HEADER LIGASE/DNA 18-JAN-21 7LFQ TITLE PYROCOCCUS RNA LIGASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA-SPLICING LIGASE RTCB; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: 3'-PHOSPHATE/5'-HYDROXY NUCLEIC ACID LIGASE; COMPND 5 EC: 6.5.1.8,3.1.-.-,6.5.1.8,3.1.-.-; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (5'-D(*AP*TP*GP*TP*CP*C)-3'); COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS HORIKOSHII; SOURCE 3 ORGANISM_TAXID: 53953; SOURCE 4 STRAIN: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3; SOURCE 5 GENE: RTCB, PH1602; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 866768; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 11 ORGANISM_TAXID: 32630 KEYWDS RNA REPAIR, LIGASE, LIGASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Y.GOLDGUR,S.SHUMAN,A.BANERJEE REVDAT 6 15-NOV-23 7LFQ 1 REMARK REVDAT 5 25-OCT-23 7LFQ 1 REMARK REVDAT 4 07-DEC-22 7LFQ 1 JRNL REVDAT 3 29-JUN-22 7LFQ 1 COMPND SOURCE REMARK SEQADV REVDAT 3 2 1 SEQRES REVDAT 2 10-MAR-21 7LFQ 1 JRNL REVDAT 1 03-MAR-21 7LFQ 0 JRNL AUTH A.BANERJEE,Y.GOLDGUR,S.SHUMAN JRNL TITL STRUCTURE OF 3'-PO 4 /5'-OH RNA LIGASE RTCB IN COMPLEX WITH JRNL TITL 2 A 5'-OH OLIGONUCLEOTIDE. JRNL REF RNA V. 27 584 2021 JRNL REFN ESSN 1469-9001 JRNL PMID 33619169 JRNL DOI 10.1261/RNA.078692.121 REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2_3874+SVN 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.87 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 26752 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.193 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.480 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 47.8700 - 6.5100 1.00 1927 155 0.1603 0.1800 REMARK 3 2 6.5100 - 5.1700 1.00 1812 147 0.1856 0.2042 REMARK 3 3 5.1700 - 4.5200 1.00 1797 145 0.1545 0.1896 REMARK 3 4 4.5100 - 4.1000 1.00 1763 143 0.1590 0.1704 REMARK 3 5 4.1000 - 3.8100 1.00 1779 144 0.1813 0.2028 REMARK 3 6 3.8100 - 3.5800 1.00 1741 141 0.2015 0.2362 REMARK 3 7 3.5800 - 3.4000 1.00 1778 142 0.2209 0.2466 REMARK 3 8 3.4000 - 3.2600 1.00 1733 141 0.2206 0.2569 REMARK 3 9 3.2600 - 3.1300 1.00 1758 142 0.2333 0.2500 REMARK 3 10 3.1300 - 3.0200 1.00 1725 140 0.2364 0.2606 REMARK 3 11 3.0200 - 2.9300 1.00 1744 141 0.2446 0.2842 REMARK 3 12 2.9300 - 2.8400 1.00 1742 140 0.2622 0.3280 REMARK 3 13 2.8400 - 2.7700 1.00 1733 140 0.2802 0.3099 REMARK 3 14 2.7700 - 2.7000 1.00 1720 139 0.3031 0.3167 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.322 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.111 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 67.81 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 70.12 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 : 0.011 3981 REMARK 3 ANGLE : 1.351 5397 REMARK 3 CHIRALITY : 0.063 575 REMARK 3 PLANARITY : 0.009 689 REMARK 3 DIHEDRAL : 22.443 595 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 8 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 126 ) REMARK 3 ORIGIN FOR THE GROUP (A): 52.4142 25.4538 18.4405 REMARK 3 T TENSOR REMARK 3 T11: 0.4389 T22: 0.4464 REMARK 3 T33: 0.4538 T12: 0.1140 REMARK 3 T13: -0.0207 T23: 0.0631 REMARK 3 L TENSOR REMARK 3 L11: 2.8850 L22: 2.2714 REMARK 3 L33: 1.6481 L12: 0.6091 REMARK 3 L13: 0.5013 L23: 0.4243 REMARK 3 S TENSOR REMARK 3 S11: -0.0693 S12: -0.1367 S13: 0.4795 REMARK 3 S21: -0.1205 S22: 0.0154 S23: 0.0347 REMARK 3 S31: -0.4281 S32: -0.0740 S33: 0.1245 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 127 THROUGH 157 ) REMARK 3 ORIGIN FOR THE GROUP (A): 25.0510 17.9438 12.1801 REMARK 3 T TENSOR REMARK 3 T11: 0.5618 T22: 0.9450 REMARK 3 T33: 1.0211 T12: 0.0428 REMARK 3 T13: -0.0107 T23: 0.0358 REMARK 3 L TENSOR REMARK 3 L11: 6.6508 L22: 1.7346 REMARK 3 L33: 4.7079 L12: -2.3820 REMARK 3 L13: -0.7786 L23: 2.2462 REMARK 3 S TENSOR REMARK 3 S11: 0.3319 S12: 0.3377 S13: 0.8266 REMARK 3 S21: -0.6535 S22: 0.2023 S23: 0.8492 REMARK 3 S31: -0.5228 S32: -1.5800 S33: -0.5781 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 158 THROUGH 221 ) REMARK 3 ORIGIN FOR THE GROUP (A): 37.5234 13.8970 13.4570 REMARK 3 T TENSOR REMARK 3 T11: 0.4126 T22: 0.5062 REMARK 3 T33: 0.4527 T12: 0.0288 REMARK 3 T13: -0.0434 T23: 0.0413 REMARK 3 L TENSOR REMARK 3 L11: 3.7918 L22: 3.4247 REMARK 3 L33: 3.4488 L12: -0.5001 REMARK 3 L13: -1.5240 L23: 0.9589 REMARK 3 S TENSOR REMARK 3 S11: -0.0696 S12: -0.1740 S13: -0.0410 REMARK 3 S21: 0.2289 S22: 0.0153 S23: 0.6014 REMARK 3 S31: 0.1445 S32: -0.4783 S33: 0.0924 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 222 THROUGH 275 ) REMARK 3 ORIGIN FOR THE GROUP (A): 39.8989 28.3766 22.0036 REMARK 3 T TENSOR REMARK 3 T11: 0.5110 T22: 0.6709 REMARK 3 T33: 0.7490 T12: 0.2124 REMARK 3 T13: 0.0761 T23: 0.0115 REMARK 3 L TENSOR REMARK 3 L11: 2.0511 L22: 3.3566 REMARK 3 L33: 2.4869 L12: 0.1674 REMARK 3 L13: 0.3216 L23: 0.5288 REMARK 3 S TENSOR REMARK 3 S11: -0.0473 S12: -0.5201 S13: 0.8678 REMARK 3 S21: 0.2079 S22: 0.2074 S23: 0.2636 REMARK 3 S31: -0.7094 S32: -0.4424 S33: -0.0101 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 276 THROUGH 384 ) REMARK 3 ORIGIN FOR THE GROUP (A): 41.8282 12.7365 18.1041 REMARK 3 T TENSOR REMARK 3 T11: 0.3180 T22: 0.4930 REMARK 3 T33: 0.4771 T12: 0.0502 REMARK 3 T13: 0.0636 T23: 0.0871 REMARK 3 L TENSOR REMARK 3 L11: 2.9286 L22: 3.2890 REMARK 3 L33: 4.3145 L12: 0.5374 REMARK 3 L13: 0.7374 L23: 2.0021 REMARK 3 S TENSOR REMARK 3 S11: 0.0446 S12: -0.1169 S13: 0.0050 REMARK 3 S21: 0.0672 S22: -0.1014 S23: 0.4602 REMARK 3 S31: -0.0205 S32: -0.3216 S33: 0.0702 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 385 THROUGH 413 ) REMARK 3 ORIGIN FOR THE GROUP (A): 53.9059 20.2062 17.1994 REMARK 3 T TENSOR REMARK 3 T11: 0.5158 T22: 0.4308 REMARK 3 T33: 0.4676 T12: 0.1152 REMARK 3 T13: -0.0480 T23: 0.0012 REMARK 3 L TENSOR REMARK 3 L11: 3.6946 L22: 1.7046 REMARK 3 L33: 3.0087 L12: 1.1362 REMARK 3 L13: -0.9219 L23: 1.6709 REMARK 3 S TENSOR REMARK 3 S11: -0.1319 S12: -0.0198 S13: 0.3165 REMARK 3 S21: -0.2645 S22: 0.1152 S23: 0.4427 REMARK 3 S31: -0.5537 S32: -0.0627 S33: 0.0229 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 414 THROUGH 481 ) REMARK 3 ORIGIN FOR THE GROUP (A): 52.0055 22.4070 0.6271 REMARK 3 T TENSOR REMARK 3 T11: 0.7303 T22: 0.6669 REMARK 3 T33: 0.6805 T12: 0.0328 REMARK 3 T13: 0.0459 T23: 0.1515 REMARK 3 L TENSOR REMARK 3 L11: 3.2910 L22: 2.3760 REMARK 3 L33: 3.2293 L12: -0.2656 REMARK 3 L13: 1.5173 L23: 0.4019 REMARK 3 S TENSOR REMARK 3 S11: 0.0215 S12: 0.7597 S13: 0.7085 REMARK 3 S21: -0.7272 S22: -0.0759 S23: -0.0024 REMARK 3 S31: -0.3001 S32: 0.3743 S33: 0.0497 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1 THROUGH 6 ) REMARK 3 ORIGIN FOR THE GROUP (A): 34.2833 35.6165 8.8988 REMARK 3 T TENSOR REMARK 3 T11: 1.3369 T22: 1.4791 REMARK 3 T33: 1.9989 T12: 0.2630 REMARK 3 T13: -0.4771 T23: -0.1370 REMARK 3 L TENSOR REMARK 3 L11: 1.8873 L22: 8.4935 REMARK 3 L33: 6.8655 L12: -0.6224 REMARK 3 L13: 2.7340 L23: -5.8218 REMARK 3 S TENSOR REMARK 3 S11: -1.2428 S12: 0.0640 S13: 2.0394 REMARK 3 S21: 0.5340 S22: 1.7203 S23: 2.0087 REMARK 3 S31: -1.1240 S32: 0.3111 S33: -0.4710 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 7LFQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-JAN-21. REMARK 100 THE DEPOSITION ID IS D_1000254224. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-NOV-19 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 : APS REMARK 200 BEAMLINE : 24-ID-E REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26802 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 10.90 REMARK 200 R MERGE (I) : 0.08400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.75 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 11.10 REMARK 200 R MERGE FOR SHELL (I) : 1.31100 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: PHENIX REMARK 200 STARTING MODEL: 4DWR REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 69.66 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.05 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MORPHEUS G6, PH 7.5, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 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+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 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 41.16850 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 75.68950 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 75.68950 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 61.75275 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 75.68950 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 75.68950 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 20.58425 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 75.68950 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 75.68950 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 61.75275 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 75.68950 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 75.68950 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 20.58425 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 41.16850 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 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 -19 REMARK 465 GLY A -18 REMARK 465 SER A -17 REMARK 465 SER A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 SER A -9 REMARK 465 SER A -8 REMARK 465 GLY A -7 REMARK 465 LEU A -6 REMARK 465 VAL A -5 REMARK 465 PRO A -4 REMARK 465 ARG A -3 REMARK 465 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 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 OD1 ASP A 211 O HOH A 601 2.15 REMARK 500 NH2 ARG A 420 OD2 ASP A 422 2.15 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 LYS A 6 CD - CE - NZ ANGL. DEV. = -29.6 DEGREES REMARK 500 GLU A 84 CA - CB - CG ANGL. DEV. = 13.3 DEGREES REMARK 500 ARG A 186 NH1 - CZ - NH2 ANGL. DEV. = -7.2 DEGREES REMARK 500 ARG A 186 NE - CZ - NH1 ANGL. DEV. = 5.8 DEGREES REMARK 500 MET A 285 CA - CB - CG ANGL. DEV. = 10.8 DEGREES REMARK 500 ARG A 343 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG A 343 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 DT B 2 O4' - C4' - C3' ANGL. DEV. = -2.5 DEGREES REMARK 500 DT B 2 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 DG B 3 O4' - C1' - N9 ANGL. DEV. = 2.2 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 LYS A 58 -38.54 72.93 REMARK 500 TYR A 59 158.50 169.90 REMARK 500 ASP A 65 2.19 -69.71 REMARK 500 PRO A 128 26.62 -72.37 REMARK 500 SER A 129 138.96 -33.11 REMARK 500 SER A 200 -158.59 -147.84 REMARK 500 LEU A 268 51.76 -92.19 REMARK 500 GLU A 316 -66.05 -91.11 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 ASP A 65 0.07 SIDE CHAIN 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 K A 502 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 206 OE1 REMARK 620 2 GLU A 206 OE2 40.7 REMARK 620 3 THR A 383 O 148.3 108.9 REMARK 620 4 SER A 385 OG 104.4 106.3 91.9 REMARK 620 N 1 2 3 DBREF 7LFQ A 1 96 UNP O59245 RTCB_PYRHO 1 96 DBREF 7LFQ A 97 481 UNP O59245 RTCB_PYRHO 487 871 DBREF 7LFQ B 1 6 PDB 7LFQ 7LFQ 1 6 SEQADV 7LFQ MET A -19 UNP O59245 INITIATING METHIONINE SEQADV 7LFQ GLY A -18 UNP O59245 EXPRESSION TAG SEQADV 7LFQ SER A -17 UNP O59245 EXPRESSION TAG SEQADV 7LFQ SER A -16 UNP O59245 EXPRESSION TAG SEQADV 7LFQ HIS A -15 UNP O59245 EXPRESSION TAG SEQADV 7LFQ HIS A -14 UNP O59245 EXPRESSION TAG SEQADV 7LFQ HIS A -13 UNP O59245 EXPRESSION TAG SEQADV 7LFQ HIS A -12 UNP O59245 EXPRESSION TAG SEQADV 7LFQ HIS A -11 UNP O59245 EXPRESSION TAG SEQADV 7LFQ HIS A -10 UNP O59245 EXPRESSION TAG SEQADV 7LFQ SER A -9 UNP O59245 EXPRESSION TAG SEQADV 7LFQ SER A -8 UNP O59245 EXPRESSION TAG SEQADV 7LFQ GLY A -7 UNP O59245 EXPRESSION TAG SEQADV 7LFQ LEU A -6 UNP O59245 EXPRESSION TAG SEQADV 7LFQ VAL A -5 UNP O59245 EXPRESSION TAG SEQADV 7LFQ PRO A -4 UNP O59245 EXPRESSION TAG SEQADV 7LFQ ARG A -3 UNP O59245 EXPRESSION TAG SEQADV 7LFQ GLY A -2 UNP O59245 EXPRESSION TAG SEQADV 7LFQ SER A -1 UNP O59245 EXPRESSION TAG SEQADV 7LFQ HIS A 0 UNP O59245 EXPRESSION TAG SEQRES 1 A 501 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 501 LEU VAL PRO ARG GLY SER HIS MET VAL VAL PRO LEU LYS SEQRES 3 A 501 ARG ILE ASP LYS ILE ARG TRP GLU ILE PRO LYS PHE ASP SEQRES 4 A 501 LYS ARG MET ARG VAL PRO GLY ARG VAL TYR ALA ASP GLU SEQRES 5 A 501 VAL LEU LEU GLU LYS MET LYS ASN ASP ARG THR LEU GLU SEQRES 6 A 501 GLN ALA THR ASN VAL ALA MET LEU PRO GLY ILE TYR LYS SEQRES 7 A 501 TYR SER ILE VAL MET PRO ASP GLY HIS GLN GLY TYR GLY SEQRES 8 A 501 PHE PRO ILE GLY GLY VAL ALA ALA PHE ASP VAL LYS GLU SEQRES 9 A 501 GLY VAL ILE SER PRO GLY GLY ILE GLY TYR ASP ILE ASN SEQRES 10 A 501 OCS GLY VAL ARG LEU ILE ARG THR ASN LEU THR GLU LYS SEQRES 11 A 501 GLU VAL ARG PRO ARG ILE LYS GLN LEU VAL ASP THR LEU SEQRES 12 A 501 PHE LYS ASN VAL PRO SER GLY VAL GLY SER GLN GLY ARG SEQRES 13 A 501 ILE LYS LEU HIS TRP THR GLN ILE ASP ASP VAL LEU VAL SEQRES 14 A 501 ASP GLY ALA LYS TRP ALA VAL ASP ASN GLY TYR GLY TRP SEQRES 15 A 501 GLU ARG ASP LEU GLU ARG LEU GLU GLU GLY GLY ARG MET SEQRES 16 A 501 GLU GLY ALA ASP PRO GLU ALA VAL SER GLN ARG ALA LYS SEQRES 17 A 501 GLN ARG GLY ALA PRO GLN LEU GLY SER LEU GLY SER GLY SEQRES 18 A 501 ASN HIS PHE LEU GLU VAL GLN VAL VAL ASP LYS ILE PHE SEQRES 19 A 501 ASP PRO GLU VAL ALA LYS ALA TYR GLY LEU PHE GLU GLY SEQRES 20 A 501 GLN VAL VAL VAL MET VAL HIS THR GLY SER ARG GLY LEU SEQRES 21 A 501 GLY HIS GLN VAL ALA SER ASP TYR LEU ARG ILE MET GLU SEQRES 22 A 501 ARG ALA ILE ARG LYS TYR ARG ILE PRO TRP PRO ASP ARG SEQRES 23 A 501 GLU LEU VAL SER VAL PRO PHE GLN SER GLU GLU GLY GLN SEQRES 24 A 501 ARG TYR PHE SER ALA MET LYS ALA ALA ALA ASN PHE ALA SEQRES 25 A 501 TRP ALA ASN ARG GLN MET ILE THR HIS TRP VAL ARG GLU SEQRES 26 A 501 SER PHE GLN GLU VAL PHE LYS GLN ASP PRO GLU GLY ASP SEQRES 27 A 501 LEU GLY MET ASP ILE VAL TYR ASP VAL ALA HIS ASN ILE SEQRES 28 A 501 GLY LYS VAL GLU GLU HIS GLU VAL ASP GLY LYS ARG VAL SEQRES 29 A 501 LYS VAL ILE VAL HIS ARG LYS GLY ALA THR ARG ALA PHE SEQRES 30 A 501 PRO PRO GLY HIS GLU ALA VAL PRO ARG LEU TYR ARG ASP SEQRES 31 A 501 VAL GLY GLN PRO VAL LEU ILE PRO GLY SER MET GLY THR SEQRES 32 A 501 ALA SER TYR ILE LEU ALA GLY THR GLU GLY ALA MET LYS SEQRES 33 A 501 GLU THR PHE GLY SER THR CYS HIS GLY ALA GLY ARG VAL SEQRES 34 A 501 LEU SER ARG LYS ALA ALA THR ARG GLN TYR ARG GLY ASP SEQRES 35 A 501 ARG ILE ARG GLN GLU LEU LEU ASN ARG GLY ILE TYR VAL SEQRES 36 A 501 ARG ALA ALA SER MET ARG VAL VAL ALA GLU GLU ALA PRO SEQRES 37 A 501 GLY ALA TYR LYS ASN VAL ASP ASN VAL VAL LYS VAL VAL SEQRES 38 A 501 SER GLU ALA GLY ILE ALA LYS LEU VAL ALA ARG MET ARG SEQRES 39 A 501 PRO ILE GLY VAL ALA LYS GLY SEQRES 1 B 6 DA DT DG DT DC DC MODRES 7LFQ OCS A 98 CYS MODIFIED RESIDUE HET OCS A 98 9 HET SO4 A 501 5 HET K A 502 1 HETNAM OCS CYSTEINESULFONIC ACID HETNAM SO4 SULFATE ION HETNAM K POTASSIUM ION FORMUL 1 OCS C3 H7 N O5 S FORMUL 3 SO4 O4 S 2- FORMUL 4 K K 1+ FORMUL 5 HOH *17(H2 O) HELIX 1 AA1 ASP A 31 LYS A 39 1 9 HELIX 2 AA2 ARG A 42 ALA A 51 1 10 HELIX 3 AA3 SER A 88 ILE A 92 5 5 HELIX 4 AA4 GLU A 109 ARG A 113 1 5 HELIX 5 AA5 ARG A 115 VAL A 127 1 13 HELIX 6 AA6 HIS A 140 GLN A 143 5 4 HELIX 7 AA7 ILE A 144 ASN A 158 1 15 HELIX 8 AA8 TRP A 162 ARG A 174 5 13 HELIX 9 AA9 ASP A 179 VAL A 183 5 5 HELIX 10 AB1 SER A 184 LEU A 195 1 12 HELIX 11 AB2 ASP A 215 TYR A 222 1 8 HELIX 12 AB3 GLY A 239 ILE A 256 1 18 HELIX 13 AB4 SER A 275 LYS A 312 1 38 HELIX 14 AB5 THR A 391 PHE A 399 1 9 HELIX 15 AB6 LYS A 413 TYR A 419 1 7 HELIX 16 AB7 ARG A 420 ASN A 430 1 11 HELIX 17 AB8 SER A 439 GLU A 446 1 8 HELIX 18 AB9 ALA A 447 TYR A 451 5 5 HELIX 19 AC1 ASN A 453 GLY A 465 1 13 SHEET 1 AA1 7 LYS A 6 ARG A 7 0 SHEET 2 AA1 7 ARG A 12 ILE A 15 -1 O GLU A 14 N LYS A 6 SHEET 3 AA1 7 GLY A 26 TYR A 29 -1 O VAL A 28 N TRP A 13 SHEET 4 AA1 7 SER A 60 HIS A 67 1 O SER A 60 N ARG A 27 SHEET 5 AA1 7 ILE A 74 ASP A 81 -1 O GLY A 75 N MET A 63 SHEET 6 AA1 7 LYS A 342 LYS A 351 -1 O HIS A 349 N ALA A 78 SHEET 7 AA1 7 ASN A 330 VAL A 339 -1 N LYS A 333 O VAL A 348 SHEET 1 AA2 2 VAL A 86 ILE A 87 0 SHEET 2 AA2 2 VAL A 271 PRO A 272 -1 O VAL A 271 N ILE A 87 SHEET 1 AA3 7 ILE A 323 ALA A 328 0 SHEET 2 AA3 7 GLY A 99 THR A 108 -1 N LEU A 102 O VAL A 324 SHEET 3 AA3 7 GLN A 228 THR A 235 -1 O VAL A 231 N ILE A 103 SHEET 4 AA3 7 PHE A 204 ILE A 213 -1 N GLN A 208 O VAL A 230 SHEET 5 AA3 7 LYS A 468 ALA A 479 -1 O ALA A 479 N LEU A 205 SHEET 6 AA3 7 SER A 385 ALA A 389 -1 N SER A 385 O MET A 473 SHEET 7 AA3 7 PRO A 374 ILE A 377 -1 N VAL A 375 O LEU A 388 SHEET 1 AA4 6 ILE A 323 ALA A 328 0 SHEET 2 AA4 6 GLY A 99 THR A 108 -1 N LEU A 102 O VAL A 324 SHEET 3 AA4 6 GLN A 228 THR A 235 -1 O VAL A 231 N ILE A 103 SHEET 4 AA4 6 PHE A 204 ILE A 213 -1 N GLN A 208 O VAL A 230 SHEET 5 AA4 6 LYS A 468 ALA A 479 -1 O ALA A 479 N LEU A 205 SHEET 6 AA4 6 TYR A 434 ARG A 436 1 N TYR A 434 O ILE A 476 SHEET 1 AA5 2 THR A 354 ARG A 355 0 SHEET 2 AA5 2 SER A 401 THR A 402 -1 O THR A 402 N THR A 354 LINK C ASN A 97 N OCS A 98 1555 1555 1.32 LINK C OCS A 98 N GLY A 99 1555 1555 1.33 LINK OE1 GLU A 206 K K A 502 1555 1555 3.21 LINK OE2 GLU A 206 K K A 502 1555 1555 2.70 LINK O THR A 383 K K A 502 1555 1555 3.01 LINK OG SER A 385 K K A 502 1555 1555 3.20 CRYST1 151.379 151.379 82.337 90.00 90.00 90.00 P 43 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 0.006606 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006606 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012145 0.00000