BIOLOGICAL UNIT CONTAINS PROTEIN CHAINS A AND B, AND DNA STRANDS C AND D. THE TETRAMER (ACCORDING TO PDB CONVENTIONS) IS A COMPLEX OF THE DIMERIC RESTRICTION ENZYME WITH ITS SUBSTRATE, DOUBLE STRANDED DNA.
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Components
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Protein , 1 types, 2 molecules AB
#1: Protein
restrictionendonucleaseTHAI / Putative uncharacterized protein Ta0828
Mass: 26417.373 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermoplasma acidophilum (acidophilic) / Strain: ATCC25905 / Gene: Ta0828 / Plasmid: PET15BMOD / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 / References: UniProt: Q9HJY3
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DNA chain , 2 types, 2 molecules CD
#2: DNA chain
DNA (5'-D(*G*GP*TP*AP*CP*GP*CP*GP*AP*TP*G)-3')
Mass: 3414.234 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain
DNA (5'-D(*C*CP*AP*TP*CP*GP*CP*GP*TP*AP*C)-3')
Mass: 3294.162 Da / Num. of mol.: 1 / Source method: obtained synthetically
Mass: 18.015 Da / Num. of mol.: 470 / Source method: isolated from a natural source / Formula: H2O
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Details
Nonpolymer details
THE IDENTITY OF THE METAL IONS IS UNCERTAIN. THE DEPOSITORS SUSPECT THEM TO BE SODIUM OR CALCIUM ...THE IDENTITY OF THE METAL IONS IS UNCERTAIN. THE DEPOSITORS SUSPECT THEM TO BE SODIUM OR CALCIUM IONS, WHICH ARE BOTH PRESENT IN THE BUFFER.
Sequence details
ALTHOUGH AN N-TERMINAL TAG HAS BEEN ASSIGNED TO CHAIN A, THE TAG MIGHT BE A PART OF CHAIN A, CHAIN ...ALTHOUGH AN N-TERMINAL TAG HAS BEEN ASSIGNED TO CHAIN A, THE TAG MIGHT BE A PART OF CHAIN A, CHAIN B OR A SYMMETRY MATE.
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 2.09 Å3/Da / Density % sol: 41.14 %
Crystal grow
Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 0.1M sodium acetate PH 4.5, 200MM, ammonium sulfate, 30% PEG400, 1.5% 1,2,3-heptanetriol, VAPOR, DIFFUSION, SITTING DROP, TEMPERATURE 294K, VAPOR DIFFUSION, HANGING DROP
Type: MARRESEARCH / Detector: CCD / Date: Dec 18, 2008 / Details: BENT MIRROR
Radiation
Monochromator: TRIANGULAR MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.976 Å / Relative weight: 1
Reflection
Resolution: 1.3→20 Å / Num. all: 118539 / Num. obs: 118539 / % possible obs: 98.7 % / Redundancy: 2.8 % / Biso Wilson estimate: 14.24 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 5
Reflection shell
Resolution: 1.3→1.37 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.266 / Mean I/σ(I) obs: 2.8 / Num. unique all: 17399 / Rsym value: 0.266 / % possible all: 99.4
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Processing
Software
Name
Version
Classification
MAR345
datacollection
SHELXCD
phasing
SHELXD
phasing
SHELXE
modelbuilding
SHARP
phasing
ARP/wARP
modelbuilding
REFMAC
5.2.0019
refinement
MOSFLM
datareduction
SCALA
datascaling
Refinement
Method to determine structure: SIRAS / Resolution: 1.3→19.51 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.968 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / ESU R Free: 0.054 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: CNS has been used for DNA refinement. No sugar pucker constraints have been applied. Hydrogens have been added in the riding positions. TLS refinement has been used.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.18318
5962
5 %
RANDOM
Rwork
0.17173
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all
0.1723
118512
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obs
0.1723
118512
98.61 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
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