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- PDB-3fuy: Structure from the mobile metagenome of Cole Harbour Salt Marsh: ... -

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Basic information

Entry
Database: PDB / ID: 3fuy
TitleStructure from the mobile metagenome of Cole Harbour Salt Marsh: Integron Cassette Protein HFX_CASS1
ComponentsPutative integron gene cassette protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Integron cassette protein / Mobile Metagenome / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologyPutative integron gene cassette protein
Function and homology information
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsSureshan, V. / Deshpande, C.N. / Harrop, S.J. / Kudrytska, M. / Koenig, J.E. / Evdokimova, E. / Osipiuk, J. / Edwards, A. / Savchenko, A. / Joachimiak, A. / Doolittle, W.F. / Stokes, H.W. / Curmi, P.M.G. / Mabbutt, B.C. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Plos One / Year: 2013
Title: Integron gene cassettes: a repository of novel protein folds with distinct interaction sites
Authors: Sureshan, V. / Deshpande, C.N. / Boucher, Y. / Koenig, J.E. / Stokes, H.W. / Harrop, S.J. / Curmi, P.M.G. / Mabbutt, B.C.
Validation Report
SummaryFull reportAbout validation report
History
DepositionJan 15, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 6, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative integron gene cassette protein
B: Putative integron gene cassette protein
C: Putative integron gene cassette protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,6924
Polymers61,5963
Non-polymers961
Water2,936163
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4380 Å2
ΔGint-32 kcal/mol
Surface area21190 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)71.572, 71.572, 92.725
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32

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Components

#1: Protein/peptide Putative integron gene cassette protein / HFX_CASS1


Mass: 20532.076 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium (environmental samples)
Gene: ORF1 / Plasmid: p15TV LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL / References: UniProt: B0BGB0
#2: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 163 / Source method: isolated from a natural source / Formula: H2O / Water

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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: 2.23 Å3/Da / Density % sol: 44.75 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M ammonium sulfate, 25% PEG 3350 pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source

Beamline: 19-ID / Site: APS / Wavelength: 0.97929 Å / Source: SYNCHROTRON

Diffraction-ID
1
2
Detector

Detector: CCD / Date: Oct 25, 2008 / Type: ADSC QUANTUM 315

Diffraction-ID
1
2
Radiation

Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray / Wavelength-ID: 1

Diffraction-ID
1
2
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 2→92.85 Å / Num. obs: 35948 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Biso Wilson estimate: 39.7 Å2 / Rmerge(I) obs: 0.082 / Rsym value: 0.082 / Net I/σ(I): 15.3 / Num. measured all: 202528
Reflection shellResolution: 2→2.11 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 4.2 / Rsym value: 0.56 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
PHENIXrefinement
PDB_EXTRACT3.006data extraction
ADSCQuantumdata collection
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2→37.126 Å / Occupancy max: 1 / Occupancy min: 0.59 / FOM work R set: 0.83 / SU ML: 0.3 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0.01 / σ(I): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2341 6704 9.71 %RANDOM
Rwork0.1946 ---
All0.199 ---
Obs0.1985 35948 96.15 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.835 Å2 / ksol: 0.383 e/Å3
Displacement parametersBiso max: 99.29 Å2 / Biso mean: 38.766 Å2 / Biso min: 18.86 Å2
Baniso -1Baniso -2Baniso -3
1-4.9997 Å2-0 Å2-0 Å2
2--4.9997 Å20 Å2
3----9.9994 Å2
Refinement stepCycle: LAST / Resolution: 2→37.126 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3714 0 5 163 3882
Refine LS restraints

Refinement-ID: X-RAY DIFFRACTION

TypeDev idealNumber
f_bond_d0.0073778
f_angle_d0.9895091
f_chiral_restr0.068562
f_plane_restr0.004677
f_dihedral_angle_d15.7421405
LS refinement shell

Refinement-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.0230.2912190.2531848206786
2.023-2.0470.2771920.2431998219088
2.047-2.0720.2882110.2361886209790
2.072-2.0980.2682350.2351978221391
2.098-2.1250.2742270.2341940216791
2.125-2.1550.312040.2382028223293
2.155-2.1850.2822020.2131998220093
2.185-2.2180.32460.2292047229395
2.218-2.2530.242060.2112102230895
2.253-2.2890.2312010.2142041224295
2.289-2.3290.3172360.2212017225396
2.329-2.3710.2612320.2022126235896
2.371-2.4170.2522420.22032227496
2.417-2.4660.282150.2072132234797
2.466-2.520.2522200.1892076229698
2.52-2.5780.2582170.1992152236998
2.578-2.6430.2332360.192148238498
2.643-2.7140.252160.1942151236798
2.714-2.7940.2582110.1992139235099
2.794-2.8840.2642390.2142121236099
2.884-2.9870.2672280.2082154238299
2.987-3.1070.212470.1962140238799
3.107-3.2480.2542270.1952154238199
3.248-3.4190.232120.1962132234499
3.419-3.6340.2332380.1922147238599
3.634-3.9140.2232250.17521682393100
3.914-4.3070.1882280.1621632391100
4.307-4.9290.1852310.1612083231499
4.929-6.2050.1942340.1882146238098
6.205-37.1320.2092270.1892118234598

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