HEADER LIGASE/TRNA 18-APR-06 2DLC TITLE CRYSTAL STRUCTURE OF THE TERNARY COMPLEX OF YEAST TYROSYL-TRNA TITLE 2 SYNTHETASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: T-RNA (76-MER); COMPND 3 CHAIN: Y; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: TYROSYL-TRNA SYNTHETASE, CYTOPLASMIC; COMPND 7 CHAIN: X; COMPND 8 SYNONYM: TYROSYL-TRNA LIGASE, TYRRS; COMPND 9 EC: 6.1.1.1; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 5 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 6 ORGANISM_TAXID: 4932; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET21A KEYWDS TYRRS, TRNA, LIGASE-TRNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.TSUNODA,Y.KUSAKABE,N.TANAKA,K.T.NAKAMURA REVDAT 5 13-MAR-24 2DLC 1 REMARK SEQADV HETSYN LINK REVDAT 4 12-JUL-17 2DLC 1 JRNL REVDAT 3 13-JUL-11 2DLC 1 VERSN REVDAT 2 24-FEB-09 2DLC 1 VERSN REVDAT 1 12-JUN-07 2DLC 0 JRNL AUTH M.TSUNODA,Y.KUSAKABE,N.TANAKA,S.OHNO,M.NAKAMURA,T.SENDA, JRNL AUTH 2 T.MORIGUCHI,N.ASAI,M.SEKINE,T.YOKOGAWA,K.NISHIKAWA, JRNL AUTH 3 K.T.NAKAMURA JRNL TITL STRUCTURAL BASIS FOR RECOGNITION OF COGNATE TRNA BY JRNL TITL 2 TYROSYL-TRNA SYNTHETASE FROM THREE KINGDOMS. JRNL REF NUCLEIC ACIDS RES. V. 35 4289 2007 JRNL REFN ESSN 1362-4962 JRNL PMID 17576676 JRNL DOI 10.1093/NAR/GKM417 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.24 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 26411 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) : 0.247 REMARK 3 R VALUE (WORKING SET) : 0.245 REMARK 3 FREE R VALUE : 0.289 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1403 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) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.46 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1929 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3470 REMARK 3 BIN FREE R VALUE SET COUNT : 93 REMARK 3 BIN FREE R VALUE : 0.4050 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2698 REMARK 3 NUCLEIC ACID ATOMS : 1472 REMARK 3 HETEROGEN ATOMS : 36 REMARK 3 SOLVENT ATOMS : 57 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.97 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.06000 REMARK 3 B22 (A**2) : 0.06000 REMARK 3 B33 (A**2) : -0.12000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.405 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.284 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.224 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.713 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.916 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.882 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4436 ; 0.006 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6332 ; 1.124 ; 2.399 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 337 ; 5.300 ; 5.000 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): 687 ; 0.067 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2799 ; 0.003 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1901 ; 0.176 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 143 ; 0.138 ; 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): 56 ; 0.176 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 9 ; 0.071 ; 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): 1702 ; 0.253 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2754 ; 0.477 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2734 ; 0.521 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 3578 ; 0.742 ; 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 : X 8 X 355 REMARK 3 ORIGIN FOR THE GROUP (A): 1.9659 37.9452 157.1791 REMARK 3 T TENSOR REMARK 3 T11: 0.1316 T22: 0.0299 REMARK 3 T33: 0.1034 T12: 0.0590 REMARK 3 T13: 0.0329 T23: -0.0035 REMARK 3 L TENSOR REMARK 3 L11: 2.9757 L22: 2.1459 REMARK 3 L33: 2.2524 L12: -1.3594 REMARK 3 L13: 1.3710 L23: -0.5641 REMARK 3 S TENSOR REMARK 3 S11: 0.0499 S12: -0.0419 S13: 0.2734 REMARK 3 S21: -0.3818 S22: -0.0259 S23: 0.0064 REMARK 3 S31: -0.1400 S32: -0.2631 S33: -0.0240 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : Y 501 Y 507 REMARK 3 RESIDUE RANGE : Y 566 Y 576 REMARK 3 ORIGIN FOR THE GROUP (A): 18.9730 -1.7124 153.6096 REMARK 3 T TENSOR REMARK 3 T11: 0.3375 T22: 0.1965 REMARK 3 T33: 0.3143 T12: -0.0736 REMARK 3 T13: -0.0282 T23: -0.1269 REMARK 3 L TENSOR REMARK 3 L11: 6.1595 L22: 4.9383 REMARK 3 L33: 7.7586 L12: -0.6236 REMARK 3 L13: 1.1745 L23: -1.9687 REMARK 3 S TENSOR REMARK 3 S11: 0.1391 S12: 0.2554 S13: -0.6674 REMARK 3 S21: -0.3126 S22: -0.0500 S23: -0.0804 REMARK 3 S31: -0.0538 S32: 0.1863 S33: -0.0891 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 : Y 508 Y 546 REMARK 3 ORIGIN FOR THE GROUP (A): -6.9423 11.8703 133.7603 REMARK 3 T TENSOR REMARK 3 T11: 0.8565 T22: 0.6993 REMARK 3 T33: 0.6437 T12: -0.0075 REMARK 3 T13: -0.0477 T23: 0.0582 REMARK 3 L TENSOR REMARK 3 L11: 6.1478 L22: 10.0368 REMARK 3 L33: 1.2701 L12: -7.8631 REMARK 3 L13: -3.1497 L23: 4.7739 REMARK 3 S TENSOR REMARK 3 S11: -0.0558 S12: 0.5943 S13: -0.2453 REMARK 3 S21: -0.5797 S22: -0.1040 S23: 0.3640 REMARK 3 S31: 0.0718 S32: 0.0342 S33: 0.1598 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 : Y 547 Y 565 REMARK 3 ORIGIN FOR THE GROUP (A): 17.4751 -2.8245 127.9050 REMARK 3 T TENSOR REMARK 3 T11: 0.5990 T22: 0.5348 REMARK 3 T33: 0.2813 T12: -0.0518 REMARK 3 T13: 0.1777 T23: -0.1281 REMARK 3 L TENSOR REMARK 3 L11: 15.2993 L22: 7.5516 REMARK 3 L33: 12.5780 L12: 3.8536 REMARK 3 L13: 0.5405 L23: 1.3512 REMARK 3 S TENSOR REMARK 3 S11: -0.4418 S12: 0.9699 S13: -0.4158 REMARK 3 S21: -0.6862 S22: 0.4261 S23: -0.3073 REMARK 3 S31: -0.1386 S32: 0.5097 S33: 0.0156 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 : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2DLC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-APR-06. REMARK 100 THE DEPOSITION ID IS D_1000025551. 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 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL38B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9798, 0.9801, 0.9819, 0.9727 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : MOSFLM REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27897 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04800 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.01 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.46 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: TRIS, PEG 400, PH 7.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 165.16700 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 31.92700 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 31.92700 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 82.58350 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 31.92700 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 31.92700 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 247.75050 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 31.92700 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 31.92700 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 82.58350 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 31.92700 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 31.92700 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 247.75050 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 165.16700 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 19860 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 48750 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -28.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: Y, X 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 BIOMT1 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 330.33400 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 H2U Y 517 REMARK 465 C Y 532 REMARK 465 MET X 1 REMARK 465 SER X 2 REMARK 465 SER X 3 REMARK 465 ALA X 4 REMARK 465 ALA X 5 REMARK 465 THR X 6 REMARK 465 VAL X 7 REMARK 465 GLN X 224 REMARK 465 GLY X 225 REMARK 465 GLY X 226 REMARK 465 LYS X 227 REMARK 465 MET X 228 REMARK 465 SER X 229 REMARK 465 ALA X 230 REMARK 465 SER X 231 REMARK 465 ASP X 232 REMARK 465 PRO X 233 REMARK 465 VAL X 357 REMARK 465 ALA X 358 REMARK 465 THR X 359 REMARK 465 PRO X 360 REMARK 465 GLN X 361 REMARK 465 LYS X 362 REMARK 465 SER X 363 REMARK 465 LYS X 364 REMARK 465 LYS X 365 REMARK 465 ALA X 366 REMARK 465 LYS X 367 REMARK 465 LYS X 368 REMARK 465 PRO X 369 REMARK 465 LYS X 370 REMARK 465 ASN X 371 REMARK 465 LYS X 372 REMARK 465 GLY X 373 REMARK 465 THR X 374 REMARK 465 LYS X 375 REMARK 465 TYR X 376 REMARK 465 PRO X 377 REMARK 465 GLY X 378 REMARK 465 ALA X 379 REMARK 465 THR X 380 REMARK 465 LYS X 381 REMARK 465 THR X 382 REMARK 465 ASN X 383 REMARK 465 GLU X 384 REMARK 465 ILE X 385 REMARK 465 ALA X 386 REMARK 465 THR X 387 REMARK 465 LYS X 388 REMARK 465 LEU X 389 REMARK 465 GLU X 390 REMARK 465 GLU X 391 REMARK 465 THR X 392 REMARK 465 LYS X 393 REMARK 465 LEU X 394 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 2MG Y 510 CM2 REMARK 470 U Y 516 C5' C4' O4' C3' O3' C2' O2' REMARK 470 U Y 516 C1' N1 C2 O2 N3 C4 O4 REMARK 470 U Y 516 C5 C6 REMARK 470 OMG Y 518 CM2 REMARK 470 G Y 520 C5' C4' O4' C3' O3' C2' O2' REMARK 470 G Y 520 C1' N9 C8 N7 C5 C6 O6 REMARK 470 G Y 520 N1 C2 N2 N3 C4 REMARK 470 M2G Y 526 CM1 CM2 REMARK 470 A Y 528 O2' REMARK 470 A Y 529 O2' REMARK 470 G Y 530 O2' REMARK 470 A Y 531 C5' C4' O4' C3' O3' C2' O2' REMARK 470 A Y 531 C1' N9 C8 N7 C5 C6 N6 REMARK 470 A Y 531 N1 C2 N3 C4 REMARK 470 U Y 533 P OP1 OP2 O5' C5' C4' O4' REMARK 470 U Y 533 C3' C2' O2' C1' N1 C2 O2 REMARK 470 U Y 533 N3 C4 O4 C5 C6 REMARK 470 6IA Y 537 C12 C13 C14 C15 C16 REMARK 470 PSU Y 539 N1 C2 N3 C4 C5 C6 O2 REMARK 470 PSU Y 539 O4 REMARK 470 C Y 540 N1 C2 O2 N3 C4 N4 C5 REMARK 470 C Y 540 C6 REMARK 470 U Y 541 N1 C2 O2 N3 C4 O4 C5 REMARK 470 U Y 541 C6 REMARK 470 G Y 546 C5' C4' O4' C3' O3' C2' O2' REMARK 470 G Y 546 C1' N9 C8 N7 C5 C6 O6 REMARK 470 G Y 546 N1 C2 N2 N3 C4 REMARK 470 U Y 547 O2' 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 A Y 528 O4' - C1' - N9 ANGL. DEV. = 5.6 DEGREES REMARK 500 ASP X 85 CB - CG - OD2 ANGL. DEV. = 5.6 DEGREES REMARK 500 ASP X 177 CB - CG - OD2 ANGL. DEV. = 5.7 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 PRO X 48 80.65 -64.96 REMARK 500 THR X 49 -110.80 -110.52 REMARK 500 LEU X 91 -100.19 12.09 REMARK 500 CYS X 255 90.58 -162.69 REMARK 500 LYS X 280 -89.46 -71.95 REMARK 500 PHE X 281 149.22 -172.59 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 X 801 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ALA X 47 O REMARK 620 2 TYR X 56 OH 124.6 REMARK 620 3 TYR X 101 OH 72.7 86.4 REMARK 620 4 YMP X 601 O2P 87.2 65.8 127.3 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 X 801 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE YMP X 601 DBREF 2DLC X 2 394 UNP P36421 SYYC_YEAST 1 393 DBREF 2DLC Y 501 576 PDB 2DLC 2DLC 501 576 SEQADV 2DLC MET X 1 UNP P36421 INITIATING METHIONINE SEQRES 1 Y 76 C U C U C G G U A 2MG C C A SEQRES 2 Y 76 A G U H2U OMG G G A A G G C M2G SEQRES 3 Y 76 C A A G A C U G PSU A 6IA A PSU SEQRES 4 Y 76 C U U G A G G U 5MC G G G C SEQRES 5 Y 76 G 5MU PSU C G 1MA C U C G C C C SEQRES 6 Y 76 C C G G G A G A C C A SEQRES 1 X 394 MET SER SER ALA ALA THR VAL ASP PRO ASN GLU ALA PHE SEQRES 2 X 394 GLY LEU ILE THR LYS ASN LEU GLN GLU VAL LEU ASN PRO SEQRES 3 X 394 GLN ILE ILE LYS ASP VAL LEU GLU VAL GLN LYS ARG HIS SEQRES 4 X 394 LEU LYS LEU TYR TRP GLY THR ALA PRO THR GLY ARG PRO SEQRES 5 X 394 HIS CYS GLY TYR PHE VAL PRO MET THR LYS LEU ALA ASP SEQRES 6 X 394 PHE LEU LYS ALA GLY CYS GLU VAL THR VAL LEU LEU ALA SEQRES 7 X 394 ASP LEU HIS ALA PHE LEU ASP ASN MET LYS ALA PRO LEU SEQRES 8 X 394 GLU VAL VAL ASN TYR ARG ALA LYS TYR TYR GLU LEU THR SEQRES 9 X 394 ILE LYS ALA ILE LEU ARG SER ILE ASN VAL PRO ILE GLU SEQRES 10 X 394 LYS LEU LYS PHE VAL VAL GLY SER SER TYR GLN LEU THR SEQRES 11 X 394 PRO ASP TYR THR MET ASP ILE PHE ARG LEU SER ASN ILE SEQRES 12 X 394 VAL SER GLN ASN ASP ALA LYS ARG ALA GLY ALA ASP VAL SEQRES 13 X 394 VAL LYS GLN VAL ALA ASN PRO LEU LEU SER GLY LEU ILE SEQRES 14 X 394 TYR PRO LEU MET GLN ALA LEU ASP GLU GLN PHE LEU ASP SEQRES 15 X 394 VAL ASP CYS GLN PHE GLY GLY VAL ASP GLN ARG LYS ILE SEQRES 16 X 394 PHE VAL LEU ALA GLU GLU ASN LEU PRO SER LEU GLY TYR SEQRES 17 X 394 LYS LYS ARG ALA HIS LEU MET ASN PRO MET VAL PRO GLY SEQRES 18 X 394 LEU ALA GLN GLY GLY LYS MET SER ALA SER ASP PRO ASN SEQRES 19 X 394 SER LYS ILE ASP LEU LEU GLU GLU PRO LYS GLN VAL LYS SEQRES 20 X 394 LYS LYS ILE ASN SER ALA PHE CYS SER PRO GLY ASN VAL SEQRES 21 X 394 GLU GLU ASN GLY LEU LEU SER PHE VAL GLN TYR VAL ILE SEQRES 22 X 394 ALA PRO ILE GLN GLU LEU LYS PHE GLY THR ASN HIS PHE SEQRES 23 X 394 GLU PHE PHE ILE ASP ARG PRO GLU LYS PHE GLY GLY PRO SEQRES 24 X 394 ILE THR TYR LYS SER PHE GLU GLU MET LYS LEU ALA PHE SEQRES 25 X 394 LYS GLU GLU LYS LEU SER PRO PRO ASP LEU LYS ILE GLY SEQRES 26 X 394 VAL ALA ASP ALA ILE ASN GLU LEU LEU GLU PRO ILE ARG SEQRES 27 X 394 GLN GLU PHE ALA ASN ASN LYS GLU PHE GLN GLU ALA SER SEQRES 28 X 394 GLU LYS GLY TYR PRO VAL ALA THR PRO GLN LYS SER LYS SEQRES 29 X 394 LYS ALA LYS LYS PRO LYS ASN LYS GLY THR LYS TYR PRO SEQRES 30 X 394 GLY ALA THR LYS THR ASN GLU ILE ALA THR LYS LEU GLU SEQRES 31 X 394 GLU THR LYS LEU MODRES 2DLC 2MG Y 510 G 2N-METHYLGUANOSINE-5'-MONOPHOSPHATE MODRES 2DLC OMG Y 518 G O2'-METHYLGUANOSINE-5'-MONOPHOSPHATE MODRES 2DLC M2G Y 526 G N2-DIMETHYLGUANOSINE-5'-MONOPHOSPHATE MODRES 2DLC PSU Y 535 U PSEUDOURIDINE-5'-MONOPHOSPHATE MODRES 2DLC 6IA Y 537 A MODRES 2DLC PSU Y 539 U PSEUDOURIDINE-5'-MONOPHOSPHATE MODRES 2DLC 5MC Y 548 C 5-METHYLCYTIDINE-5'-MONOPHOSPHATE MODRES 2DLC 5MU Y 554 U 5-METHYLURIDINE 5'-MONOPHOSPHATE MODRES 2DLC PSU Y 555 U PSEUDOURIDINE-5'-MONOPHOSPHATE MODRES 2DLC 1MA Y 558 A HET 2MG Y 510 23 HET OMG Y 518 23 HET M2G Y 526 23 HET PSU Y 535 20 HET 6IA Y 537 22 HET PSU Y 539 12 HET 5MC Y 548 21 HET 5MU Y 554 21 HET PSU Y 555 20 HET 1MA Y 558 23 HET MG X 801 1 HET YMP X 601 35 HETNAM 2MG 2N-METHYLGUANOSINE-5'-MONOPHOSPHATE HETNAM OMG O2'-METHYLGUANOSINE-5'-MONOPHOSPHATE HETNAM M2G N2-DIMETHYLGUANOSINE-5'-MONOPHOSPHATE HETNAM PSU PSEUDOURIDINE-5'-MONOPHOSPHATE HETNAM 6IA N6-ISOPENTENYL-ADENOSINE-5'-MONOPHOSPHATE HETNAM 5MC 5-METHYLCYTIDINE-5'-MONOPHOSPHATE HETNAM 5MU 5-METHYLURIDINE 5'-MONOPHOSPHATE HETNAM 1MA 6-HYDRO-1-METHYLADENOSINE-5'-MONOPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM YMP O-(ADENOSINE-5'-O-YL)-N-(L-TYROSYL)PHOSPHORAMIDATE HETSYN YMP TYROSYL-ADENYLATE ANALOGUE; TYR-AMP ANALOGUE FORMUL 1 2MG C11 H16 N5 O8 P FORMUL 1 OMG C11 H16 N5 O8 P FORMUL 1 M2G C12 H18 N5 O8 P FORMUL 1 PSU 3(C9 H13 N2 O9 P) FORMUL 1 6IA C15 H24 N5 O7 P FORMUL 1 5MC C10 H16 N3 O8 P FORMUL 1 5MU C10 H15 N2 O9 P FORMUL 1 1MA C11 H16 N5 O7 P FORMUL 3 MG MG 2+ FORMUL 4 YMP C19 H24 N7 O8 P FORMUL 5 HOH *57(H2 O) HELIX 1 1 ASP X 8 LYS X 18 1 11 HELIX 2 2 ASN X 25 VAL X 35 1 11 HELIX 3 3 HIS X 53 GLY X 55 5 3 HELIX 4 4 TYR X 56 ALA X 69 1 14 HELIX 5 5 ALA X 78 ASP X 85 1 8 HELIX 6 6 GLU X 92 ILE X 112 1 21 HELIX 7 7 GLY X 124 LEU X 129 1 6 HELIX 8 8 THR X 130 ASN X 142 1 13 HELIX 9 9 SER X 145 GLY X 153 1 9 HELIX 10 10 LEU X 165 LEU X 181 1 17 HELIX 11 11 GLN X 192 LEU X 203 1 12 HELIX 12 12 PRO X 204 GLY X 207 5 4 HELIX 13 13 GLU X 242 ALA X 253 1 12 HELIX 14 14 ASN X 263 VAL X 272 1 10 HELIX 15 15 VAL X 272 LEU X 279 1 8 HELIX 16 16 PRO X 293 GLY X 297 5 5 HELIX 17 17 SER X 304 GLU X 314 1 11 HELIX 18 18 SER X 318 ASN X 344 1 27 HELIX 19 19 ASN X 344 TYR X 355 1 12 SHEET 1 A 6 GLU X 22 LEU X 24 0 SHEET 2 A 6 ALA X 212 ASN X 216 -1 O HIS X 213 N LEU X 24 SHEET 3 A 6 CYS X 185 GLY X 189 1 N GLY X 188 O LEU X 214 SHEET 4 A 6 LYS X 41 THR X 46 1 N TYR X 43 O PHE X 187 SHEET 5 A 6 GLU X 72 LEU X 77 1 O LEU X 76 N THR X 46 SHEET 6 A 6 LYS X 120 VAL X 123 1 O LYS X 120 N VAL X 75 SHEET 1 B 2 PHE X 288 ILE X 290 0 SHEET 2 B 2 ILE X 300 TYR X 302 -1 O TYR X 302 N PHE X 288 LINK O3' A Y 509 P 2MG Y 510 1555 1555 1.61 LINK O3' 2MG Y 510 P C Y 511 1555 1555 1.61 LINK O3' OMG Y 518 P G Y 519 1555 1555 1.60 LINK O3' C Y 525 P M2G Y 526 1555 1555 1.60 LINK O3' M2G Y 526 P C Y 527 1555 1555 1.61 LINK O3' G Y 534 P PSU Y 535 1555 1555 1.60 LINK O3' PSU Y 535 P A Y 536 1555 1555 1.60 LINK O3' A Y 536 P 6IA Y 537 1555 1555 1.60 LINK O3' 6IA Y 537 P A Y 538 1555 1555 1.60 LINK O3' A Y 538 P PSU Y 539 1555 1555 1.60 LINK O3' PSU Y 539 P C Y 540 1555 1555 1.60 LINK O3' U Y 547 P 5MC Y 548 1555 1555 1.61 LINK O3' 5MC Y 548 P G Y 549 1555 1555 1.61 LINK O3' G Y 553 P 5MU Y 554 1555 1555 1.60 LINK O3' 5MU Y 554 P PSU Y 555 1555 1555 1.60 LINK O3' PSU Y 555 P C Y 556 1555 1555 1.61 LINK O3' G Y 557 P 1MA Y 558 1555 1555 1.60 LINK O3' 1MA Y 558 P C Y 559 1555 1555 1.60 LINK O ALA X 47 MG MG X 801 1555 1555 2.74 LINK OH TYR X 56 MG MG X 801 1555 1555 2.80 LINK OH TYR X 101 MG MG X 801 1555 1555 2.93 LINK O2P YMP X 601 MG MG X 801 1555 1555 2.61 SITE 1 AC1 5 ALA X 47 THR X 49 TYR X 56 TYR X 101 SITE 2 AC1 5 YMP X 601 SITE 1 AC2 27 TYR X 43 TRP X 44 GLY X 45 THR X 46 SITE 2 AC2 27 ALA X 47 HIS X 53 GLY X 55 TYR X 56 SITE 3 AC2 27 LEU X 76 ALA X 78 HIS X 81 VAL X 156 SITE 4 AC2 27 TYR X 170 GLN X 174 ASP X 177 GLN X 186 SITE 5 AC2 27 GLY X 188 GLY X 189 ASP X 191 GLN X 192 SITE 6 AC2 27 ASN X 216 PRO X 217 MET X 218 VAL X 219 SITE 7 AC2 27 MG X 801 HOH X 821 HOH X 834 CRYST1 63.854 63.854 330.334 90.00 90.00 90.00 P 41 21 2 8 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 0.015661 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015661 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003027 0.00000