HEADER TRANSFERASE/RNA 13-APR-04 1VFG TITLE CRYSTAL STRUCTURE OF TRNA NUCLEOTIDYLTRANSFERASE COMPLEXED WITH A TITLE 2 PRIMER TRNA AND AN INCOMING ATP ANALOG COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (75-MER); COMPND 3 CHAIN: C, D; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: POLY A POLYMERASE; COMPND 7 CHAIN: A, B; COMPND 8 FRAGMENT: RESIDUES 1-390; COMPND 9 SYNONYM: A-ADDING ENZYME; COMPND 10 EC: 2.7.7.19; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: RNA WAS PREPARED BY IN VITRO TRANSCRIPTION WITH T7 SOURCE 4 RNA POLYMERASE IN THERMOTOGA MARITIMA; SOURCE 5 MOL_ID: 2; SOURCE 6 ORGANISM_SCIENTIFIC: AQUIFEX AEOLICUS; SOURCE 7 ORGANISM_TAXID: 63363; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 10 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 11 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 12 EXPRESSION_SYSTEM_PLASMID: PET KEYWDS TRANSFERASE, RNA, RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE, KEYWDS 2 RSGI, STRUCTURAL GENOMICS, TRANSFERASE-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR K.TOMITA,S.FUKAI,R.ISHITANI,T.UEDA,N.TAKEUCHI,D.G.VASSYLYEV,O.NUREKI, AUTHOR 2 RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 3 27-DEC-23 1VFG 1 REMARK SEQADV REVDAT 2 24-FEB-09 1VFG 1 VERSN REVDAT 1 10-AUG-04 1VFG 0 JRNL AUTH K.TOMITA,S.FUKAI,R.ISHITANI,T.UEDA,N.TAKEUCHI,D.G.VASSYLYEV, JRNL AUTH 2 O.NUREKI JRNL TITL STRUCTURAL BASIS FOR TEMPLATE-INDEPENDENT RNA JRNL TITL 2 POLYMERIZATION. JRNL REF NATURE V. 430 700 2004 JRNL REFN ISSN 0028-0836 JRNL PMID 15295603 JRNL DOI 10.1038/NATURE02712 REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 39038 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.230 REMARK 3 FREE R VALUE : 0.287 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1945 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.90 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3013 REMARK 3 BIN FREE R VALUE : 0.3263 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 180 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5794 REMARK 3 NUCLEIC ACID ATOMS : 1384 REMARK 3 HETEROGEN ATOMS : 62 REMARK 3 SOLVENT ATOMS : 79 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 87.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.36 REMARK 3 ESD FROM SIGMAA (A) : 0.42 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.41 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.55 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.012 REMARK 3 BOND ANGLES (DEGREES) : 1.520 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.10 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.230 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 THIS CRYSTAL HAS A PSEUDO-MEROHEDRAL PERFECT TWINNING IN P2, WHICH REMARK 3 PRETENDS P2(1)2(1)2. BETA IS 90 DEGREE SINCE DEPOSITORS PROCESSED REMARK 3 THE DATA WITH P2(1)2(1)2, AND EXPANDED THEM TO THE P2 SPACE GROUP. REMARK 3 THE FILE CONTAINS FRIEDEL PAIRS. REMARK 4 REMARK 4 1VFG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-APR-04. REMARK 100 THE DEPOSITION ID IS D_1000006557. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-DEC-03 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL41XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000, 0.9793, 0.9795, 0.9843, REMARK 200 0.9743 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : SI(111) REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS V REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39382 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 6.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06700 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 22.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.87 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.7 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.39800 REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: MLPHARE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: THE FILE CONTAINS FRIEDEL PAIRS REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 70.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MPD, MAGNESIUM ACETATE, PH 6.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-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 0.00000 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: D, 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 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 U C 8 REMARK 465 A C 9 REMARK 465 G C 10 REMARK 465 C C 11 REMARK 465 U C 12 REMARK 465 C C 13 REMARK 465 A C 14 REMARK 465 G C 15 REMARK 465 U C 16 REMARK 465 U C 17 REMARK 465 G C 18 REMARK 465 G C 19 REMARK 465 U C 20 REMARK 465 A C 21 REMARK 465 G C 22 REMARK 465 A C 23 REMARK 465 G C 24 REMARK 465 C C 25 REMARK 465 A C 26 REMARK 465 C C 27 REMARK 465 U C 28 REMARK 465 G C 29 REMARK 465 G C 30 REMARK 465 A C 31 REMARK 465 C C 32 REMARK 465 U C 33 REMARK 465 G C 34 REMARK 465 A C 35 REMARK 465 A C 36 REMARK 465 A C 37 REMARK 465 A C 38 REMARK 465 U C 39 REMARK 465 C C 40 REMARK 465 C C 41 REMARK 465 A C 42 REMARK 465 G C 43 REMARK 465 G C 44 REMARK 465 U C 45 REMARK 465 G C 46 REMARK 465 U C 47 REMARK 465 C C 48 REMARK 465 A C 73 REMARK 465 C C 74 REMARK 465 C C 75 REMARK 465 U D 8 REMARK 465 A D 9 REMARK 465 G D 10 REMARK 465 C D 11 REMARK 465 U D 12 REMARK 465 C D 13 REMARK 465 A D 14 REMARK 465 G D 15 REMARK 465 U D 16 REMARK 465 U D 17 REMARK 465 G D 18 REMARK 465 G D 19 REMARK 465 U D 20 REMARK 465 A D 21 REMARK 465 G D 22 REMARK 465 A D 23 REMARK 465 G D 24 REMARK 465 C D 25 REMARK 465 A D 26 REMARK 465 C D 27 REMARK 465 U D 28 REMARK 465 G D 29 REMARK 465 G D 30 REMARK 465 A D 31 REMARK 465 C D 32 REMARK 465 U D 33 REMARK 465 G D 34 REMARK 465 A D 35 REMARK 465 A D 36 REMARK 465 A D 37 REMARK 465 A D 38 REMARK 465 U D 39 REMARK 465 C D 40 REMARK 465 C D 41 REMARK 465 A D 42 REMARK 465 G D 43 REMARK 465 G D 44 REMARK 465 U D 45 REMARK 465 G D 46 REMARK 465 U D 47 REMARK 465 C D 48 REMARK 465 TYR A 83 REMARK 465 PRO A 84 REMARK 465 ARG A 85 REMARK 465 PRO A 86 REMARK 465 GLY A 87 REMARK 465 ALA A 88 REMARK 465 TYR A 89 REMARK 465 PRO A 90 REMARK 465 LYS A 91 REMARK 465 LYS A 352 REMARK 465 GLU A 353 REMARK 465 LYS A 354 REMARK 465 ILE A 355 REMARK 465 GLU A 356 REMARK 465 GLU A 357 REMARK 465 LEU A 358 REMARK 465 LYS A 359 REMARK 465 LYS A 360 REMARK 465 GLN A 361 REMARK 465 GLY A 362 REMARK 465 LEU A 363 REMARK 465 LYS A 364 REMARK 465 GLY A 365 REMARK 465 LYS A 366 REMARK 465 GLU A 367 REMARK 465 LEU A 368 REMARK 465 GLY A 369 REMARK 465 GLU A 370 REMARK 465 ARG A 371 REMARK 465 ILE A 372 REMARK 465 GLU A 373 REMARK 465 GLU A 374 REMARK 465 LEU A 375 REMARK 465 LYS A 376 REMARK 465 ARG A 377 REMARK 465 GLU A 378 REMARK 465 ILE A 379 REMARK 465 MET A 380 REMARK 465 ASN A 381 REMARK 465 LYS A 382 REMARK 465 ILE A 383 REMARK 465 LYS A 384 REMARK 465 LEU A 385 REMARK 465 ALA A 386 REMARK 465 ALA A 387 REMARK 465 ALA A 388 REMARK 465 LEU A 389 REMARK 465 GLU A 390 REMARK 465 TYR B 83 REMARK 465 PRO B 84 REMARK 465 ARG B 85 REMARK 465 PRO B 86 REMARK 465 GLY B 87 REMARK 465 ALA B 88 REMARK 465 TYR B 89 REMARK 465 PRO B 90 REMARK 465 LYS B 91 REMARK 465 LYS B 352 REMARK 465 GLU B 353 REMARK 465 LYS B 354 REMARK 465 ILE B 355 REMARK 465 GLU B 356 REMARK 465 GLU B 357 REMARK 465 LEU B 358 REMARK 465 LYS B 359 REMARK 465 LYS B 360 REMARK 465 GLN B 361 REMARK 465 GLY B 362 REMARK 465 LEU B 363 REMARK 465 LYS B 364 REMARK 465 GLY B 365 REMARK 465 LYS B 366 REMARK 465 GLU B 367 REMARK 465 LEU B 368 REMARK 465 GLY B 369 REMARK 465 GLU B 370 REMARK 465 ARG B 371 REMARK 465 ILE B 372 REMARK 465 GLU B 373 REMARK 465 GLU B 374 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O GLU B 309 N TYR B 311 2.11 REMARK 500 O GLU A 309 N TYR A 311 2.13 REMARK 500 O TRP B 244 OE2 GLU B 248 2.16 REMARK 500 O ILE B 263 OG SER B 266 2.17 REMARK 500 REMARK 500 REMARK: NULL 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 C 1 P G C 1 OP3 -0.085 REMARK 500 G D 1 P G D 1 OP3 -0.085 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 MET A 9 36.34 -99.14 REMARK 500 HIS A 56 79.84 -119.36 REMARK 500 GLU A 60 -28.68 77.22 REMARK 500 ARG A 79 -156.36 -166.68 REMARK 500 ARG A 80 49.47 -143.46 REMARK 500 GLU A 93 -176.30 63.04 REMARK 500 ALA A 95 114.47 76.24 REMARK 500 ASP A 105 -99.20 -57.84 REMARK 500 LYS A 136 73.40 58.03 REMARK 500 PRO A 150 2.66 -61.62 REMARK 500 PRO A 188 97.04 -52.84 REMARK 500 ARG A 189 -48.85 -29.82 REMARK 500 GLN A 226 131.26 -178.72 REMARK 500 GLU A 248 -77.59 -77.65 REMARK 500 PHE A 249 33.79 -70.00 REMARK 500 ARG A 253 -145.46 -113.87 REMARK 500 ILE A 254 162.09 174.32 REMARK 500 SER A 266 160.92 -47.73 REMARK 500 LEU A 268 164.08 -31.69 REMARK 500 ASP A 269 -86.16 -124.64 REMARK 500 PRO A 283 174.96 -56.52 REMARK 500 GLU A 288 -66.11 -91.62 REMARK 500 LYS A 305 -6.82 -59.03 REMARK 500 LYS A 308 -61.15 -91.43 REMARK 500 GLU A 309 -136.71 -160.84 REMARK 500 ASN A 310 -30.63 27.93 REMARK 500 LEU A 320 -17.49 -46.32 REMARK 500 THR A 322 -73.51 -18.16 REMARK 500 SER A 323 -61.82 -6.09 REMARK 500 LEU A 330 30.30 -77.08 REMARK 500 GLU A 331 71.89 -155.58 REMARK 500 GLU A 332 -66.31 -2.53 REMARK 500 LEU A 334 42.80 -91.80 REMARK 500 GLU B 60 -29.73 76.11 REMARK 500 ARG B 79 -155.96 -166.18 REMARK 500 ARG B 80 54.48 -141.47 REMARK 500 GLU B 81 -6.45 72.71 REMARK 500 GLU B 93 -177.23 63.82 REMARK 500 ALA B 95 115.31 75.94 REMARK 500 ASP B 105 -101.51 -52.12 REMARK 500 LYS B 136 72.42 58.60 REMARK 500 PRO B 150 3.59 -63.66 REMARK 500 PRO B 188 97.55 -52.36 REMARK 500 GLU B 223 -81.99 -46.02 REMARK 500 GLN B 226 129.28 -179.62 REMARK 500 GLU B 248 -78.74 -78.30 REMARK 500 PHE B 249 31.22 -67.88 REMARK 500 ARG B 253 -146.49 -115.54 REMARK 500 ILE B 254 162.99 175.31 REMARK 500 SER B 266 160.50 -48.47 REMARK 500 REMARK 500 THIS ENTRY HAS 68 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 U C 59 0.07 SIDE CHAIN REMARK 500 U D 59 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE APC A 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE APC B 1500 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1MIW RELATED DB: PDB REMARK 900 RELATED ID: 1OU5 RELATED DB: PDB REMARK 900 RELATED ID: 1UET RELATED DB: PDB REMARK 900 RELATED ID: 1R89 RELATED DB: PDB REMARK 900 RELATED ID: AR_001000505.1 RELATED DB: TARGETDB DBREF 1VFG A 2 383 UNP O66728 O66728_AQUAE 443 824 DBREF 1VFG B 2 383 UNP O66728 O66728_AQUAE 443 824 DBREF 1VFG C 1 75 PDB 1VFG 1VFG 1 75 DBREF 1VFG D 1 75 PDB 1VFG 1VFG 1 75 SEQADV 1VFG MET A 1 UNP O66728 INITIATING METHIONINE SEQADV 1VFG LYS A 384 UNP O66728 CLONING ARTIFACT SEQADV 1VFG LEU A 385 UNP O66728 CLONING ARTIFACT SEQADV 1VFG ALA A 386 UNP O66728 CLONING ARTIFACT SEQADV 1VFG ALA A 387 UNP O66728 CLONING ARTIFACT SEQADV 1VFG ALA A 388 UNP O66728 CLONING ARTIFACT SEQADV 1VFG LEU A 389 UNP O66728 CLONING ARTIFACT SEQADV 1VFG GLU A 390 UNP O66728 CLONING ARTIFACT SEQADV 1VFG MET B 1 UNP O66728 INITIATING METHIONINE SEQADV 1VFG LYS B 384 UNP O66728 CLONING ARTIFACT SEQADV 1VFG LEU B 385 UNP O66728 CLONING ARTIFACT SEQADV 1VFG ALA B 386 UNP O66728 CLONING ARTIFACT SEQADV 1VFG ALA B 387 UNP O66728 CLONING ARTIFACT SEQADV 1VFG ALA B 388 UNP O66728 CLONING ARTIFACT SEQADV 1VFG LEU B 389 UNP O66728 CLONING ARTIFACT SEQADV 1VFG GLU B 390 UNP O66728 CLONING ARTIFACT SEQRES 1 C 75 G G C C A G G U A G C U C SEQRES 2 C 75 A G U U G G U A G A G C A SEQRES 3 C 75 C U G G A C U G A A A A U SEQRES 4 C 75 C C A G G U G U C G G C G SEQRES 5 C 75 G U U C G A U U C C G C C SEQRES 6 C 75 C C U G G C C A C C SEQRES 1 D 75 G G C C A G G U A G C U C SEQRES 2 D 75 A G U U G G U A G A G C A SEQRES 3 D 75 C U G G A C U G A A A A U SEQRES 4 D 75 C C A G G U G U C G G C G SEQRES 5 D 75 G U U C G A U U C C G C C SEQRES 6 D 75 C C U G G C C A C C SEQRES 1 A 390 MET VAL GLY GLN ILE ALA LYS GLU MET GLY LEU ARG ALA SEQRES 2 A 390 TYR ILE VAL GLY GLY VAL VAL ARG ASP ILE LEU LEU GLY SEQRES 3 A 390 LYS GLU VAL TRP ASP VAL ASP PHE VAL VAL GLU GLY ASN SEQRES 4 A 390 ALA ILE GLU LEU ALA LYS GLU LEU ALA ARG ARG HIS GLY SEQRES 5 A 390 VAL ASN VAL HIS PRO PHE PRO GLU PHE GLY THR ALA HIS SEQRES 6 A 390 LEU LYS ILE GLY LYS LEU LYS LEU GLU PHE ALA THR ALA SEQRES 7 A 390 ARG ARG GLU THR TYR PRO ARG PRO GLY ALA TYR PRO LYS SEQRES 8 A 390 VAL GLU PRO ALA SER LEU LYS GLU ASP LEU ILE ARG ARG SEQRES 9 A 390 ASP PHE THR ILE ASN ALA MET ALA ILE SER VAL ASN LEU SEQRES 10 A 390 GLU ASP TYR GLY THR LEU ILE ASP TYR PHE GLY GLY LEU SEQRES 11 A 390 ARG ASP LEU LYS ASP LYS VAL ILE ARG VAL LEU HIS PRO SEQRES 12 A 390 VAL SER PHE ILE GLU ASP PRO VAL ARG ILE LEU ARG ALA SEQRES 13 A 390 LEU ARG PHE ALA GLY ARG LEU ASN PHE LYS LEU SER ARG SEQRES 14 A 390 SER THR GLU LYS LEU LEU LYS GLN ALA VAL ASN LEU GLY SEQRES 15 A 390 LEU LEU LYS GLU ALA PRO ARG GLY ARG LEU ILE ASN GLU SEQRES 16 A 390 ILE LYS LEU ALA LEU ARG GLU ASP ARG PHE LEU GLU ILE SEQRES 17 A 390 LEU GLU LEU TYR ARG LYS TYR ARG VAL LEU GLU GLU ILE SEQRES 18 A 390 ILE GLU GLY PHE GLN TRP ASN GLU LYS VAL LEU GLN LYS SEQRES 19 A 390 LEU TYR ALA LEU ARG LYS VAL VAL ASP TRP HIS ALA LEU SEQRES 20 A 390 GLU PHE SER GLU GLU ARG ILE ASP TYR GLY TRP LEU TYR SEQRES 21 A 390 LEU LEU ILE LEU ILE SER ASN LEU ASP TYR GLU ARG GLY SEQRES 22 A 390 LYS HIS PHE LEU GLU GLU MET SER ALA PRO SER TRP VAL SEQRES 23 A 390 ARG GLU THR TYR LYS PHE MET LYS PHE LYS LEU GLY SER SEQRES 24 A 390 LEU LYS GLU GLU LEU LYS LYS ALA LYS GLU ASN TYR GLU SEQRES 25 A 390 VAL TYR ARG LEU LEU LYS PRO LEU HIS THR SER VAL LEU SEQRES 26 A 390 LEU LEU LEU MET LEU GLU GLU GLU LEU LYS GLU LYS ILE SEQRES 27 A 390 LYS LEU TYR LEU GLU LYS LEU ARG LYS VAL LYS LEU PRO SEQRES 28 A 390 LYS GLU LYS ILE GLU GLU LEU LYS LYS GLN GLY LEU LYS SEQRES 29 A 390 GLY LYS GLU LEU GLY GLU ARG ILE GLU GLU LEU LYS ARG SEQRES 30 A 390 GLU ILE MET ASN LYS ILE LYS LEU ALA ALA ALA LEU GLU SEQRES 1 B 390 MET VAL GLY GLN ILE ALA LYS GLU MET GLY LEU ARG ALA SEQRES 2 B 390 TYR ILE VAL GLY GLY VAL VAL ARG ASP ILE LEU LEU GLY SEQRES 3 B 390 LYS GLU VAL TRP ASP VAL ASP PHE VAL VAL GLU GLY ASN SEQRES 4 B 390 ALA ILE GLU LEU ALA LYS GLU LEU ALA ARG ARG HIS GLY SEQRES 5 B 390 VAL ASN VAL HIS PRO PHE PRO GLU PHE GLY THR ALA HIS SEQRES 6 B 390 LEU LYS ILE GLY LYS LEU LYS LEU GLU PHE ALA THR ALA SEQRES 7 B 390 ARG ARG GLU THR TYR PRO ARG PRO GLY ALA TYR PRO LYS SEQRES 8 B 390 VAL GLU PRO ALA SER LEU LYS GLU ASP LEU ILE ARG ARG SEQRES 9 B 390 ASP PHE THR ILE ASN ALA MET ALA ILE SER VAL ASN LEU SEQRES 10 B 390 GLU ASP TYR GLY THR LEU ILE ASP TYR PHE GLY GLY LEU SEQRES 11 B 390 ARG ASP LEU LYS ASP LYS VAL ILE ARG VAL LEU HIS PRO SEQRES 12 B 390 VAL SER PHE ILE GLU ASP PRO VAL ARG ILE LEU ARG ALA SEQRES 13 B 390 LEU ARG PHE ALA GLY ARG LEU ASN PHE LYS LEU SER ARG SEQRES 14 B 390 SER THR GLU LYS LEU LEU LYS GLN ALA VAL ASN LEU GLY SEQRES 15 B 390 LEU LEU LYS GLU ALA PRO ARG GLY ARG LEU ILE ASN GLU SEQRES 16 B 390 ILE LYS LEU ALA LEU ARG GLU ASP ARG PHE LEU GLU ILE SEQRES 17 B 390 LEU GLU LEU TYR ARG LYS TYR ARG VAL LEU GLU GLU ILE SEQRES 18 B 390 ILE GLU GLY PHE GLN TRP ASN GLU LYS VAL LEU GLN LYS SEQRES 19 B 390 LEU TYR ALA LEU ARG LYS VAL VAL ASP TRP HIS ALA LEU SEQRES 20 B 390 GLU PHE SER GLU GLU ARG ILE ASP TYR GLY TRP LEU TYR SEQRES 21 B 390 LEU LEU ILE LEU ILE SER ASN LEU ASP TYR GLU ARG GLY SEQRES 22 B 390 LYS HIS PHE LEU GLU GLU MET SER ALA PRO SER TRP VAL SEQRES 23 B 390 ARG GLU THR TYR LYS PHE MET LYS PHE LYS LEU GLY SER SEQRES 24 B 390 LEU LYS GLU GLU LEU LYS LYS ALA LYS GLU ASN TYR GLU SEQRES 25 B 390 VAL TYR ARG LEU LEU LYS PRO LEU HIS THR SER VAL LEU SEQRES 26 B 390 LEU LEU LEU MET LEU GLU GLU GLU LEU LYS GLU LYS ILE SEQRES 27 B 390 LYS LEU TYR LEU GLU LYS LEU ARG LYS VAL LYS LEU PRO SEQRES 28 B 390 LYS GLU LYS ILE GLU GLU LEU LYS LYS GLN GLY LEU LYS SEQRES 29 B 390 GLY LYS GLU LEU GLY GLU ARG ILE GLU GLU LEU LYS ARG SEQRES 30 B 390 GLU ILE MET ASN LYS ILE LYS LEU ALA ALA ALA LEU GLU HET APC A 500 31 HET APC B1500 31 HETNAM APC DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER HETSYN APC ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE FORMUL 5 APC 2(C11 H18 N5 O12 P3) FORMUL 7 HOH *79(H2 O) HELIX 1 1 MET A 1 MET A 9 1 9 HELIX 2 2 GLY A 17 LEU A 25 1 9 HELIX 3 3 ASN A 39 GLY A 52 1 14 HELIX 4 4 SER A 96 ARG A 103 1 8 HELIX 5 5 PHE A 106 ALA A 110 5 5 HELIX 6 6 ASN A 116 TYR A 120 5 5 HELIX 7 7 GLY A 128 ASP A 135 1 8 HELIX 8 8 VAL A 144 ASP A 149 1 6 HELIX 9 9 VAL A 151 ASN A 164 1 14 HELIX 10 10 SER A 168 LEU A 181 1 14 HELIX 11 11 GLY A 182 GLU A 186 5 5 HELIX 12 12 PRO A 188 GLU A 202 1 15 HELIX 13 13 ARG A 204 TYR A 215 1 12 HELIX 14 14 VAL A 217 ILE A 222 1 6 HELIX 15 15 ASN A 228 PHE A 249 1 22 HELIX 16 16 SER A 250 GLU A 252 5 3 HELIX 17 17 ASP A 255 SER A 266 1 12 HELIX 18 18 GLY A 273 MET A 280 1 8 HELIX 19 19 PRO A 283 LYS A 305 1 23 HELIX 20 20 TYR A 311 LEU A 316 1 6 HELIX 21 21 LEU A 317 HIS A 321 5 5 HELIX 22 22 THR A 322 MET A 329 1 8 HELIX 23 23 GLU A 331 GLU A 333 5 3 HELIX 24 24 LEU A 334 LYS A 349 1 16 HELIX 25 25 MET B 1 MET B 9 1 9 HELIX 26 26 GLY B 17 LEU B 25 1 9 HELIX 27 27 ASN B 39 GLY B 52 1 14 HELIX 28 28 SER B 96 ARG B 103 1 8 HELIX 29 29 PHE B 106 ALA B 110 5 5 HELIX 30 30 ASN B 116 TYR B 120 5 5 HELIX 31 31 GLY B 128 ASP B 135 1 8 HELIX 32 32 VAL B 144 ASP B 149 1 6 HELIX 33 33 VAL B 151 ASN B 164 1 14 HELIX 34 34 SER B 168 LEU B 181 1 14 HELIX 35 35 GLY B 182 GLU B 186 5 5 HELIX 36 36 PRO B 188 GLU B 202 1 15 HELIX 37 37 ARG B 204 TYR B 215 1 12 HELIX 38 38 VAL B 217 ILE B 222 1 6 HELIX 39 39 ASN B 228 PHE B 249 1 22 HELIX 40 40 SER B 250 GLU B 252 5 3 HELIX 41 41 ASP B 255 SER B 266 1 12 HELIX 42 42 GLY B 273 MET B 280 1 8 HELIX 43 43 PRO B 283 LYS B 305 1 23 HELIX 44 44 TYR B 311 LEU B 316 1 6 HELIX 45 45 LEU B 317 HIS B 321 5 5 HELIX 46 46 THR B 322 MET B 329 1 8 HELIX 47 47 GLU B 331 GLU B 333 5 3 HELIX 48 48 LEU B 334 LYS B 349 1 16 HELIX 49 49 LYS B 376 GLU B 390 1 15 SHEET 1 A 7 HIS A 56 PHE A 58 0 SHEET 2 A 7 THR A 63 ILE A 68 -1 O THR A 63 N PHE A 58 SHEET 3 A 7 LEU A 71 THR A 77 -1 O LEU A 71 N ILE A 68 SHEET 4 A 7 ASP A 31 VAL A 36 1 N PHE A 34 O GLU A 74 SHEET 5 A 7 ALA A 13 VAL A 16 -1 N TYR A 14 O VAL A 35 SHEET 6 A 7 ALA A 112 SER A 114 -1 O ILE A 113 N ILE A 15 SHEET 7 A 7 LEU A 123 ILE A 124 -1 O ILE A 124 N ALA A 112 SHEET 1 B 2 VAL A 137 ILE A 138 0 SHEET 2 B 2 LYS A 166 LEU A 167 1 O LYS A 166 N ILE A 138 SHEET 1 C 7 HIS B 56 PHE B 58 0 SHEET 2 C 7 THR B 63 ILE B 68 -1 O THR B 63 N PHE B 58 SHEET 3 C 7 LEU B 71 THR B 77 -1 O PHE B 75 N ALA B 64 SHEET 4 C 7 ASP B 31 VAL B 36 1 N PHE B 34 O GLU B 74 SHEET 5 C 7 ALA B 13 VAL B 16 -1 N VAL B 16 O ASP B 33 SHEET 6 C 7 ALA B 112 SER B 114 -1 O ILE B 113 N ILE B 15 SHEET 7 C 7 LEU B 123 ILE B 124 -1 O ILE B 124 N ALA B 112 SHEET 1 D 2 VAL B 137 ILE B 138 0 SHEET 2 D 2 LYS B 166 LEU B 167 1 O LYS B 166 N ILE B 138 SITE 1 AC1 14 GLY A 18 ARG A 21 ASP A 22 ARG A 104 SITE 2 AC1 14 ASP A 105 ASP A 149 ARG A 152 ARG A 155 SITE 3 AC1 14 ARG A 158 ARG A 162 ARG A 191 HOH A 501 SITE 4 AC1 14 HOH A 505 HOH A 520 SITE 1 AC2 13 GLY B 18 ARG B 21 ARG B 103 ASP B 105 SITE 2 AC2 13 ASN B 109 ASP B 149 ARG B 152 ARG B 155 SITE 3 AC2 13 ARG B 158 PHE B 159 ARG B 162 C D 75 SITE 4 AC2 13 HOH D 82 CRYST1 109.476 125.900 58.920 90.00 90.00 90.00 P 1 2 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 0.009134 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007943 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016972 0.00000