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- PDB-2qgg: X-Ray structure of the protein Q6F7I0 from Acinetobacter calcoace... -

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Basic information

Entry
Database: PDB / ID: 2qgg
TitleX-Ray structure of the protein Q6F7I0 from Acinetobacter calcoaceticus AmMS 248. Northeast Structural Genomics Consortium target AsR73.
Components16S rRNA-processing protein rimM
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / NESG / AsR73 / Acinetobacter calcoaceticus / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
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
: / Unknown ligand / Ribosome maturation factor RimM
Similarity search - Component
Biological speciesAcinetobacter calcoaceticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsKuzin, A.P. / Su, M. / Jayaraman, S. / Wang, D. / Janjua, H. / Cunningham, K. / Ma, L.-C. / Xiao, R. / Liu, J. / Baran, M.C. ...Kuzin, A.P. / Su, M. / Jayaraman, S. / Wang, D. / 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: X-Ray structure of the protein Q6F7I0 from Acinetobacter calcoaceticus AmMS 248.
Authors: Kuzin, A.P. / Su, M. / Jayaraman, S. / Wang, D. / 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
DepositionJun 28, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Remark 600 HETEROGEN THE ATOMS OF UNKNOWN LIGAND HAVE BEEN REFINED AS WATER OXYGEN ATOMS.
Remark 999 SEQUENCE AUTHORS STATE THAT THE SEQUENCE DIFFERENCE IS DUE TO ANNOTATION ERROR OF THE ENTRY Q6F7I0. ... SEQUENCE AUTHORS STATE THAT THE SEQUENCE DIFFERENCE IS DUE TO ANNOTATION ERROR OF THE ENTRY Q6F7I0. THE AUTHOR'S SEQUENCE CONTAINS 13 NATURAL (NOT ENGINEERED) REPLACEMENTS FROM ANNOTATED Q6F7I0.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 16S rRNA-processing protein rimM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0833
Polymers21,0441
Non-polymers392
Water93752
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.899, 37.588, 69.200
Angle α, β, γ (deg.)90.00, 97.23, 90.00
Int Tables number3
Space group name H-MP121

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Components

#1: Protein 16S rRNA-processing protein rimM


Mass: 21043.771 Da / Num. of mol.: 1
Mutation: F46Y, N74G, N79T, A80G, I85V, G86A, T88N, V91I, T99A, E119D, A147P, V150I, A152S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter calcoaceticus (bacteria) / Strain: ADP1, AmMS 248 / Gene: rimM, ACIAD3312 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6F7I0
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.75 Å3/Da / Density % sol: 55.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 15% PEG 20000, 0.1M Potassium acetate, 0.1M MOPS, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 27, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 9040 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Redundancy: 13.5 % / Biso Wilson estimate: 27.5 Å2 / Rmerge(I) obs: 0.078
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.243 / % possible all: 85.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→19.86 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 438858.54 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.256 421 5.4 %RANDOM
Rwork0.207 ---
obs0.207 7729 84 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 23.779 Å2 / ksol: 0.306619 e/Å3
Displacement parametersBiso mean: 29.2 Å2
Baniso -1Baniso -2Baniso -3
1-11.05 Å20 Å2-3.96 Å2
2---4.68 Å20 Å2
3----6.37 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.47 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.4→19.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1417 0 8 52 1477
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.71
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.661.5
X-RAY DIFFRACTIONc_mcangle_it2.922
X-RAY DIFFRACTIONc_scbond_it2.142
X-RAY DIFFRACTIONc_scangle_it3.22.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.054 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.362 45 5.1 %
Rwork0.272 845 -
obs--58.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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