HEADER HYDROLASE/RNA 29-AUG-16 5GUH TITLE CRYSTAL STRUCTURE OF SILKWORM PIWI-CLADE ARGONAUTE SIWI BOUND TO PIRNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: PIWI; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PIWI,SIWI,UNCHARACTERIZED PROTEIN; COMPND 5 OTHER_DETAILS: THE N-TERMINAL REGION (RESIDUES 1-129) WAS TRUNCATED COMPND 6 BY THERMOLYSIN TREATMENT.; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: RNA (28-MER); COMPND 9 CHAIN: B; COMPND 10 OTHER_DETAILS: THE BOUND RNAS ARE CO-PURIFIED ENDOGENOUS PIRNAS, COMPND 11 WHICH HAVE DIVERGENT SEQUENCES AND LENGTHS. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOMBYX MORI; SOURCE 3 ORGANISM_COMMON: SILK MOTH; SOURCE 4 ORGANISM_TAXID: 7091; SOURCE 5 MOL_ID: 2; SOURCE 6 ORGANISM_SCIENTIFIC: BOMBYX MORI; SOURCE 7 ORGANISM_TAXID: 7091 KEYWDS NUCLEASE, RNASEH, HYDROLASE-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR N.MATSUMOTO,H.NISHIMASU,R.ISHITANI,O.NUREKI REVDAT 3 08-NOV-23 5GUH 1 LINK REVDAT 2 27-SEP-17 5GUH 1 REMARK REVDAT 1 19-OCT-16 5GUH 0 JRNL AUTH N.MATSUMOTO,H.NISHIMASU,K.SAKAKIBARA,K.M.NISHIDA,T.HIRANO, JRNL AUTH 2 R.ISHITANI,H.SIOMI,M.C.SIOMI,O.NUREKI JRNL TITL CRYSTAL STRUCTURE OF SILKWORM PIWI-CLADE ARGONAUTE SIWI JRNL TITL 2 BOUND TO PIRNA JRNL REF CELL V. 167 484 2016 JRNL REFN ISSN 1097-4172 JRNL PMID 27693359 JRNL DOI 10.1016/J.CELL.2016.09.002 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10_2155: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 87.84 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.680 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 38660 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.211 REMARK 3 R VALUE (WORKING SET) : 0.209 REMARK 3 FREE R VALUE : 0.236 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.170 REMARK 3 FREE R VALUE TEST SET COUNT : 2000 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 2.4600 - 2.4000 0.00 0 0 0.2988 0.3474 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.330 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.010 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 67.43 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 130 THROUGH 449 ) REMARK 3 ORIGIN FOR THE GROUP (A): 51.5816 -1.7219 102.9133 REMARK 3 T TENSOR REMARK 3 T11: 0.4147 T22: 0.4565 REMARK 3 T33: 0.5625 T12: 0.0398 REMARK 3 T13: -0.0158 T23: 0.1042 REMARK 3 L TENSOR REMARK 3 L11: 0.6186 L22: 1.1714 REMARK 3 L33: 3.3523 L12: 0.3986 REMARK 3 L13: -1.4375 L23: -1.4813 REMARK 3 S TENSOR REMARK 3 S11: -0.0812 S12: -0.1752 S13: -0.1942 REMARK 3 S21: 0.2300 S22: -0.0521 S23: -0.0436 REMARK 3 S31: -0.2503 S32: 0.1790 S33: 0.1258 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 450 THROUGH 899 ) REMARK 3 ORIGIN FOR THE GROUP (A): 40.0522 28.2669 87.0827 REMARK 3 T TENSOR REMARK 3 T11: 0.2833 T22: 0.3590 REMARK 3 T33: 0.2731 T12: -0.0435 REMARK 3 T13: -0.0361 T23: -0.0034 REMARK 3 L TENSOR REMARK 3 L11: 1.3458 L22: 1.5296 REMARK 3 L33: 0.6870 L12: -0.5384 REMARK 3 L13: -0.2637 L23: 0.0188 REMARK 3 S TENSOR REMARK 3 S11: -0.0423 S12: -0.2512 S13: 0.1451 REMARK 3 S21: 0.2508 S22: -0.0024 S23: -0.1365 REMARK 3 S31: -0.0164 S32: -0.0040 S33: 0.0204 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1 THROUGH 28 ) REMARK 3 ORIGIN FOR THE GROUP (A): 49.8983 19.8274 103.0020 REMARK 3 T TENSOR REMARK 3 T11: 0.5280 T22: 0.7018 REMARK 3 T33: 0.8755 T12: 0.0189 REMARK 3 T13: -0.1259 T23: 0.0376 REMARK 3 L TENSOR REMARK 3 L11: 0.1033 L22: 2.6334 REMARK 3 L33: 5.9383 L12: -0.4142 REMARK 3 L13: 0.3311 L23: -3.2031 REMARK 3 S TENSOR REMARK 3 S11: 0.2593 S12: 0.0616 S13: -0.0941 REMARK 3 S21: -1.2413 S22: -0.8874 S23: -0.5134 REMARK 3 S31: 1.1866 S32: 0.4114 S33: 0.5291 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5GUH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 02-SEP-16. REMARK 100 THE DEPOSITION ID IS D_1300001476. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-DEC-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL 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 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DIALS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 38755 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 114.620 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 5.000 REMARK 200 R MERGE (I) : 0.12100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.0000 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) : 2.49 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 4OLB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.95 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50MM POTASSIUM PHOSPHATE MONOBASIC, REMARK 280 20% PEG8000, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 30.94950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 68.35900 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 57.30950 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 68.35900 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 30.94950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 57.30950 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2760 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 33490 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -39.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 MET A 1 REMARK 465 SER A 2 REMARK 465 GLU A 3 REMARK 465 PRO A 4 REMARK 465 ARG A 5 REMARK 465 GLY A 6 REMARK 465 ARG A 7 REMARK 465 GLY A 8 REMARK 465 ARG A 9 REMARK 465 ALA A 10 REMARK 465 ARG A 11 REMARK 465 GLY A 12 REMARK 465 ARG A 13 REMARK 465 ALA A 14 REMARK 465 GLY A 15 REMARK 465 ARG A 16 REMARK 465 GLY A 17 REMARK 465 GLY A 18 REMARK 465 ASP A 19 REMARK 465 GLY A 20 REMARK 465 GLY A 21 REMARK 465 GLY A 22 REMARK 465 PRO A 23 REMARK 465 ALA A 24 REMARK 465 PRO A 25 REMARK 465 ARG A 26 REMARK 465 ARG A 27 REMARK 465 PRO A 28 REMARK 465 GLY A 29 REMARK 465 GLU A 30 REMARK 465 GLN A 31 REMARK 465 ALA A 32 REMARK 465 GLY A 33 REMARK 465 PRO A 34 REMARK 465 SER A 35 REMARK 465 GLN A 36 REMARK 465 GLN A 37 REMARK 465 SER A 38 REMARK 465 MET A 39 REMARK 465 PRO A 40 REMARK 465 PRO A 41 REMARK 465 GLY A 42 REMARK 465 PRO A 43 REMARK 465 ARG A 44 REMARK 465 PRO A 45 REMARK 465 GLN A 46 REMARK 465 PRO A 47 REMARK 465 PRO A 48 REMARK 465 SER A 49 REMARK 465 GLY A 50 REMARK 465 TRP A 51 REMARK 465 GLY A 52 REMARK 465 PRO A 53 REMARK 465 GLN A 54 REMARK 465 SER A 55 REMARK 465 SER A 56 REMARK 465 VAL A 57 REMARK 465 PRO A 58 REMARK 465 PRO A 59 REMARK 465 VAL A 60 REMARK 465 ARG A 61 REMARK 465 ALA A 62 REMARK 465 GLY A 63 REMARK 465 VAL A 64 REMARK 465 PRO A 65 REMARK 465 THR A 66 REMARK 465 PRO A 67 REMARK 465 THR A 68 REMARK 465 ALA A 69 REMARK 465 GLN A 70 REMARK 465 ALA A 71 REMARK 465 GLY A 72 REMARK 465 ARG A 73 REMARK 465 ALA A 74 REMARK 465 SER A 75 REMARK 465 HIS A 76 REMARK 465 ARG A 77 REMARK 465 VAL A 78 REMARK 465 THR A 79 REMARK 465 PRO A 80 REMARK 465 THR A 81 REMARK 465 THR A 82 REMARK 465 HIS A 83 REMARK 465 GLU A 84 REMARK 465 HIS A 85 REMARK 465 PRO A 86 REMARK 465 GLY A 87 REMARK 465 ASP A 88 REMARK 465 ILE A 89 REMARK 465 ASP A 90 REMARK 465 VAL A 91 REMARK 465 GLN A 92 REMARK 465 GLN A 93 REMARK 465 ARG A 94 REMARK 465 MET A 95 REMARK 465 GLN A 96 REMARK 465 LYS A 97 REMARK 465 LEU A 98 REMARK 465 GLU A 99 REMARK 465 LEU A 100 REMARK 465 GLY A 101 REMARK 465 PRO A 102 REMARK 465 HIS A 103 REMARK 465 SER A 104 REMARK 465 SER A 105 REMARK 465 GLY A 106 REMARK 465 GLY A 107 REMARK 465 GLY A 108 REMARK 465 ASP A 109 REMARK 465 ALA A 110 REMARK 465 SER A 111 REMARK 465 SER A 112 REMARK 465 VAL A 113 REMARK 465 VAL A 114 REMARK 465 GLY A 115 REMARK 465 ARG A 116 REMARK 465 GLY A 117 REMARK 465 SER A 118 REMARK 465 ARG A 119 REMARK 465 ARG A 120 REMARK 465 GLY A 121 REMARK 465 GLY A 122 REMARK 465 GLY A 123 REMARK 465 ARG A 124 REMARK 465 VAL A 125 REMARK 465 LEU A 126 REMARK 465 PRO A 127 REMARK 465 GLU A 128 REMARK 465 THR A 129 REMARK 465 GLY A 330 REMARK 465 ASN A 331 REMARK 465 ASN A 332 REMARK 465 TYR A 333 REMARK 465 LYS A 334 REMARK 465 TRP A 362 REMARK 465 THR A 704 REMARK 465 SER A 705 REMARK 465 GLY A 706 REMARK 465 GLU A 707 REMARK 465 GLU A 708 REMARK 465 A B 6 REMARK 465 A B 7 REMARK 465 A B 8 REMARK 465 A B 9 REMARK 465 A B 10 REMARK 465 A B 11 REMARK 465 A B 12 REMARK 465 A B 13 REMARK 465 A B 14 REMARK 465 A B 15 REMARK 465 A B 16 REMARK 465 A B 17 REMARK 465 A B 18 REMARK 465 A B 19 REMARK 465 A B 20 REMARK 465 A B 21 REMARK 465 A B 22 REMARK 465 A B 23 REMARK 465 A B 24 REMARK 465 A B 25 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 GLU A 138 CG CD OE1 OE2 REMARK 470 VAL A 140 CG1 CG2 REMARK 470 THR A 141 OG1 CG2 REMARK 470 LYS A 165 CG CD CE NZ REMARK 470 LYS A 194 CG CD CE NZ REMARK 470 ASP A 215 CG OD1 OD2 REMARK 470 GLU A 218 CG CD OE1 OE2 REMARK 470 ASP A 222 CG OD1 OD2 REMARK 470 LYS A 224 CG CD CE NZ REMARK 470 THR A 225 OG1 CG2 REMARK 470 ASP A 226 CG OD1 OD2 REMARK 470 ASN A 227 CG OD1 ND2 REMARK 470 ARG A 229 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 235 CG CD CE NZ REMARK 470 GLU A 239 CG CD OE1 OE2 REMARK 470 TYR A 245 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 GLN A 249 CG CD OE1 NE2 REMARK 470 LYS A 263 CG CD CE NZ REMARK 470 ARG A 269 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 275 CG CD OE1 OE2 REMARK 470 GLU A 324 CG CD OE1 OE2 REMARK 470 THR A 328 OG1 CG2 REMARK 470 LYS A 329 CG CD CE NZ REMARK 470 LYS A 335 CG CD CE NZ REMARK 470 ILE A 336 CG1 CG2 CD1 REMARK 470 GLU A 339 CG CD OE1 OE2 REMARK 470 ASP A 340 CG OD1 OD2 REMARK 470 LYS A 344 CG CD CE NZ REMARK 470 LYS A 352 CG CD CE NZ REMARK 470 ARG A 356 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 373 CG CD NE CZ NH1 NH2 REMARK 470 TYR A 384 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS A 385 CG CD CE NZ REMARK 470 ASN A 388 CG OD1 ND2 REMARK 470 ARG A 390 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 392 CG CD OE1 NE2 REMARK 470 ARG A 402 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 404 CG CD CE NZ REMARK 470 ARG A 406 CG CD NE CZ NH1 NH2 REMARK 470 LEU A 428 CG CD1 CD2 REMARK 470 SER A 429 OG REMARK 470 ASP A 430 CG OD1 OD2 REMARK 470 GLU A 431 CG CD OE1 OE2 REMARK 470 MET A 432 CG SD CE REMARK 470 ARG A 433 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 440 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 452 CG CD CE NZ REMARK 470 ARG A 463 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 484 CG CD OE1 OE2 REMARK 470 GLU A 513 CG CD OE1 OE2 REMARK 470 ARG A 517 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 529 CG CD OE1 NE2 REMARK 470 GLU A 539 CG CD OE1 OE2 REMARK 470 ARG A 543 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 564 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 572 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 585 CG CD OE1 OE2 REMARK 470 ARG A 589 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 590 CG CD CE NZ REMARK 470 ARG A 601 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 633 CG CD CE NZ REMARK 470 ARG A 676 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 678 CG CD CE NZ REMARK 470 GLU A 679 CG CD OE1 OE2 REMARK 470 ARG A 781 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 823 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 824 CG CD OE1 OE2 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 U B 1 P U B 1 OP3 -0.130 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 VAL A 140 75.40 -69.37 REMARK 500 ASN A 156 49.51 -78.75 REMARK 500 GLU A 178 66.04 60.98 REMARK 500 THR A 204 -42.28 -138.44 REMARK 500 SER A 221 -169.51 -123.41 REMARK 500 GLU A 228 -178.59 -67.84 REMARK 500 VAL A 240 96.81 -62.08 REMARK 500 TYR A 298 -162.91 -103.04 REMARK 500 ARG A 373 -131.10 58.78 REMARK 500 ASP A 374 39.11 -93.95 REMARK 500 ASN A 388 63.56 60.34 REMARK 500 GLN A 500 -167.00 -118.32 REMARK 500 ASP A 574 56.72 -97.65 REMARK 500 ASN A 602 74.10 -68.56 REMARK 500 VAL A 616 -73.63 -94.34 REMARK 500 SER A 634 33.21 -98.42 REMARK 500 GLU A 679 18.48 59.73 REMARK 500 SER A 793 -155.74 -111.45 REMARK 500 VAL A 806 -65.99 67.68 REMARK 500 SER A 819 -47.23 -133.56 REMARK 500 SER A 861 48.65 -85.32 REMARK 500 SER A 883 -53.19 -132.46 REMARK 500 LEU A 896 48.92 -88.47 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 A 901 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLN A 645 OE1 REMARK 620 2 LEU A 899 O 89.7 REMARK 620 3 LEU A 899 OXT 86.1 57.0 REMARK 620 4 HOH A1027 O 175.6 89.9 90.1 REMARK 620 5 U B 1 OP3 85.5 151.6 94.6 92.8 REMARK 620 6 U B 3 OP1 99.7 107.0 163.3 84.6 101.4 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 902 DBREF 5GUH A 1 899 UNP A8D8P8 A8D8P8_BOMMO 1 899 DBREF 5GUH B 1 28 PDB 5GUH 5GUH 1 28 SEQRES 1 A 899 MET SER GLU PRO ARG GLY ARG GLY ARG ALA ARG GLY ARG SEQRES 2 A 899 ALA GLY ARG GLY GLY ASP GLY GLY GLY PRO ALA PRO ARG SEQRES 3 A 899 ARG PRO GLY GLU GLN ALA GLY PRO SER GLN GLN SER MET SEQRES 4 A 899 PRO PRO GLY PRO ARG PRO GLN PRO PRO SER GLY TRP GLY SEQRES 5 A 899 PRO GLN SER SER VAL PRO PRO VAL ARG ALA GLY VAL PRO SEQRES 6 A 899 THR PRO THR ALA GLN ALA GLY ARG ALA SER HIS ARG VAL SEQRES 7 A 899 THR PRO THR THR HIS GLU HIS PRO GLY ASP ILE ASP VAL SEQRES 8 A 899 GLN GLN ARG MET GLN LYS LEU GLU LEU GLY PRO HIS SER SEQRES 9 A 899 SER GLY GLY GLY ASP ALA SER SER VAL VAL GLY ARG GLY SEQRES 10 A 899 SER ARG ARG GLY GLY GLY ARG VAL LEU PRO GLU THR ILE SEQRES 11 A 899 SER ILE LEU ARG THR ARG PRO GLU ALA VAL THR SER LYS SEQRES 12 A 899 LYS GLY THR SER GLY THR PRO LEU ASP LEU LEU ALA ASN SEQRES 13 A 899 TYR PHE THR VAL GLU THR THR PRO LYS TRP GLY LEU TYR SEQRES 14 A 899 GLN TYR HIS VAL ASP ILE SER PRO GLU GLU ASP SER THR SEQRES 15 A 899 GLY VAL ARG LYS ALA LEU MET ARG VAL HIS SER LYS THR SEQRES 16 A 899 LEU GLY GLY TYR LEU PHE ASP GLY THR VAL LEU TYR THR SEQRES 17 A 899 VAL ASN ARG LEU HIS PRO ASP PRO MET GLU LEU TYR SER SEQRES 18 A 899 ASP ARG LYS THR ASP ASN GLU ARG MET ARG ILE LEU ILE SEQRES 19 A 899 LYS LEU THR CYS GLU VAL SER PRO GLY ASP TYR HIS TYR SEQRES 20 A 899 ILE GLN ILE PHE ASN ILE ILE ILE ARG LYS CYS PHE ASN SEQRES 21 A 899 LEU LEU LYS LEU GLN LEU MET GLY ARG ASP TYR PHE ASP SEQRES 22 A 899 PRO GLU ALA LYS ILE ASP ILE PRO GLU PHE LYS LEU GLN SEQRES 23 A 899 ILE TRP PRO GLY TYR LYS THR THR ILE ASN GLN TYR GLU SEQRES 24 A 899 ASP ARG LEU LEU LEU VAL THR GLU ILE ALA HIS LYS VAL SEQRES 25 A 899 LEU ARG MET ASP THR VAL LEU GLN MET LEU SER GLU TYR SEQRES 26 A 899 ALA ALA THR LYS GLY ASN ASN TYR LYS LYS ILE PHE LEU SEQRES 27 A 899 GLU ASP VAL VAL GLY LYS ILE VAL MET THR ASP TYR ASN SEQRES 28 A 899 LYS ARG THR TYR ARG VAL ASP ASP VAL ALA TRP ASN VAL SEQRES 29 A 899 SER PRO LYS SER THR PHE LYS MET ARG ASP GLU ASN ILE SEQRES 30 A 899 THR TYR ILE GLU TYR TYR TYR LYS LYS TYR ASN LEU ARG SEQRES 31 A 899 ILE GLN ASP PRO GLY GLN PRO LEU LEU ILE SER ARG SER SEQRES 32 A 899 LYS PRO ARG GLU ILE ARG ALA GLY LEU PRO GLU LEU ILE SEQRES 33 A 899 TYR LEU VAL PRO GLU LEU CYS ARG GLN THR GLY LEU SER SEQRES 34 A 899 ASP GLU MET ARG ALA ASN PHE LYS LEU MET ARG SER LEU SEQRES 35 A 899 ASP VAL HIS THR LYS ILE GLY PRO ASP LYS ARG ILE GLU SEQRES 36 A 899 LYS LEU ASN ASN PHE ASN ARG ARG PHE THR SER THR PRO SEQRES 37 A 899 GLU VAL VAL GLU GLU LEU ALA THR TRP SER LEU LYS LEU SEQRES 38 A 899 SER LYS GLU LEU VAL LYS ILE LYS GLY ARG GLN LEU PRO SEQRES 39 A 899 PRO GLU ASN ILE ILE GLN ALA ASN ASN VAL LYS TYR PRO SEQRES 40 A 899 ALA GLY ASP THR THR GLU GLY TRP THR ARG ASP MET ARG SEQRES 41 A 899 SER LYS HIS LEU LEU ALA ILE ALA GLN LEU ASN SER TRP SEQRES 42 A 899 VAL VAL ILE THR PRO GLU ARG GLN ARG ARG ASP THR GLU SEQRES 43 A 899 SER PHE ILE ASP LEU ILE ILE LYS THR GLY GLY GLY VAL SEQRES 44 A 899 GLY PHE ARG MET ARG SER PRO ASP LEU VAL VAL ILE ARG SEQRES 45 A 899 HIS ASP GLY PRO ILE GLU TYR ALA ASN MET CYS GLU GLU SEQRES 46 A 899 VAL ILE ALA ARG LYS ASN PRO ALA LEU ILE LEU CYS VAL SEQRES 47 A 899 LEU ALA ARG ASN TYR ALA ASP ARG TYR GLU ALA ILE LYS SEQRES 48 A 899 LYS LYS CYS THR VAL ASP ARG ALA VAL PRO THR GLN VAL SEQRES 49 A 899 VAL CYS ALA ARG ASN MET SER SER LYS SER ALA MET SER SEQRES 50 A 899 ILE ALA THR LYS VAL ALA ILE GLN ILE ASN CYS LYS LEU SEQRES 51 A 899 GLY GLY SER PRO TRP THR VAL ASP ILE PRO LEU PRO SER SEQRES 52 A 899 LEU MET VAL VAL GLY TYR ASP VAL CYS HIS ASP THR ARG SEQRES 53 A 899 SER LYS GLU LYS SER PHE GLY ALA PHE VAL ALA THR LEU SEQRES 54 A 899 ASP LYS GLN MET THR GLN TYR TYR SER ILE VAL ASN ALA SEQRES 55 A 899 HIS THR SER GLY GLU GLU LEU SER SER HIS MET GLY PHE SEQRES 56 A 899 ASN ILE ALA SER ALA VAL LYS LYS PHE ARG GLU LYS ASN SEQRES 57 A 899 GLY THR TYR PRO ALA ARG ILE PHE ILE TYR ARG ASP GLY SEQRES 58 A 899 VAL GLY ASP GLY GLN ILE PRO TYR VAL HIS SER HIS GLU SEQRES 59 A 899 VAL ALA GLU ILE LYS LYS LYS LEU ALA GLU ILE TYR ALA SEQRES 60 A 899 GLY VAL GLU ILE LYS LEU ALA PHE ILE ILE VAL SER LYS SEQRES 61 A 899 ARG ILE ASN THR ARG ILE PHE VAL GLN ARG GLY ARG SER SEQRES 62 A 899 GLY GLU ASN PRO ARG PRO GLY THR VAL ILE ASP ASP VAL SEQRES 63 A 899 VAL THR LEU PRO GLU ARG TYR ASP PHE TYR LEU VAL SER SEQRES 64 A 899 GLN ASN VAL ARG GLU GLY THR ILE ALA PRO THR SER TYR SEQRES 65 A 899 ASN VAL ILE GLU ASP THR THR GLY LEU ASN PRO ASP ARG SEQRES 66 A 899 ILE GLN ARG LEU THR TYR LYS LEU THR HIS LEU TYR PHE SEQRES 67 A 899 ASN CYS SER SER GLN VAL ARG VAL PRO SER VAL CYS GLN SEQRES 68 A 899 TYR ALA HIS LYS LEU ALA PHE LEU ALA ALA ASN SER LEU SEQRES 69 A 899 HIS ASN GLN PRO HIS TYR SER LEU ASN GLU THR LEU TYR SEQRES 70 A 899 PHE LEU SEQRES 1 B 28 U A U U U A A A A A A A A SEQRES 2 B 28 A A A A A A A A A A A A U SEQRES 3 B 28 U OMU HET OMU B 28 21 HET MG A 901 1 HET MG A 902 1 HETNAM OMU O2'-METHYLURIDINE 5'-MONOPHOSPHATE HETNAM MG MAGNESIUM ION FORMUL 2 OMU C10 H15 N2 O9 P FORMUL 3 MG 2(MG 2+) FORMUL 5 HOH *84(H2 O) HELIX 1 AA1 SER A 181 VAL A 191 1 11 HELIX 2 AA2 HIS A 192 GLY A 197 1 6 HELIX 3 AA3 ASP A 244 LEU A 262 1 19 HELIX 4 AA4 PRO A 274 LYS A 277 5 4 HELIX 5 AA5 PRO A 281 PHE A 283 5 3 HELIX 6 AA6 VAL A 318 LYS A 329 1 12 HELIX 7 AA7 ILE A 336 VAL A 342 1 7 HELIX 8 AA8 TYR A 379 TYR A 387 1 9 HELIX 9 AA9 VAL A 419 GLU A 421 5 3 HELIX 10 AB1 SER A 429 ASN A 435 1 7 HELIX 11 AB2 ASN A 435 LYS A 447 1 13 HELIX 12 AB3 GLY A 449 SER A 466 1 18 HELIX 13 AB4 THR A 467 THR A 476 1 10 HELIX 14 AB5 ALA A 501 ASN A 503 5 3 HELIX 15 AB6 TRP A 515 ARG A 520 1 6 HELIX 16 AB7 GLN A 541 VAL A 559 1 19 HELIX 17 AB8 GLY A 575 LYS A 590 1 16 HELIX 18 AB9 TYR A 603 VAL A 616 1 14 HELIX 19 AC1 ALA A 627 SER A 631 1 5 HELIX 20 AC2 SER A 634 LEU A 650 1 17 HELIX 21 AC3 SER A 710 GLY A 729 1 20 HELIX 22 AC4 GLY A 743 GLY A 745 5 3 HELIX 23 AC5 GLN A 746 HIS A 753 1 8 HELIX 24 AC6 HIS A 753 ALA A 767 1 15 HELIX 25 AC7 ASN A 842 THR A 854 1 13 HELIX 26 AC8 PRO A 867 SER A 883 1 17 HELIX 27 AC9 HIS A 889 ASN A 893 5 5 SHEET 1 AA112 TYR A 696 HIS A 703 0 SHEET 2 AA112 SER A 681 THR A 688 -1 N ALA A 687 O TYR A 697 SHEET 3 AA112 LEU A 664 HIS A 673 -1 N ASP A 670 O ALA A 684 SHEET 4 AA112 ARG A 734 ASP A 740 1 O TYR A 738 N VAL A 667 SHEET 5 AA112 LEU A 773 SER A 779 1 O ILE A 776 N ILE A 737 SHEET 6 AA112 THR A 830 ASP A 837 -1 O ASN A 833 N ILE A 777 SHEET 7 AA112 ASP A 814 LEU A 817 -1 N LEU A 817 O THR A 830 SHEET 8 AA112 THR A 801 ILE A 803 -1 N ILE A 803 O TYR A 816 SHEET 9 AA112 VAL A 486 GLN A 492 -1 N ARG A 491 O VAL A 802 SHEET 10 AA112 THR A 149 ALA A 155 -1 N LEU A 153 O ILE A 488 SHEET 11 AA112 ILE A 786 ARG A 790 -1 O PHE A 787 N LEU A 154 SHEET 12 AA112 SER A 793 GLU A 795 -1 O GLU A 795 N VAL A 788 SHEET 1 AA2 7 GLN A 265 MET A 267 0 SHEET 2 AA2 7 ASP A 270 PHE A 272 -1 O ASP A 270 N MET A 267 SHEET 3 AA2 7 LEU A 285 GLN A 297 -1 O TYR A 291 N TYR A 271 SHEET 4 AA2 7 LEU A 302 THR A 317 -1 O ALA A 309 N GLY A 290 SHEET 5 AA2 7 CYS A 423 THR A 426 -1 O GLN A 425 N ARG A 314 SHEET 6 AA2 7 ILE A 345 THR A 348 -1 N MET A 347 O ARG A 424 SHEET 7 AA2 7 ARG A 353 ARG A 356 -1 O TYR A 355 N VAL A 346 SHEET 1 AA3 5 ILE A 278 ILE A 280 0 SHEET 2 AA3 5 LEU A 285 GLN A 297 -1 O LEU A 285 N ILE A 280 SHEET 3 AA3 5 LEU A 302 THR A 317 -1 O ALA A 309 N GLY A 290 SHEET 4 AA3 5 TYR A 157 THR A 162 -1 N PHE A 158 O LEU A 304 SHEET 5 AA3 5 LEU A 479 LEU A 481 -1 O LYS A 480 N GLU A 161 SHEET 1 AA4 5 TYR A 199 PHE A 201 0 SHEET 2 AA4 5 VAL A 205 THR A 208 -1 O TYR A 207 N LEU A 200 SHEET 3 AA4 5 LEU A 168 ILE A 175 -1 N TYR A 171 O LEU A 206 SHEET 4 AA4 5 MET A 230 VAL A 240 -1 O LYS A 235 N HIS A 172 SHEET 5 AA4 5 GLU A 218 SER A 221 -1 N LEU A 219 O ILE A 232 SHEET 1 AA5 3 ASP A 359 ALA A 361 0 SHEET 2 AA5 3 LEU A 398 SER A 403 -1 O LEU A 398 N ALA A 361 SHEET 3 AA5 3 GLU A 414 LEU A 418 -1 O ILE A 416 N SER A 401 SHEET 1 AA6 2 THR A 369 MET A 372 0 SHEET 2 AA6 2 GLU A 375 THR A 378 -1 O GLU A 375 N MET A 372 SHEET 1 AA7 2 ASN A 497 ILE A 499 0 SHEET 2 AA7 2 LYS A 505 PRO A 507 -1 O TYR A 506 N ILE A 498 SHEET 1 AA8 4 ASP A 567 ILE A 571 0 SHEET 2 AA8 4 TRP A 533 PRO A 538 1 N VAL A 535 O VAL A 569 SHEET 3 AA8 4 LEU A 594 LEU A 599 1 O VAL A 598 N ILE A 536 SHEET 4 AA8 4 THR A 622 CYS A 626 1 O VAL A 625 N LEU A 599 LINK O3' U B 27 P OMU B 28 1555 1555 1.61 LINK OE1 GLN A 645 MG MG A 901 1555 1555 2.15 LINK O LEU A 899 MG MG A 901 1555 1555 1.98 LINK OXT LEU A 899 MG MG A 901 1555 1555 2.38 LINK MG MG A 901 O HOH A1027 1555 1555 2.13 LINK MG MG A 901 OP3 U B 1 1555 1555 1.97 LINK MG MG A 901 OP1 U B 3 1555 1555 1.98 CISPEP 1 HIS A 213 PRO A 214 0 2.82 SITE 1 AC1 5 GLN A 645 LEU A 899 HOH A1027 U B 1 SITE 2 AC1 5 U B 3 SITE 1 AC2 2 ASP A 740 LYS A 780 CRYST1 61.899 114.619 136.718 90.00 90.00 90.00 P 21 21 21 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 0.016155 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008725 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007314 0.00000