ma, L.-C. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionDec 5, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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: BH1328 protein
B: BH1328 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0807
Polymers28,7642
Non-polymers3165
Water70339
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.936, 32.021, 59.546
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein BH1328 protein


Mass: 14382.027 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans (bacteria) / Gene: BH1328 / Plasmid: pet21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: Q9KD89
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 1.99 Å3/Da / Density % sol: 38.11 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 11% PEG 400, 100mM MES pH 6.0, 200mM MnSO4, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97903, 0.97937, 0.96791
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979031
20.979371
30.967911
Reflection

D res low: 50 Å

Redundancy (%)IDAv σ(I) over netINumberRmerge(I) obsΧ2D res high (Å)Num. obs% possible obs
7.6112.71158920.0951.152.51534299.8
7.7210929670.1121.132.71212899.9
7.638.2849180.1271.062.81111699.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.385099.710.0471.017.4
4.275.3810010.0521.0427.6
3.734.2799.910.0651.0417.7
3.393.7399.910.0841.0157.7
3.153.3999.910.1231.0887.8
2.963.1510010.1661.0617.8
2.822.9699.710.241.2197.6
2.692.8210010.3541.2667.6
2.592.6999.310.4881.4057.3
2.52.5910010.5921.3887.1
5.815099.820.0451.0517.6
4.625.8110020.0571.0787.7
4.034.6210020.0650.9397.8
3.664.0399.920.0930.9647.8
3.43.6699.920.1331.0697.7
3.23.499.820.1911.0537.9
3.043.210020.2841.1777.7
2.913.0499.820.3641.2637.8
2.82.9199.720.5261.3247.4
2.72.810020.7391.4127.3
6.035099.830.0471.0087.5
4.796.0310030.0671.1167.7
4.184.7910030.0690.9437.8
3.84.1810030.1080.9697.8
3.533.899.930.1491.0217.8
3.323.5310030.2111.0147.8
3.153.3299.830.3411.1197.7
3.023.1510030.4481.1587.7
2.93.0299.530.5881.1617.5
2.82.910030.7551.1136.9
ReflectionResolution: 2.7→50 Å / Num. obs: 12143 / % possible obs: 99.8 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 10.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obs% possible all
2.7-2.86.30.36999.5
2.8-2.916.50.27599.7
2.91-3.046.70.299.7
3.04-3.270.16699.8
3.2-3.47.20.123100
3.4-3.667.40.09999.9
3.66-4.037.60.079100
4.03-4.627.70.065100
4.62-5.817.80.061100
5.81-507.60.05199.7

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Phasing

Phasing dmFOM : 0.65 / FOM acentric: 0.65 / FOM centric: 0.64 / Reflection: 7964 / Reflection acentric: 6486 / Reflection centric: 1478
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
7.1-42.2560.890.930.84421239182
4.5-7.10.870.890.821164866298
3.6-4.50.860.870.7814071133274
3.1-3.60.730.750.6213911154237
2.7-3.10.50.510.4523091982327
2.5-2.70.30.30.2412721112160

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
RESOLVE2.08phasing
CNS1.1refinement
PDB_EXTRACT2data extraction
HKL-2000data reduction
SnBphasing
RefinementMethod to determine structure: MAD / Resolution: 2.7→20 Å / σ(F): 2 / Stereochemistry target values: ENGH & HUBER
Details: Non-crystallographic restrains were used during the refinement, they were not relaxed.
RfactorNum. reflection% reflection
Rfree0.2783 1092 9 %
Rwork0.2511 --
obs0.2511 10990 90.6 %
Solvent computationBsol: 38.54 Å2
Displacement parametersBiso mean: 42.31 Å2
Baniso -1Baniso -2Baniso -3
1-2.404 Å20 Å20 Å2
2--2.837 Å20 Å2
3----5.241 Å2
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1723 0 9 39 1771
LS refinement shellResolution: 2.7→2.74 Å / Total num. of bins used: 21 /
RfactorNum. reflection
Rfree0.4259 30
Rwork0.2941 357
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PAR
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3ION.PARAM

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