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- PDB-3h9n: Crystal structure of the ribosome maturation factor rimm (hi0203)... -

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Basic information

Entry
Database: PDB / ID: 3h9n
TitleCrystal structure of the ribosome maturation factor rimm (hi0203) from h.influenzae. northeast structural genomics consortium target IR66.
ComponentsRibosome maturation factor rimM
KeywordsRIBOSOMAL PROTEIN / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / IR66 / rimM / Chaperone / Cytoplasm / Ribosome biogenesis
Function / homology
Function and homology information


rRNA processing / ribosomal small subunit biogenesis / ribosome binding / ribosome / cytoplasm
Similarity search - Function
RimM / PRC-barrel domain / RimM, N-terminal / 16S rRNA processing protein RimM / RimM, N-terminal domain superfamily / RimM N-terminal domain / PRC-barrel domain / PRC-barrel domain / PRC-barrel-like superfamily / Elongation Factor Tu (Ef-tu); domain 3 ...RimM / PRC-barrel domain / RimM, N-terminal / 16S rRNA processing protein RimM / RimM, N-terminal domain superfamily / RimM N-terminal domain / PRC-barrel domain / PRC-barrel domain / PRC-barrel-like superfamily / Elongation Factor Tu (Ef-tu); domain 3 / SH3 type barrels. / Translation protein, beta-barrel domain superfamily / Roll / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Ribosome maturation factor RimM
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å
AuthorsKuzin, A. / Su, M. / Seetharaman, J. / Mao, M. / Xiao, R. / Maglaqui, M. / Zhao, L. / Everett, J.K. / Nair, R. / Acton, T.B. ...Kuzin, A. / Su, M. / Seetharaman, J. / Mao, M. / Xiao, R. / Maglaqui, M. / Zhao, L. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Northeast Structural Genomics Consortium Target IR66
Authors: Kuzin, A. / Su, M. / Seetharaman, J. / Mao, M. / Xiao, R. / Maglaqui, M. / Zhao, L. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionApr 30, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 19, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribosome maturation factor rimM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0215
Polymers20,6371
Non-polymers3844
Water362
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Ribosome maturation factor rimM
hetero molecules

A: Ribosome maturation factor rimM
hetero molecules

A: Ribosome maturation factor rimM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,06315
Polymers61,9103
Non-polymers1,15312
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555z+1/2,-x+1/2,-y1
crystal symmetry operation12_554-y+1/2,-z,x-1/21
Buried area12510 Å2
ΔGint-176 kcal/mol
Surface area23880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.642, 129.642, 129.642
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number199
Space group name H-MI213

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Components

#1: Protein Ribosome maturation factor rimM


Mass: 20636.738 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: HI0203, rimM / Plasmid: pET21 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: P44568
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 2 / 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: 4.4 Å3/Da / Density % sol: 72.04 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 5.6
Details: 0.4M Li2SO4, 0.1M Na3Citrate, 0.2M NH42SO4, ph 5.6, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97901 0.97927 0.96790
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 2, 2009 / Details: mirror
RadiationMonochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979011
20.979271
30.96791
ReflectionResolution: 2.7→50 Å / Num. obs: 19211 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 34.6 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 46.3
Reflection shellResolution: 2.7→2.8 Å / Rmerge(I) obs: 0.523 / Mean I/σ(I) obs: 5 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3data extraction
RefinementMethod to determine structure: MAD / Resolution: 2.7→20 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.237 872 4.5 %
Rwork0.211 --
obs-17302 89.8 %
Solvent computationBsol: 30.952 Å2
Displacement parametersBiso mean: 59.099 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1448 0 20 2 1470
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_d1.3
X-RAY DIFFRACTIONc_mcbond_it1.421.5
X-RAY DIFFRACTIONc_scbond_it1.9442
X-RAY DIFFRACTIONc_mcangle_it2.492
X-RAY DIFFRACTIONc_scangle_it2.9932.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.paramCNS_TOPPAR:dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top

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