HEADER TRANSFERASE/DNA 21-APR-25 9OAY TITLE TNA POLYMERASE, 8-64, TERNARY COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: 8-64, TNA POLYMERASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: TEMPLATE; COMPND 7 CHAIN: T; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: PRIMER; COMPND 11 CHAIN: P; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOCOCCUS KODAKARENSIS; SOURCE 3 ORGANISM_TAXID: 311400; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 MOL_ID: 2; SOURCE 7 SYNTHETIC: YES; SOURCE 8 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 9 ORGANISM_TAXID: 32630; SOURCE 10 MOL_ID: 3; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 13 ORGANISM_TAXID: 32630 KEYWDS ENZYME ENGINEERING, B-FAMILY POLYMERASE, TNA POLYMERASE, POLYMERASE, KEYWDS 2 TERNARY COMPLEX, TRANSFERASE, TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.J.LEE,V.A.MAOLA,N.CHIM,J.C.CHAPUT REVDAT 3 04-FEB-26 9OAY 1 JRNL REVDAT 2 31-DEC-25 9OAY 1 JRNL REVDAT 1 10-DEC-25 9OAY 0 JRNL AUTH M.HAJJAR,V.A.MAOLA,J.J.LEE,M.J.HOLGUIN,R.N.QUIJANO, JRNL AUTH 2 K.K.NGUYEN,K.L.HO,J.V.MEDINA,E.BOTELLO-CORNEJO,B.BARPUZARY, JRNL AUTH 3 N.CHIM,J.C.CHAPUT JRNL TITL DIRECTED EVOLUTION OF A TNA POLYMERASE IDENTIFIES JRNL TITL 2 INDEPENDENT PATHS TO FIDELITY AND CATALYSIS. JRNL REF NAT COMMUN V. 17 925 2025 JRNL REFN ESSN 2041-1723 JRNL PMID 41413390 JRNL DOI 10.1038/S41467-025-67652-1 REMARK 2 REMARK 2 RESOLUTION. 2.38 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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) : 2.38 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.59 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 35755 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.219 REMARK 3 R VALUE (WORKING SET) : 0.216 REMARK 3 FREE R VALUE : 0.266 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.580 REMARK 3 FREE R VALUE TEST SET COUNT : 1994 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 48.5900 - 5.7300 1.00 2585 158 0.2019 0.2292 REMARK 3 2 5.7300 - 4.5500 1.00 2455 140 0.1965 0.2247 REMARK 3 3 4.5500 - 3.9800 1.00 2434 154 0.1870 0.2529 REMARK 3 4 3.9800 - 3.6100 1.00 2440 128 0.2072 0.2635 REMARK 3 5 3.6100 - 3.3500 1.00 2392 149 0.2184 0.2742 REMARK 3 6 3.3500 - 3.1600 1.00 2415 139 0.2331 0.2719 REMARK 3 7 3.1600 - 3.0000 1.00 2382 143 0.2232 0.3099 REMARK 3 8 3.0000 - 2.8700 1.00 2396 144 0.2345 0.2778 REMARK 3 9 2.8700 - 2.7600 1.00 2379 144 0.2425 0.3034 REMARK 3 10 2.7600 - 2.6600 1.00 2383 139 0.2715 0.3364 REMARK 3 11 2.6600 - 2.5800 1.00 2387 130 0.2626 0.3157 REMARK 3 12 2.5800 - 2.5100 1.00 2355 147 0.2683 0.3204 REMARK 3 13 2.5100 - 2.4400 1.00 2419 133 0.2628 0.3120 REMARK 3 14 2.4400 - 2.3800 1.00 2339 146 0.2619 0.3447 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.307 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.753 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 46.91 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 59.48 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 : 0.003 7019 REMARK 3 ANGLE : 0.522 9612 REMARK 3 CHIRALITY : 0.040 1031 REMARK 3 PLANARITY : 0.004 1121 REMARK 3 DIHEDRAL : 18.854 1152 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 123 ) REMARK 3 ORIGIN FOR THE GROUP (A): -24.9163 -5.3821 24.4213 REMARK 3 T TENSOR REMARK 3 T11: 0.3612 T22: 0.5164 REMARK 3 T33: 0.3373 T12: -0.0664 REMARK 3 T13: -0.0056 T23: 0.0334 REMARK 3 L TENSOR REMARK 3 L11: 1.6977 L22: 1.6862 REMARK 3 L33: 1.9655 L12: 0.1618 REMARK 3 L13: 0.0483 L23: 0.5344 REMARK 3 S TENSOR REMARK 3 S11: 0.0916 S12: -0.0817 S13: -0.0783 REMARK 3 S21: -0.0301 S22: -0.1159 S23: 0.0381 REMARK 3 S31: 0.2454 S32: -0.5059 S33: -0.0001 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 124 THROUGH 255 ) REMARK 3 ORIGIN FOR THE GROUP (A): -2.9440 14.5734 43.9333 REMARK 3 T TENSOR REMARK 3 T11: 0.6267 T22: 0.4834 REMARK 3 T33: 0.4490 T12: -0.0079 REMARK 3 T13: 0.0282 T23: -0.0193 REMARK 3 L TENSOR REMARK 3 L11: 2.5070 L22: 2.5717 REMARK 3 L33: 1.6925 L12: 1.2204 REMARK 3 L13: 0.4052 L23: 0.6169 REMARK 3 S TENSOR REMARK 3 S11: 0.3190 S12: -0.4551 S13: -0.1363 REMARK 3 S21: 0.5004 S22: -0.2290 S23: -0.1539 REMARK 3 S31: 0.3082 S32: 0.0197 S33: -0.0001 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 256 THROUGH 364 ) REMARK 3 ORIGIN FOR THE GROUP (A): 2.1924 15.7128 30.2803 REMARK 3 T TENSOR REMARK 3 T11: 0.5191 T22: 0.4528 REMARK 3 T33: 0.4716 T12: 0.0687 REMARK 3 T13: -0.0330 T23: -0.0180 REMARK 3 L TENSOR REMARK 3 L11: 1.0556 L22: 1.4311 REMARK 3 L33: 1.0209 L12: 0.8596 REMARK 3 L13: -0.0991 L23: 0.7941 REMARK 3 S TENSOR REMARK 3 S11: 0.0841 S12: 0.1141 S13: 0.1780 REMARK 3 S21: 0.2303 S22: 0.0944 S23: -0.1650 REMARK 3 S31: 0.0381 S32: 0.3750 S33: 0.0000 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 365 THROUGH 652 ) REMARK 3 ORIGIN FOR THE GROUP (A): 7.9476 10.9986 2.5542 REMARK 3 T TENSOR REMARK 3 T11: 0.4682 T22: 0.3512 REMARK 3 T33: 0.4701 T12: -0.0070 REMARK 3 T13: -0.0367 T23: 0.0333 REMARK 3 L TENSOR REMARK 3 L11: 1.5758 L22: 0.7857 REMARK 3 L33: 1.1101 L12: 0.5601 REMARK 3 L13: -0.5461 L23: 0.0290 REMARK 3 S TENSOR REMARK 3 S11: -0.0998 S12: 0.0817 S13: 0.1306 REMARK 3 S21: -0.0878 S22: 0.0689 S23: -0.1473 REMARK 3 S31: -0.3390 S32: 0.0546 S33: 0.0001 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 653 THROUGH 750 ) REMARK 3 ORIGIN FOR THE GROUP (A): 26.3576 3.8764 27.9066 REMARK 3 T TENSOR REMARK 3 T11: 0.5293 T22: 0.8184 REMARK 3 T33: 0.7093 T12: 0.0520 REMARK 3 T13: -0.0445 T23: 0.1318 REMARK 3 L TENSOR REMARK 3 L11: 1.3298 L22: 1.7709 REMARK 3 L33: 0.9982 L12: -0.4068 REMARK 3 L13: 0.4947 L23: 0.2531 REMARK 3 S TENSOR REMARK 3 S11: -0.0307 S12: -0.9440 S13: -0.6408 REMARK 3 S21: 0.5104 S22: 0.0408 S23: -0.4572 REMARK 3 S31: -0.2643 S32: 0.3063 S33: 0.0012 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'T' AND (RESID 4 THROUGH 8 ) REMARK 3 ORIGIN FOR THE GROUP (A): -7.2167 -3.3719 26.1461 REMARK 3 T TENSOR REMARK 3 T11: 0.8593 T22: 1.1705 REMARK 3 T33: 0.9752 T12: 0.1457 REMARK 3 T13: 0.1104 T23: 0.1393 REMARK 3 L TENSOR REMARK 3 L11: 0.0778 L22: 0.0679 REMARK 3 L33: 0.0592 L12: 0.0722 REMARK 3 L13: 0.0543 L23: 0.0564 REMARK 3 S TENSOR REMARK 3 S11: 0.1940 S12: -0.4468 S13: 0.4891 REMARK 3 S21: -0.3267 S22: -0.5769 S23: -1.5700 REMARK 3 S31: 0.6764 S32: 0.4880 S33: -0.0003 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'T' AND (RESID 9 THROUGH 21 ) REMARK 3 ORIGIN FOR THE GROUP (A): 20.5240 -4.4786 13.8638 REMARK 3 T TENSOR REMARK 3 T11: 0.4800 T22: 0.5558 REMARK 3 T33: 0.7780 T12: 0.1684 REMARK 3 T13: -0.0678 T23: 0.0063 REMARK 3 L TENSOR REMARK 3 L11: 0.4839 L22: 0.6333 REMARK 3 L33: 0.6820 L12: 0.5312 REMARK 3 L13: 0.1789 L23: 0.3793 REMARK 3 S TENSOR REMARK 3 S11: -0.3605 S12: 0.0091 S13: -0.5421 REMARK 3 S21: 0.4830 S22: 0.2447 S23: -0.4702 REMARK 3 S31: 0.1857 S32: 0.2870 S33: 0.0007 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'P' AND (RESID 1 THROUGH 11 ) REMARK 3 ORIGIN FOR THE GROUP (A): 23.0485 -5.0505 14.2374 REMARK 3 T TENSOR REMARK 3 T11: 0.5120 T22: 0.8886 REMARK 3 T33: 1.0397 T12: 0.2274 REMARK 3 T13: 0.0222 T23: 0.1642 REMARK 3 L TENSOR REMARK 3 L11: 0.0578 L22: 0.1695 REMARK 3 L33: 0.2843 L12: 0.0696 REMARK 3 L13: 0.1293 L23: 0.1712 REMARK 3 S TENSOR REMARK 3 S11: -0.0892 S12: 0.4574 S13: -0.8921 REMARK 3 S21: -0.0511 S22: -0.4230 S23: 0.0438 REMARK 3 S31: 0.2845 S32: 0.9821 S33: -0.0088 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 9OAY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-APR-25. REMARK 100 THE DEPOSITION ID IS D_1000295079. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-MAY-23 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 : ALS REMARK 200 BEAMLINE : 5.0.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : POINTLESS, AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 38977 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.380 REMARK 200 RESOLUTION RANGE LOW (A) : 48.590 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : 0.07340 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.4500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.38 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.47 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.76580 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: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.88 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.99 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM IODIDE, 20 % POLYETHYLENE REMARK 280 GLYCOL 3350, AND 0.1 M TAURINE, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 298K 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 38.85650 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 55.33750 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 50.76500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 55.33750 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 38.85650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 50.76500 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, T, P 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 DT T 1 REMARK 465 DA T 2 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 LYS A 467 OG1 THR A 471 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OE1 GLU A 399 NH1 ARG A 466 4555 2.15 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 ASP A 164 -152.65 -144.59 REMARK 500 PHE A 214 -91.21 -137.18 REMARK 500 ALA A 231 84.31 -67.82 REMARK 500 MET A 244 64.14 -110.69 REMARK 500 THR A 267 -49.57 -130.79 REMARK 500 ASP A 373 -177.86 -69.88 REMARK 500 GLN A 437 -57.44 64.19 REMARK 500 TRP A 505 46.94 -90.37 REMARK 500 CYS A 507 85.94 -156.47 REMARK 500 ASP A 541 -137.48 -120.82 REMARK 500 LYS A 633 -63.59 -96.18 REMARK 500 PRO A 696 117.41 -39.66 REMARK 500 LEU A 746 50.94 -112.90 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 802 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 405 OD2 REMARK 620 2 PHE A 406 O 79.0 REMARK 620 3 ASP A 543 OD2 108.4 111.8 REMARK 620 4 9O7 A 801 O1A 103.3 177.4 66.3 REMARK 620 5 9O7 A 801 O2B 161.6 110.2 83.5 68.0 REMARK 620 6 9O7 A 801 O1G 71.0 93.7 154.1 88.3 92.1 REMARK 620 N 1 2 3 4 5 DBREF 9OAY A 1 750 PDB 9OAY 9OAY 1 750 DBREF 9OAY T 1 21 PDB 9OAY 9OAY 1 21 DBREF 9OAY P 1 12 PDB 9OAY 9OAY 1 12 SEQRES 1 A 750 MET ILE LEU ASP THR ASP TYR ILE THR GLU ASP GLY LYS SEQRES 2 A 750 PRO VAL ILE ARG ILE PHE LYS LYS GLU ASN GLY GLU PHE SEQRES 3 A 750 LYS ILE GLU TYR ASP ARG THR PHE GLU PRO TYR PHE TYR SEQRES 4 A 750 ALA LEU LEU LYS ASP ASP SER ALA ILE GLU GLU VAL LYS SEQRES 5 A 750 LYS ILE THR ALA GLU ARG HIS GLY THR VAL VAL THR VAL SEQRES 6 A 750 LYS ARG VAL GLU LYS VAL GLN LYS LYS PHE LEU GLY ARG SEQRES 7 A 750 PRO VAL GLU VAL TRP LYS LEU TYR PHE THR HIS PRO GLN SEQRES 8 A 750 ASP VAL PRO ALA ILE ARG ASP ARG ILE ARG ALA HIS PRO SEQRES 9 A 750 ALA VAL VAL ASP ILE TYR GLU TYR ASP ILE PRO PHE ALA SEQRES 10 A 750 LYS ARG TYR LEU ILE ASP LYS GLY LEU ILE PRO MET GLU SEQRES 11 A 750 GLY ASP GLU GLU LEU THR MET LEU ALA PHE ALA ILE ALA SEQRES 12 A 750 THR LEU TYR HIS GLU GLY GLU GLU PHE ALA GLU GLY PRO SEQRES 13 A 750 ILE LEU MET ILE SER TYR ALA ASP GLU GLU GLY ALA ARG SEQRES 14 A 750 VAL ILE THR TRP LYS ASN VAL ASP LEU PRO TYR VAL ASP SEQRES 15 A 750 VAL VAL SER THR GLU ARG GLU MET ILE LYS ARG PHE LEU SEQRES 16 A 750 ARG VAL VAL LYS GLU LYS ASP PRO ASP VAL LEU ILE THR SEQRES 17 A 750 TYR ASN GLY ASP ASN PHE ASP PHE ALA TYR LEU LYS LYS SEQRES 18 A 750 ARG CYS GLU LYS LEU GLY ILE ASN PHE ALA LEU GLY ARG SEQRES 19 A 750 ASP GLY SER GLU PRO LYS ILE GLN ARG MET GLY ASP ARG SEQRES 20 A 750 PHE ALA VAL GLU VAL LYS GLY ARG ILE HIS PHE ASP LEU SEQRES 21 A 750 TYR PRO VAL ILE ARG ARG THR ILE ASN LEU PRO THR TYR SEQRES 22 A 750 THR LEU GLU ALA VAL TYR GLU ALA VAL PHE GLY LYS PRO SEQRES 23 A 750 LYS GLU LYS VAL TYR ALA GLU GLU ILE ALA GLN ALA TRP SEQRES 24 A 750 GLU THR GLY GLU GLY LEU GLU ARG VAL ALA ARG TYR SER SEQRES 25 A 750 MET GLU ASP ALA LYS VAL THR TYR GLU LEU GLY LYS GLU SEQRES 26 A 750 PHE LEU PRO MET GLU ALA GLN LEU SER ARG LEU VAL GLY SEQRES 27 A 750 GLN PRO LEU TRP ASP VAL SER ARG SER SER THR GLY ASN SEQRES 28 A 750 LEU VAL GLU TRP TYR LEU LEU ARG LYS ALA TYR GLU ARG SEQRES 29 A 750 ASN GLU LEU ALA PRO ASN LYS PRO ASP GLU ARG GLU TYR SEQRES 30 A 750 GLU ARG ARG LEU ARG GLU SER TYR ALA GLY GLY TYR VAL SEQRES 31 A 750 LYS GLU PRO GLU LYS GLY LEU TRP GLU ASN ILE VAL TYR SEQRES 32 A 750 LEU ASP PHE ARG SER LEU TYR PRO SER ILE ILE ILE THR SEQRES 33 A 750 HIS ASN VAL SER PRO ASP THR LEU ASN ARG GLU GLY CYS SEQRES 34 A 750 LYS GLU TYR ASP VAL ALA PRO GLN VAL GLY HIS ARG PHE SEQRES 35 A 750 CYS LYS ASP PHE PRO GLY PHE ILE PRO SER LEU LEU GLY SEQRES 36 A 750 ASP LEU LEU GLU GLU ARG GLN LYS ILE LYS ARG LYS MET SEQRES 37 A 750 LYS ALA THR VAL ASP PRO LEU GLU LYS LYS LEU LEU ASP SEQRES 38 A 750 TYR ARG GLN ARG ARG ILE LYS ILE LEU ALA SER SER TYR SEQRES 39 A 750 TYR GLY TYR TYR GLY TYR ALA ARG ALA ARG TRP TYR CYS SEQRES 40 A 750 LYS GLU CYS ALA GLU SER VAL THR ALA TRP GLY ARG GLN SEQRES 41 A 750 TYR ILE GLU THR THR ILE ARG GLU ILE GLU GLU LYS PHE SEQRES 42 A 750 GLY PHE LYS VAL LEU TYR ALA ASP THR ASP GLY PHE PHE SEQRES 43 A 750 ALA THR ILE PRO GLY ALA ASP ALA GLU THR VAL LYS LYS SEQRES 44 A 750 LYS ALA LYS GLU PHE LEU ASP TYR ILE ASN ALA LYS LEU SEQRES 45 A 750 PRO GLY LEU LEU GLU LEU GLU TYR GLU GLY PHE TYR LYS SEQRES 46 A 750 ARG GLY PHE PHE VAL THR LYS LYS LYS TYR ALA VAL ILE SEQRES 47 A 750 ASP GLU GLU ASP LYS ILE THR THR GLY GLY LEU GLU ILE SEQRES 48 A 750 VAL ARG ARG GLY TRP SER GLU ILE ALA LYS GLU THR GLN SEQRES 49 A 750 ALA ARG VAL LEU GLU ALA LEU LEU LYS ASP GLY ASP VAL SEQRES 50 A 750 GLU LYS ALA VAL ARG ILE VAL LYS GLU VAL THR GLU LYS SEQRES 51 A 750 LEU SER LYS TYR GLU VAL PRO PRO GLU LYS LEU VAL ILE SEQRES 52 A 750 HIS GLU GLN ILE THR ARG ASP LEU ARG ASP TYR LYS ALA SEQRES 53 A 750 THR GLY PRO HIS VAL ALA VAL ALA LYS ARG LEU ALA ALA SEQRES 54 A 750 ARG GLY VAL LYS ILE ARG PRO GLY THR VAL ILE SER TYR SEQRES 55 A 750 ILE VAL LEU LYS GLY SER GLY ARG ILE GLY ASP ARG ALA SEQRES 56 A 750 ILE SER PHE ASP GLU PHE ASP PRO ALA LYS HIS LYS TYR SEQRES 57 A 750 ASP ALA GLU TYR TYR ILE GLU ASN GLN VAL LEU PRO PRO SEQRES 58 A 750 VAL GLU ARG ILE LEU ARG ALA CYS GLY SEQRES 1 T 21 DT DA DT DG DC DA DC DG DT DA DC DG DC SEQRES 2 T 21 DA DG DT DT DC DG DC DG SEQRES 1 P 12 DC DG DC DG DA DA DC DT DG DC DG YTI HET YTI P 12 18 HET 9O7 A 801 29 HET MG A 802 1 HET IOD A 803 1 HET CL A 804 1 HETNAM YTI (3R,5R)-5-(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN- HETNAM 2 YTI 1(2H)-YL)OXOLAN-3-YL DIHYDROGEN PHOSPHATE HETNAM 9O7 [(3~{S},4~{R},5~{R})-5-(6-AMINOPURIN-9-YL)-4-OXIDANYL- HETNAM 2 9O7 OXOLAN-3-YL] [OXIDANYL(PHOSPHONOOXY)PHOSPHORYL] HETNAM 3 9O7 HYDROGEN PHOSPHATE HETNAM MG MAGNESIUM ION HETNAM IOD IODIDE ION HETNAM CL CHLORIDE ION FORMUL 3 YTI C9 H13 N2 O7 P FORMUL 4 9O7 C9 H14 N5 O12 P3 FORMUL 5 MG MG 2+ FORMUL 6 IOD I 1- FORMUL 7 CL CL 1- FORMUL 8 HOH *68(H2 O) HELIX 1 AA1 ASP A 44 SER A 46 5 3 HELIX 2 AA2 ALA A 47 LYS A 52 1 6 HELIX 3 AA3 GLN A 91 ALA A 102 1 12 HELIX 4 AA4 PRO A 115 LYS A 124 1 10 HELIX 5 AA5 THR A 186 ASP A 202 1 17 HELIX 6 AA6 PHE A 214 GLY A 227 1 14 HELIX 7 AA7 LEU A 260 ARG A 266 1 7 HELIX 8 AA8 THR A 274 GLY A 284 1 11 HELIX 9 AA9 TYR A 291 GLY A 302 1 12 HELIX 10 AB1 GLY A 304 GLY A 338 1 35 HELIX 11 AB2 PRO A 340 SER A 345 1 6 HELIX 12 AB3 SER A 348 ARG A 364 1 17 HELIX 13 AB4 ASP A 373 GLU A 383 1 11 HELIX 14 AB5 SER A 408 ASN A 418 1 11 HELIX 15 AB6 ILE A 450 ALA A 470 1 21 HELIX 16 AB7 ASP A 473 GLY A 499 1 27 HELIX 17 AB8 CYS A 507 LYS A 532 1 26 HELIX 18 AB9 ASP A 553 ALA A 570 1 18 HELIX 19 AC1 SER A 617 LYS A 633 1 17 HELIX 20 AC2 ASP A 636 LYS A 653 1 18 HELIX 21 AC3 PRO A 657 VAL A 662 5 6 HELIX 22 AC4 ASP A 670 TYR A 674 5 5 HELIX 23 AC5 GLY A 678 ARG A 690 1 13 HELIX 24 AC6 ASP A 729 GLN A 737 1 9 HELIX 25 AC7 VAL A 738 ARG A 744 1 7 SHEET 1 AA1 3 ILE A 2 GLU A 10 0 SHEET 2 AA1 3 LYS A 13 GLU A 22 -1 O PHE A 19 N LEU A 3 SHEET 3 AA1 3 GLU A 25 ASP A 31 -1 O LYS A 27 N LYS A 20 SHEET 1 AA2 4 ARG A 67 PHE A 75 0 SHEET 2 AA2 4 ARG A 78 TYR A 86 -1 O LYS A 84 N GLU A 69 SHEET 3 AA2 4 TYR A 37 LEU A 42 -1 N PHE A 38 O LEU A 85 SHEET 4 AA2 4 VAL A 106 TYR A 110 -1 O ASP A 108 N LEU A 41 SHEET 1 AA3 2 ALA A 56 ARG A 58 0 SHEET 2 AA3 2 THR A 61 VAL A 63 -1 O VAL A 63 N ALA A 56 SHEET 1 AA4 6 VAL A 181 VAL A 183 0 SHEET 2 AA4 6 GLY A 167 THR A 172 1 N VAL A 170 O ASP A 182 SHEET 3 AA4 6 ILE A 157 ASP A 164 -1 N ILE A 160 O ILE A 171 SHEET 4 AA4 6 MET A 137 THR A 144 -1 N ALA A 139 O ALA A 163 SHEET 5 AA4 6 VAL A 205 THR A 208 1 O ILE A 207 N LEU A 138 SHEET 6 AA4 6 ILE A 256 ASP A 259 1 O PHE A 258 N LEU A 206 SHEET 1 AA5 2 LYS A 240 MET A 244 0 SHEET 2 AA5 2 ARG A 247 GLU A 251 -1 O ALA A 249 N GLN A 242 SHEET 1 AA6 6 LYS A 536 ALA A 540 0 SHEET 2 AA6 6 GLY A 544 THR A 548 -1 O THR A 548 N LYS A 536 SHEET 3 AA6 6 LEU A 397 PHE A 406 -1 N VAL A 402 O ALA A 547 SHEET 4 AA6 6 LEU A 578 THR A 591 -1 O GLU A 579 N ASP A 405 SHEET 5 AA6 6 LYS A 594 ILE A 598 -1 O ILE A 598 N ARG A 586 SHEET 6 AA6 6 ILE A 604 GLY A 607 -1 O GLY A 607 N TYR A 595 SHEET 1 AA7 2 TYR A 432 VAL A 434 0 SHEET 2 AA7 2 ARG A 441 CYS A 443 -1 O PHE A 442 N ASP A 433 SHEET 1 AA8 3 ILE A 663 GLN A 666 0 SHEET 2 AA8 3 VAL A 699 VAL A 704 -1 O ILE A 700 N GLU A 665 SHEET 3 AA8 3 ALA A 715 SER A 717 -1 O ILE A 716 N ILE A 703 SSBOND 1 CYS A 429 CYS A 443 1555 1555 2.04 SSBOND 2 CYS A 507 CYS A 510 1555 1555 2.05 LINK O3' DG P 11 P YTI P 12 1555 1555 1.60 LINK OD2 ASP A 405 MG MG A 802 1555 1555 2.31 LINK O PHE A 406 MG MG A 802 1555 1555 2.04 LINK OD2 ASP A 543 MG MG A 802 1555 1555 1.96 LINK O1A 9O7 A 801 MG MG A 802 1555 1555 2.70 LINK O2B 9O7 A 801 MG MG A 802 1555 1555 2.42 LINK O1G 9O7 A 801 MG MG A 802 1555 1555 2.13 CRYST1 77.713 101.530 110.675 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 0.012868 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009849 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009035 0.00000 CONECT 3343 6808 CONECT 3347 6808 CONECT 3534 3649 CONECT 3649 3534 CONECT 4194 4218 CONECT 4218 4194 CONECT 4491 6808 CONECT 6746 6760 CONECT 6760 6746 6761 6762 6766 CONECT 6761 6760 CONECT 6762 6760 CONECT 6763 6764 6765 CONECT 6764 6763 6768 CONECT 6765 6763 6766 6767 CONECT 6766 6760 6765 CONECT 6767 6765 6768 CONECT 6768 6764 6767 6769 CONECT 6769 6768 6770 6776 CONECT 6770 6769 6771 6772 CONECT 6771 6770 CONECT 6772 6770 6773 CONECT 6773 6772 6774 6775 CONECT 6774 6773 CONECT 6775 6773 6776 6777 CONECT 6776 6769 6775 CONECT 6777 6775 CONECT 6779 6780 6784 CONECT 6780 6779 6781 CONECT 6781 6780 6782 CONECT 6782 6781 6783 6788 CONECT 6783 6782 6784 6786 CONECT 6784 6779 6783 6785 CONECT 6785 6784 CONECT 6786 6783 6787 CONECT 6787 6786 6788 CONECT 6788 6782 6787 6792 CONECT 6789 6793 6797 6801 6802 CONECT 6790 6794 6798 6802 6803 CONECT 6791 6799 6803 6804 6807 CONECT 6792 6788 6795 6806 CONECT 6793 6789 6808 CONECT 6794 6790 CONECT 6795 6792 6796 6800 CONECT 6796 6795 CONECT 6797 6789 CONECT 6798 6790 6808 CONECT 6799 6791 CONECT 6800 6795 6801 6805 CONECT 6801 6789 6800 CONECT 6802 6789 6790 CONECT 6803 6790 6791 CONECT 6804 6791 CONECT 6805 6800 6806 CONECT 6806 6792 6805 CONECT 6807 6791 6808 CONECT 6808 3343 3347 4491 6793 CONECT 6808 6798 6807 MASTER 406 0 5 25 28 0 0 6 6875 3 57 61 END