HEADER NUCLEIC ACID 24-APR-06 2CKY TITLE STRUCTURE OF THE ARABIDOPSIS THALIANA THIAMINE PYROPHOSPHATE TITLE 2 RIBOSWITCH WITH ITS REGULATORY LIGAND COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEIC ACID; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; SOURCE 4 ORGANISM_COMMON: MOUSE-EAR CRESS; SOURCE 5 ORGANISM_TAXID: 3702 KEYWDS NUCLEIC ACID EXPDTA X-RAY DIFFRACTION AUTHOR S.THORE,M.LEIBUNDGUT,N.BAN REVDAT 5 08-MAY-24 2CKY 1 LINK REVDAT 4 13-JUL-11 2CKY 1 VERSN REVDAT 3 24-FEB-09 2CKY 1 VERSN REVDAT 2 31-MAY-06 2CKY 1 JRNL REVDAT 1 08-MAY-06 2CKY 0 JRNL AUTH S.THORE,M.LEIBUNDGUT,N.BAN JRNL TITL STRUCTURE OF THE EUKARYOTIC THIAMINE PYROPHOSPHATE JRNL TITL 2 RIBOSWITCH WITH ITS REGULATORY LIGAND. JRNL REF SCIENCE V. 312 1208 2006 JRNL REFN ISSN 0036-8075 JRNL PMID 16675665 JRNL DOI 10.1126/SCIENCE.1128451 REMARK 2 REMARK 2 RESOLUTION. 2.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 3 NUMBER OF REFLECTIONS : 8918 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 12.500 REMARK 3 FREE R VALUE TEST SET COUNT : 1270 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.97 REMARK 3 REFLECTION IN BIN (WORKING SET) : 469 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3550 REMARK 3 BIN FREE R VALUE SET COUNT : 73 REMARK 3 BIN FREE R VALUE : 0.4390 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 3310 REMARK 3 HETEROGEN ATOMS : 74 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 50.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.62000 REMARK 3 B22 (A**2) : -0.12000 REMARK 3 B33 (A**2) : -1.05000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.88000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.474 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.345 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 37.628 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.945 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.887 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3758 ; 0.011 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 1292 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5856 ; 2.218 ; 3.000 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3360 ; 1.426 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 770 ; 0.082 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1654 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 885 ; 0.178 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 1728 ; 0.247 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1414 ; 0.252 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 874 ; 0.095 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 112 ; 0.208 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 23 ; 0.207 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 23 ; 0.392 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 8 ; 0.170 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 5429 ; 1.195 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 5856 ; 2.017 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 59 REMARK 3 ORIGIN FOR THE GROUP (A): 5.2400 12.4660 -46.3580 REMARK 3 T TENSOR REMARK 3 T11: 0.2182 T22: 0.0666 REMARK 3 T33: 0.1021 T12: 0.0301 REMARK 3 T13: -0.0988 T23: -0.0389 REMARK 3 L TENSOR REMARK 3 L11: 1.0141 L22: 2.7682 REMARK 3 L33: 2.1085 L12: 0.9814 REMARK 3 L13: 0.2742 L23: 0.1554 REMARK 3 S TENSOR REMARK 3 S11: -0.0123 S12: -0.0642 S13: -0.1056 REMARK 3 S21: -0.4060 S22: 0.1671 S23: -0.0458 REMARK 3 S31: -0.0349 S32: 0.1515 S33: -0.1548 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 60 A 77 REMARK 3 ORIGIN FOR THE GROUP (A): -5.4470 4.1630 -51.4470 REMARK 3 T TENSOR REMARK 3 T11: 0.3374 T22: 0.0408 REMARK 3 T33: 0.1974 T12: -0.0355 REMARK 3 T13: -0.1973 T23: 0.0890 REMARK 3 L TENSOR REMARK 3 L11: 3.2859 L22: 3.3447 REMARK 3 L33: 5.0686 L12: 0.0667 REMARK 3 L13: -0.5135 L23: 1.7588 REMARK 3 S TENSOR REMARK 3 S11: 0.0947 S12: 0.1432 S13: -0.1806 REMARK 3 S21: -0.7329 S22: -0.2308 S23: 0.1640 REMARK 3 S31: -0.3047 S32: -0.2729 S33: 0.1361 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1 B 59 REMARK 3 ORIGIN FOR THE GROUP (A): -0.2270 -18.2660 -88.7550 REMARK 3 T TENSOR REMARK 3 T11: 0.1859 T22: 0.1406 REMARK 3 T33: 0.1514 T12: -0.0186 REMARK 3 T13: -0.0667 T23: -0.0209 REMARK 3 L TENSOR REMARK 3 L11: 0.6031 L22: 3.6733 REMARK 3 L33: 1.1279 L12: -0.4628 REMARK 3 L13: 0.2605 L23: -0.8179 REMARK 3 S TENSOR REMARK 3 S11: -0.1373 S12: -0.1238 S13: -0.0769 REMARK 3 S21: 0.0972 S22: 0.0409 S23: 0.4575 REMARK 3 S31: 0.0835 S32: -0.1009 S33: 0.0964 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 60 B 77 REMARK 3 ORIGIN FOR THE GROUP (A): -8.4630 -9.5430 -96.7110 REMARK 3 T TENSOR REMARK 3 T11: 0.2822 T22: 0.1263 REMARK 3 T33: 0.3754 T12: -0.0884 REMARK 3 T13: -0.2189 T23: -0.0157 REMARK 3 L TENSOR REMARK 3 L11: 4.4041 L22: 3.7795 REMARK 3 L33: 4.9602 L12: -1.0656 REMARK 3 L13: -2.5325 L23: 0.4980 REMARK 3 S TENSOR REMARK 3 S11: -0.1803 S12: 0.5835 S13: -0.2484 REMARK 3 S21: -0.3599 S22: -0.2259 S23: 1.0863 REMARK 3 S31: -0.0570 S32: -0.8611 S33: 0.4062 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. AN ALTERNATIVE CONFORMATION OF THE PYROPHOSPHATE THAT REMARK 3 INCLUDES AN ADDITIONAL MG ION WOULD ALSO EXPLAIN THE ELECTRON REMARK 3 DENSITY BUT DID NOT REFINE STABLY AT CURRENT RESOLUTION. ATOM REMARK 3 3333 O22 TDP Z 1 -6.837 9.528 -43.442 1.00 57.26 ATOM 3334 P2 REMARK 3 TDP Z 1 -5.700 8.586 -42.801 1.00 58.90 ATOM 3335 O23 TDP Z 1 - REMARK 3 5.792 8.782 -41.205 1.00 56.67 ATOM 3336 O21 TDP Z 1 -5.840 REMARK 3 7.175 -43.223 1.00 59.87 ATOM 3337 O11 TDP Z 1 -4.282 9.217 - REMARK 3 43.230 1.00 58.47 ATOM 3338 P1 TDP Z 1 -3.766 10.572 -42.527 REMARK 3 1.00 57.46 ATOM 3339 O13 TDP Z 1 -3.929 10.438 -40.935 1.00 REMARK 3 57.28 ATOM 3340 O12 TDP Z 1 -4.348 11.782 -43.152 1.00 57.28 REMARK 3 ATOM 3341 O5G TDP Z 1 -2.168 10.573 -42.729 1.00 56.65 ATOM 3342 REMARK 3 C5B TDP Z 1 -1.596 9.973 -43.895 1.00 58.30 ATOM 3343 C5A TDP Z REMARK 3 1 -0.879 11.035 -44.733 1.00 58.55 ATOM 3344 C5 TDP Z 1 0.286 REMARK 3 11.649 -43.960 1.00 57.40 ATOM 3345 C4 TDP Z 1 1.590 11.195 - REMARK 3 43.763 1.00 56.88 ATOM 3346 C4A TDP Z 1 2.111 9.923 -44.433 1.00 REMARK 3 58.41 ATOM 3347 S1 TDP Z 1 0.170 13.155 -43.100 1.00 63.43 ATOM REMARK 3 3348 C2 TDP Z 1 1.791 13.043 -42.459 1.00 58.90 ATOM 3349 N3 TDP REMARK 3 Z 1 2.352 11.945 - 42.971 1.00 58.30 ATOM 3350 C35 TDP Z 1 3.742 REMARK 3 11.569 -42.664 1.00 51.33 ATOM 3351 C5* TDP Z 1 4.667 12.074 - REMARK 3 43.771 1.00 48.26 ATOM 3352 C6* TDP Z 1 4.096 12.728 -44.858 REMARK 3 1.00 46.89 ATOM 3353 N1* TDP Z 1 4.858 13.191 -45.830 1.00 46.75 REMARK 3 ATOM 3354 C2* TDP Z 1 6.191 13.046 -45.794 1.00 48.28 ATOM 3355 REMARK 3 C2A TDP Z 1 7.051 13.632 -46.917 1.00 46.88 ATOM 3356 N3* TDP Z REMARK 3 1 6.783 12.419 -44.770 1.00 48.53 ATOM 3357 C4* TDP Z 1 6.048 REMARK 3 11.929 -43.760 1.00 48.94 ATOM 3358 N4* TDP Z 1 6.649 11.292 - REMARK 3 42.759 1.00 48.13 ATOM 3359 MG MG M 1 -4.149 8.720 -39.392 1.00 REMARK 3 48.53 ATOM 3360 MG MG M 2 -7.655 11.172 -43.838 1.00 68.69 ATOM REMARK 3 3361 O22 TDP Z 2 -1.323 -14.809-100.997 1.00 75.50 ATOM 3362 P2 REMARK 3 TDP Z 2 -0.700 -13.758 -99.945 1.00 73.87 ATOM 3363 O23 TDP Z 2 REMARK 3 0.797 -13.435-100.442 1.00 71.46 ATOM 3364 O21 TDP Z 2 -1.543 - REMARK 3 12.551 -99.810 1.00 73.60 ATOM 3365 O11 TDP Z 2 -0.542 -14.553 - REMARK 3 98.557 1.00 72.09 ATOM 3366 P1 TDP Z 2 0.607 -15.670 -98.393 REMARK 3 1.00 71.83 ATOM 3367 O13 TDP Z 2 1.995 - 15.124 -98.985 1.00 REMARK 3 71.01 ATOM 3368 O12 TDP Z 2 0.178 -17.018 -98.830 1.00 73.08 REMARK 3 ATOM 3369 O5G TDP Z 2 0.854 -15.664 -96.804 1.00 69.28 ATOM 3370 REMARK 3 C5B TDP Z 2 -0.265 -15.547 -95.922 1.00 69.80 ATOM 3371 C5A TDP REMARK 3 Z 2 -0.542 -16.897 -95.257 1.00 71.58 ATOM 3372 C5 TDP Z 2 0.625 REMARK 3 -17.307 -94.362 1.00 71.11 ATOM 3373 C4 TDP Z 2 1.021 -16.795 - REMARK 3 93.126 1.00 70.49 ATOM 3374 C4A TDP Z 2 0.188 -15.742 -92.391 REMARK 3 1.00 68.84 ATOM 3375 S1 TDP Z 2 1.775 -18.550 -94.770 1.00 74.34 REMARK 3 ATOM 3376 C2 TDP Z 2 2.765 - 18.232 -93.367 1.00 72.30 ATOM 3377 REMARK 3 N3 TDP Z 2 2.151 -17.298 - 92.637 1.00 70.45 ATOM 3378 C35 TDP Z REMARK 3 2 2.715 -16.846 -91.353 1.00 72.30 ATOM 3379 C5* TDP Z 2 2.073 - REMARK 3 17.621 -90.204 1.00 62.80 ATOM 3380 C6* TDP Z 2 0.999 -18.455 - REMARK 3 90.495 1.00 62.47 ATOM 3381 N1* TDP Z 2 0.373 -19.098 -89.528 REMARK 3 1.00 61.62 ATOM 3382 C2* TDP Z 2 0.754 -18.967 -88.251 1.00 REMARK 3 60.60 ATOM 3383 C2A TDP Z 2 0.029 -19.754 -87.159 1.00 60.95 REMARK 3 ATOM 3384 N3* TDP Z 2 1.783 -18.172 -87.923 1.00 60.57 ATOM 3385 REMARK 3 C4* TDP Z 2 2.451 -17.504 -88.871 1.00 62.25 ATOM 3386 N4* TDP Z REMARK 3 2 3.505 - 16.764 -88.539 1.00 61.96 ATOM 3387 MG MG M 3 3.095 - REMARK 3 13.594 - 99.566 1.00 49.90 ATOM 3388 MG MG M 4 -1.296 -16.602- REMARK 3 102.200 1.00 68.69 REMARK 4 REMARK 4 2CKY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 24-APR-06. REMARK 100 THE DEPOSITION ID IS D_1290028550. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.1397 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8918 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900 REMARK 200 RESOLUTION RANGE LOW (A) : 15.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.23500 REMARK 200 R SYM (I) : 0.17500 REMARK 200 FOR THE DATA SET : 7.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 74.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.70 REMARK 200 R MERGE FOR SHELL (I) : 0.97000 REMARK 200 R SYM FOR SHELL (I) : 0.72000 REMARK 200 FOR SHELL : 1.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SHELX, SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.57 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% 1,6-HEXANEDIOL 50MM SODIUM REMARK 280 CACODYLATE PH7.0 10MM MGSO4 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 49.33500 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 G A 30 C6 G A 30 N1 0.063 REMARK 500 G A 64 O5' G A 64 C5' -0.056 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 G A 1 O4' - C1' - N9 ANGL. DEV. = 6.5 DEGREES REMARK 500 G A 1 C4 - C5 - N7 ANGL. DEV. = 2.4 DEGREES REMARK 500 G A 1 N1 - C6 - O6 ANGL. DEV. = 3.8 DEGREES REMARK 500 G A 1 C5 - C6 - O6 ANGL. DEV. = -3.9 DEGREES REMARK 500 G A 3 C5 - C6 - O6 ANGL. DEV. = -4.1 DEGREES REMARK 500 A A 7 O4' - C1' - N9 ANGL. DEV. = 7.3 DEGREES REMARK 500 G A 13 P - O5' - C5' ANGL. DEV. = -9.8 DEGREES REMARK 500 G A 13 C4' - C3' - C2' ANGL. DEV. = -6.1 DEGREES REMARK 500 U A 19 O5' - P - OP1 ANGL. DEV. = -5.8 DEGREES REMARK 500 U A 19 C1' - O4' - C4' ANGL. DEV. = -4.4 DEGREES REMARK 500 A A 21 O4' - C4' - C3' ANGL. DEV. = -6.7 DEGREES REMARK 500 A A 23 C3' - C2' - C1' ANGL. DEV. = -4.8 DEGREES REMARK 500 U A 27 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 U A 27 C3' - O3' - P ANGL. DEV. = 8.8 DEGREES REMARK 500 G A 30 C6 - N1 - C2 ANGL. DEV. = -4.3 DEGREES REMARK 500 G A 30 N1 - C2 - N3 ANGL. DEV. = 4.4 DEGREES REMARK 500 G A 30 N1 - C6 - O6 ANGL. DEV. = 3.8 DEGREES REMARK 500 A A 31 O4' - C1' - N9 ANGL. DEV. = 5.7 DEGREES REMARK 500 A A 33 N9 - C1' - C2' ANGL. DEV. = 8.1 DEGREES REMARK 500 A A 33 O4' - C1' - N9 ANGL. DEV. = -5.3 DEGREES REMARK 500 G A 34 C4' - C3' - C2' ANGL. DEV. = -6.2 DEGREES REMARK 500 U A 35 O4' - C1' - C2' ANGL. DEV. = -6.7 DEGREES REMARK 500 U A 41 C3' - C2' - C1' ANGL. DEV. = -4.3 DEGREES REMARK 500 A A 52 C4' - C3' - C2' ANGL. DEV. = -7.6 DEGREES REMARK 500 A A 52 C3' - C2' - C1' ANGL. DEV. = -6.6 DEGREES REMARK 500 U A 59 C3' - O3' - P ANGL. DEV. = -7.4 DEGREES REMARK 500 G A 60 O4' - C1' - N9 ANGL. DEV. = 6.4 DEGREES REMARK 500 G A 73 N9 - C1' - C2' ANGL. DEV. = 8.0 DEGREES REMARK 500 G A 73 O4' - C1' - N9 ANGL. DEV. = -6.9 DEGREES REMARK 500 G B 8 O4' - C1' - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 G B 9 C3' - C2' - C1' ANGL. DEV. = -5.3 DEGREES REMARK 500 G B 11 O4' - C1' - N9 ANGL. DEV. = -5.0 DEGREES REMARK 500 G B 13 C6 - C5 - N7 ANGL. DEV. = -3.7 DEGREES REMARK 500 A B 23 O4' - C1' - N9 ANGL. DEV. = 6.7 DEGREES REMARK 500 G B 24 C3' - C2' - C1' ANGL. DEV. = -4.8 DEGREES REMARK 500 U B 27 O4' - C1' - N1 ANGL. DEV. = 7.0 DEGREES REMARK 500 A B 33 O4' - C1' - N9 ANGL. DEV. = -7.1 DEGREES REMARK 500 U B 35 C1' - O4' - C4' ANGL. DEV. = -7.5 DEGREES REMARK 500 U B 35 N1 - C1' - C2' ANGL. DEV. = 11.9 DEGREES REMARK 500 U B 35 C3' - O3' - P ANGL. DEV. = 9.5 DEGREES REMARK 500 A B 50 N9 - C1' - C2' ANGL. DEV. = 8.0 DEGREES REMARK 500 A B 50 O4' - C1' - N9 ANGL. DEV. = -6.5 DEGREES REMARK 500 A B 50 C3' - O3' - P ANGL. DEV. = 9.8 DEGREES REMARK 500 U B 59 N3 - C2 - O2 ANGL. DEV. = -4.8 DEGREES REMARK 500 G B 60 N9 - C1' - C2' ANGL. DEV. = -7.0 DEGREES REMARK 500 G B 60 O4' - C1' - N9 ANGL. DEV. = 5.6 DEGREES REMARK 500 C B 62 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 U B 63 O4' - C1' - N1 ANGL. DEV. = 5.3 DEGREES REMARK 500 G B 64 C5' - C4' - O4' ANGL. DEV. = 5.4 DEGREES REMARK 500 G B 70 O4' - C1' - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 51 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A1081 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 3 OP1 REMARK 620 2 A A 4 OP1 138.0 REMARK 620 3 A A 4 OP2 103.9 51.6 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A1082 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 48 O6 REMARK 620 2 G A 66 O6 67.2 REMARK 620 3 TPP A1084 O2B 152.9 97.8 REMARK 620 4 TPP A1084 O1A 123.3 162.4 77.7 REMARK 620 5 TPP A1084 O2A 155.7 115.2 50.7 49.0 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A1078 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 71 O6 REMARK 620 2 MG A1080 MG 82.6 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B1080 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G B 48 O6 REMARK 620 2 A B 49 N1 62.7 REMARK 620 3 G B 66 O6 86.2 116.5 REMARK 620 4 TPP B1082 O1A 125.4 122.2 120.9 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A1078 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A1079 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A1080 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A1081 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A1082 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B1078 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B1079 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B1080 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE OS B1081 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TPP A1084 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TPP B1082 DBREF 2CKY A 1 77 PDB 2CKY 2CKY 1 77 DBREF 2CKY B 1 77 PDB 2CKY 2CKY 1 77 SEQRES 1 A 77 G G G A C C A G G G G U G SEQRES 2 A 77 C U U G U U C A C A G G C SEQRES 3 A 77 U G A G A A A G U C C C U SEQRES 4 A 77 U U G A A C C U G A A C A SEQRES 5 A 77 G G G U A A U G C C U G C SEQRES 6 A 77 G C A G G G A G U G U C SEQRES 1 B 77 G G G A C C A G G G G U G SEQRES 2 B 77 C U U G U U C A C A G G C SEQRES 3 B 77 U G A G A A A G U C C C U SEQRES 4 B 77 U U G A A C C U G A A C A SEQRES 5 B 77 G G G U A A U G C C U G C SEQRES 6 B 77 G C A G G G A G U G U C HET MG A1078 1 HET MG A1079 1 HET MG A1080 1 HET MG A1081 1 HET MG A1082 1 HET OS A1083 1 HET TPP A1084 26 HET OS A1085 1 HET OS A1086 1 HET OS A1087 1 HET OS A1088 1 HET MG B1078 1 HET MG B1079 1 HET MG B1080 1 HET OS B1081 1 HET TPP B1082 26 HET MG B1083 1 HET MG B1084 1 HET OS B1085 1 HET OS B1086 1 HET OS B1087 1 HET OS B1088 1 HET OS B1089 1 HET OS B1090 1 HETNAM MG MAGNESIUM ION HETNAM OS OSMIUM ION HETNAM TPP THIAMINE DIPHOSPHATE FORMUL 3 MG 10(MG 2+) FORMUL 8 OS 12(OS 3+) FORMUL 9 TPP 2(C12 H19 N4 O7 P2 S 1+) LINK OP1 G A 3 MG MG A1081 1555 1555 3.14 LINK OP1 A A 4 MG MG A1081 1555 1555 3.03 LINK OP2 A A 4 MG MG A1081 1555 1555 2.72 LINK N7 A A 29 MG MG A1079 1555 1555 2.52 LINK O6 G A 48 MG MG A1082 1555 1555 2.64 LINK O6 G A 66 MG MG A1082 1555 1555 2.26 LINK O6 G A 71 MG MG A1078 1555 1555 3.13 LINK MG MG A1078 MG MG A1080 1555 1555 2.61 LINK MG MG A1082 O2B TPP A1084 1555 1555 3.00 LINK MG MG A1082 O1A TPP A1084 1555 1555 3.04 LINK MG MG A1082 O2A TPP A1084 1555 1555 3.06 LINK N7 A B 29 MG MG B1078 1555 1555 2.44 LINK O6 G B 48 MG MG B1080 1555 1555 2.06 LINK N1 A B 49 MG MG B1080 1555 1555 3.05 LINK O6 G B 66 MG MG B1080 1555 1555 2.04 LINK OP2 G B 70 MG MG B1079 1555 1555 2.66 LINK MG MG B1080 O1A TPP B1082 1555 1555 2.28 SITE 1 AC1 2 G A 71 MG A1080 SITE 1 AC2 1 A A 29 SITE 1 AC3 1 MG A1078 SITE 1 AC4 2 G A 3 A A 4 SITE 1 AC5 4 G A 48 C A 65 G A 66 TPP A1084 SITE 1 AC6 1 A B 29 SITE 1 AC7 2 G B 42 G B 70 SITE 1 AC8 4 G B 48 A B 49 G B 66 TPP B1082 SITE 1 AC9 1 G B 55 SITE 1 BC1 10 G A 11 G A 28 G A 30 A A 31 SITE 2 BC1 10 C A 45 G A 60 C A 61 U A 63 SITE 3 BC1 10 C A 65 MG A1082 SITE 1 BC2 11 G B 11 G B 28 G B 30 A B 31 SITE 2 BC2 11 C B 45 G B 60 U B 63 G B 64 SITE 3 BC2 11 C B 65 G B 66 MG B1080 CRYST1 46.850 98.670 54.550 90.00 104.80 90.00 P 1 21 1 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.021345 0.000000 0.005640 0.00000 SCALE2 0.000000 0.010135 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018961 0.00000