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- PDB-3ilx: Crystal structure of First ORF in transposon ISC1904 from Sulfolo... -

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Basic information

Entry
Database: PDB / ID: 3ilx
TitleCrystal structure of First ORF in transposon ISC1904 from Sulfolobus solfataricus P2
ComponentsFirst ORF in transposon ISC1904
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / transposon ISC1904 / Sulfolobus solfataricus P2 / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


DNA strand exchange activity / DNA integration / regulation of DNA-templated transcription / DNA binding
Similarity search - Function
Helix Hairpins - #2170 / IS607-like transposase, catalytic domain / : / : / Helix-turn-helix domain, group 17 / Helix-turn-helix domain / Resolvase, N-terminal catalytic domain / Recombinase, conserved site / Site-specific recombinases active site. / Resolvase/invertase-type recombinase catalytic domain profile. ...Helix Hairpins - #2170 / IS607-like transposase, catalytic domain / : / : / Helix-turn-helix domain, group 17 / Helix-turn-helix domain / Resolvase, N-terminal catalytic domain / Recombinase, conserved site / Site-specific recombinases active site. / Resolvase/invertase-type recombinase catalytic domain profile. / Resolvase, N-terminal catalytic domain / Resolvase-like, N-terminal catalytic domain superfamily / Resolvase, N terminal domain / Resolvase, N terminal domain / helix_turn_helix, mercury resistance / MerR-type HTH domain profile. / MerR-type HTH domain / Putative DNA-binding domain superfamily / Helix Hairpins / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
First ORF in transposon ISC1904
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsChang, C. / Bigelow, L. / Bearden, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of First ORF in transposon ISC1904 from Sulfolobus solfataricus P2
Authors: Chang, C. / Bigelow, L. / Bearden, J. / Joachimiak, A.
History
DepositionAug 7, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: First ORF in transposon ISC1904
B: First ORF in transposon ISC1904
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2373
Polymers33,1452
Non-polymers921
Water3,603200
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-39 kcal/mol
Surface area14280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.013, 50.013, 126.134
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein First ORF in transposon ISC1904


Mass: 16572.639 Da / Num. of mol.: 2 / Fragment: sequence database residues 55-194
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: SSO2943 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: Q97UQ9
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / 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: 2.38 Å3/Da / Density % sol: 48.31 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2M Ammonium Acetate, 0.1M Bis-Tris, 25% PEG3350, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 4, 2009
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 20869 / Num. obs: 20817 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Biso Wilson estimate: 34.7 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 38.6
Reflection shellResolution: 2→2.03 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.725 / Mean I/σ(I) obs: 2.52 / Num. unique all: 1003 / % possible all: 98.4

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
MLPHAREphasing
DMmodel building
RESOLVEmodel building
Cootmodel building
ARP/wARPmodel building
REFMAC5.5.0054refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.938 / SU B: 10.605 / SU ML: 0.129 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.192 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23628 1060 5.1 %RANDOM
Rwork0.18772 ---
all0.19013 20709 --
obs0.19013 20709 99.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.8 Å2
Baniso -1Baniso -2Baniso -3
1--1.89 Å20 Å20 Å2
2---1.89 Å20 Å2
3---3.79 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2239 0 6 200 2445
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222281
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4391.9923063
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5265279
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.15525.283106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.35215463
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5021514
X-RAY DIFFRACTIONr_chiral_restr0.090.2356
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021650
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7481.51397
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.33222259
X-RAY DIFFRACTIONr_scbond_it2.2853884
X-RAY DIFFRACTIONr_scangle_it3.6924.5804
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 90 -
Rwork0.286 1344 -
obs-1434 95.86 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.2344-0.5191-0.3353.82180.80131.68070.0574-0.07150.32570.0303-0.05470.0223-0.2150.0115-0.00270.10160.0171-0.01120.0572-0.01440.0379-10.566424.614613.0315
22.03340.1862-0.8215.17492.3793.41170.0360.18270.1137-0.1074-0.13440.20460.0322-0.19140.09840.06820.0249-0.03090.1506-0.03270.0367-19.91880.69552.6684
33.706-0.4753-0.77012.97890.40831.56180.03930.2121-0.1304-0.17750.017-0.3831-0.02810.1253-0.05630.04410.02520.01190.1445-0.02560.06386.83057.17112.1775
46.45030.3071-0.69993.16560.25623.6693-0.0768-0.5827-0.11470.46910.090.00980.0982-0.0869-0.01330.10610.03350.0070.07320.01780.0065-16.9821-1.714212.8219
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A54 - 154
2X-RAY DIFFRACTION2A155 - 194
3X-RAY DIFFRACTION3B54 - 154
4X-RAY DIFFRACTION4B155 - 194

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