- PDB-3h50: CRYSTAL STRUCTURE OF A TETRACENOMYCIN POLYKETIDE SYNTHESIS PROTEI... -
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Basic information
Entry
Database: PDB / ID: 3h50
Title
CRYSTAL STRUCTURE OF A TETRACENOMYCIN POLYKETIDE SYNTHESIS PROTEIN (TCMJ) FROM XANTHOMONAS CAMPESTRIS PV. CAMPESTRIS AT 1.60 A RESOLUTION
Components
Tetracenomycin polyketide synthesis protein
Keywords
BIOSYNTHETIC PROTEIN / TETRACENOMYCIN POLYKETIDE SYNTHESIS PROTEIN / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Mass: 18.015 Da / Num. of mol.: 152 / Source method: isolated from a natural source / Formula: H2O
Sequence details
THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE
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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: 2.19 Å3/Da / Density % sol: 43.79 %
Crystal grow
Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 35.0% 2-propanol, 0.2M Zn(OAc)2, 0.1M Imidazole pH 8.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Monochromator: Single crystal Si(111) bent monochromator (horizontal focusing) Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
ID
Wavelength (Å)
Relative weight
1
0.91837
1
2
0.979616
1
3
0.979305
1
Reflection
Resolution: 1.6→28.502 Å / Num. obs: 13913 / % possible obs: 96.8 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 11.422 Å2 / Rmerge(I) obs: 0.105 / Net I/σ(I): 9.99
Reflection shell
Resolution (Å)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured obs
Num. unique obs
Diffraction-ID
% possible all
1.59-1.65
0.61
1.9
8850
2430
1
80.3
1.65-1.71
0.535
2.3
9471
2496
1
98.6
1.71-1.79
0.424
3
10553
2860
1
98.6
1.79-1.88
0.341
3.8
10112
2689
1
98.9
1.88-2
0.233
5.7
9653
2816
1
98
2-2.16
0.167
7.9
10465
2905
1
98.7
2.16-2.37
0.123
10.4
9838
2696
1
99.3
2.37-2.72
0.096
12.7
10648
2904
1
99.1
2.72-3.42
0.055
20.6
10213
2742
1
99.4
3.42-28.502
0.034
29.8
10350
2813
1
98.4
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Phasing
Phasing
Method: MAD
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Processing
Software
Name
Version
Classification
NB
REFMAC
5.2.0019
refinement
PHENIX
refinement
SHELX
phasing
MolProbity
3beta29
modelbuilding
XSCALE
datascaling
PDB_EXTRACT
3.006
dataextraction
XDS
datareduction
SHELXD
phasing
autoSHARP
phasing
Refinement
Method to determine structure: MAD / Resolution: 1.6→28.502 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.932 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 3.667 / SU ML: 0.074 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.1 / ESU R Free: 0.1 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1). HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2). ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY 3). ZINC WAS MODELED IN FOUR SITES THAT COINCIDE WITH PEAKS IN THE ANOMALOUS DIFFERENCE ...Details: 1). HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2). ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY 3). ZINC WAS MODELED IN FOUR SITES THAT COINCIDE WITH PEAKS IN THE ANOMALOUS DIFFERENCE FOURIER. X-RAY FLUORESCENCE MEASUREMENTS CONFIRM THAT ZINC IS PRESENT AND NICKEL IS ABSENT FROM THE SAMPLE. 4). ACETATE MOLECULES FROM THE CRYSTALLIZATION SOLUTIONS HAVE BEEN MODELED INTO THE STRUCTURE. 5). UNEXPLAINED ELECTRON DENSITIES WERE OBSERVED WITHIN COORDINATION DISTANCE OF ZN 2, ZN 3, AND ZN 4. LIGANDS WERE NOT MODELED INTO THESE ELECTRON DENSITIES.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.22
696
5 %
RANDOM
Rwork
0.182
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-
-
obs
0.184
13912
98.9 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
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