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- PDB-3fyn: Crystal structure from the mobile metagenome of Cole Harbour Salt... -

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Basic information

Entry
Database: PDB / ID: 3fyn
TitleCrystal structure from the mobile metagenome of Cole Harbour Salt Marsh: Integron Cassette Protein HFX_CASS3
ComponentsIntegron gene cassette protein HFX_CASS3
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Integron Cassette Protein / Mobile Metagenome / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


N-acetyltransferase activity
Similarity search - Function
Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Putative integron gene cassette protein
Similarity search - Component
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.449 Å
AuthorsSureshan, V. / Deshpande, C.N. / Harrop, S.J. / Kudritska, M. / Koenig, J.E. / Evdokimova, E. / Osipiuk, J. / Edwards, A.M. / Savchenko, A. / Joachimiak, A. ...Sureshan, V. / Deshpande, C.N. / Harrop, S.J. / Kudritska, M. / Koenig, J.E. / Evdokimova, E. / Osipiuk, J. / Edwards, A.M. / Savchenko, A. / Joachimiak, A. / Doolittle, W.F. / Stokes, H.W. / Curmi, P.M.G. / Mabbutt, B.C. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Structure from the mobile metagenome of Cole Harbour Salt Marsh: Integron Cassette Protein HFX_CASS3
Authors: Sureshan, V. / Deshpande, C. / Harrop, S.J. / Kudritska, M. / Koenig, J.E. / Evdokimova, E. / Osipiuk, J. / Edwards, A.M. / Savchenko, A. / Joachimiak, A. / Doolittle, W.F. / Stokes, H.W. / ...Authors: Sureshan, V. / Deshpande, C. / Harrop, S.J. / Kudritska, M. / Koenig, J.E. / Evdokimova, E. / Osipiuk, J. / Edwards, A.M. / Savchenko, A. / Joachimiak, A. / Doolittle, W.F. / Stokes, H.W. / Curmi, P.M.G. / Mabbutt, B.C.
History
DepositionJan 22, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Integron gene cassette protein HFX_CASS3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3283
Polymers19,2441
Non-polymers832
Water2,198122
1
A: Integron gene cassette protein HFX_CASS3
hetero molecules

A: Integron gene cassette protein HFX_CASS3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6556
Polymers38,4892
Non-polymers1674
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area4800 Å2
ΔGint-26.7 kcal/mol
Surface area14520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.827, 62.374, 37.247
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Integron gene cassette protein HFX_CASS3


Mass: 19244.275 Da / Num. of mol.: 1
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: B0BFQ1
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 1.75 Å3/Da / Density % sol: 29.6 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Magnesium acetate, 20% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97923 Å
DetectorType: SBC-3 / Detector: CCD / Date: Oct 13, 2008
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 1.449→50 Å / Num. all: 23542 / Num. obs: 23542 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 16.14 Å2 / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Χ2: 1.707 / Net I/σ(I): 24.992
Reflection shellResolution: 1.449→1.53 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.696 / Mean I/σ(I) obs: 1.906 / Num. unique all: 1075 / Rsym value: 0.696 / Χ2: 0.84 / % possible all: 99.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.006data extraction
HKL-3000data collection
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.449→27.985 Å / Occupancy max: 1 / Occupancy min: 0.16 / SU ML: 0.19 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.207 1921 8.16 %random
Rwork0.179 ---
all0.181 23542 --
obs0.181 22399 95.79 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 72.816 Å2 / ksol: 0.407 e/Å3
Displacement parametersBiso max: 62.61 Å2 / Biso mean: 22.616 Å2 / Biso min: 8.12 Å2
Baniso -1Baniso -2Baniso -3
1--4.021 Å2-0 Å20 Å2
2---0.391 Å2-0 Å2
3---4.412 Å2
Refinement stepCycle: LAST / Resolution: 1.449→27.985 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1226 0 5 122 1353
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041263
X-RAY DIFFRACTIONf_angle_d0.9041718
X-RAY DIFFRACTIONf_chiral_restr0.058183
X-RAY DIFFRACTIONf_plane_restr0.004232
X-RAY DIFFRACTIONf_dihedral_angle_d14.609456
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.449-1.4860.2971250.2451411153689
1.486-1.5260.2891370.2271421155890
1.526-1.5710.2481110.2041463157491
1.571-1.6220.2231410.181437157892
1.622-1.6790.221380.181502164095
1.679-1.7470.2481230.161503162694
1.747-1.8260.1851350.1521550168596
1.826-1.9220.2011370.1511549168697
1.922-2.0430.1791390.1491572171199
2.043-2.20.1731490.1441619176899
2.2-2.4220.191480.1561597174599
2.422-2.7720.1961380.1721613175199
2.772-3.4910.1981430.1711652179599
3.491-27.990.1831570.1861732188999

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