HEADER TRANSFERASE/DNA 18-MAY-17 5VU7 TITLE TNA POLYMERASE, OPEN TERNARY COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: KOD-RI; COMPND 5 EC: 2.7.7.7; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA TEMPLATE; COMPND 9 CHAIN: T; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: DNA/TNA HYBRID PRIMER; COMPND 13 CHAIN: P; COMPND 14 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 PROTEIN-NUCLEIC ACID COMPLEX, TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR N.CHIM,J.C.CHAPUT REVDAT 2 13-DEC-17 5VU7 1 JRNL REVDAT 1 06-DEC-17 5VU7 0 JRNL AUTH N.CHIM,C.SHI,S.P.SAU,A.NIKOOMANZAR,J.C.CHAPUT JRNL TITL STRUCTURAL BASIS FOR TNA SYNTHESIS BY AN ENGINEERED TNA JRNL TITL 2 POLYMERASE. JRNL REF NAT COMMUN V. 8 1810 2017 JRNL REFN ESSN 2041-1723 JRNL PMID 29180809 JRNL DOI 10.1038/S41467-017-02014-0 REMARK 2 REMARK 2 RESOLUTION. 2.72 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.11.1_2575: ???) 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) : 2.72 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.10 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 3 NUMBER OF REFLECTIONS : 29340 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.218 REMARK 3 R VALUE (WORKING SET) : 0.214 REMARK 3 FREE R VALUE : 0.268 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.810 REMARK 3 FREE R VALUE TEST SET COUNT : 1998 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 49.1056 - 6.5510 0.95 2046 149 0.1781 0.2173 REMARK 3 2 6.5510 - 5.2016 0.97 1994 146 0.1892 0.2139 REMARK 3 3 5.2016 - 4.5446 0.97 1960 143 0.1628 0.2122 REMARK 3 4 4.5446 - 4.1293 0.97 1957 143 0.1684 0.2226 REMARK 3 5 4.1293 - 3.8335 0.97 1950 142 0.1903 0.2455 REMARK 3 6 3.8335 - 3.6075 0.98 1960 144 0.2083 0.2710 REMARK 3 7 3.6075 - 3.4269 0.98 1928 141 0.2240 0.2958 REMARK 3 8 3.4269 - 3.2778 0.97 1939 140 0.2424 0.3031 REMARK 3 9 3.2778 - 3.1516 0.98 1931 141 0.2790 0.3703 REMARK 3 10 3.1516 - 3.0429 0.98 1931 142 0.2836 0.3311 REMARK 3 11 3.0429 - 2.9477 0.98 1937 142 0.2765 0.3080 REMARK 3 12 2.9477 - 2.8635 0.98 1940 142 0.2922 0.3755 REMARK 3 13 2.8635 - 2.7881 0.98 1923 141 0.3079 0.3873 REMARK 3 14 2.7881 - 2.7201 0.98 1946 142 0.3304 0.3685 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) : 0.410 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.760 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 6947 REMARK 3 ANGLE : 0.624 9478 REMARK 3 CHIRALITY : 0.043 1017 REMARK 3 PLANARITY : 0.004 1123 REMARK 3 DIHEDRAL : 20.216 4111 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 156 ) REMARK 3 ORIGIN FOR THE GROUP (A): 34.7458 34.9082 328.5966 REMARK 3 T TENSOR REMARK 3 T11: 0.3328 T22: 0.3336 REMARK 3 T33: 0.4262 T12: -0.0350 REMARK 3 T13: -0.0423 T23: -0.0128 REMARK 3 L TENSOR REMARK 3 L11: 2.5415 L22: 2.1353 REMARK 3 L33: 0.8422 L12: -1.4313 REMARK 3 L13: 0.7391 L23: -0.0865 REMARK 3 S TENSOR REMARK 3 S11: 0.0177 S12: 0.0209 S13: 0.1049 REMARK 3 S21: 0.1407 S22: 0.0114 S23: -0.4929 REMARK 3 S31: 0.0224 S32: 0.2119 S33: -0.0001 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 157 THROUGH 304 ) REMARK 3 ORIGIN FOR THE GROUP (A): 9.3937 50.1824 317.5625 REMARK 3 T TENSOR REMARK 3 T11: 0.2522 T22: 0.3360 REMARK 3 T33: 0.2915 T12: -0.0270 REMARK 3 T13: 0.0224 T23: 0.0215 REMARK 3 L TENSOR REMARK 3 L11: 1.8289 L22: 3.1768 REMARK 3 L33: 2.0536 L12: -0.4898 REMARK 3 L13: 0.4938 L23: -0.8292 REMARK 3 S TENSOR REMARK 3 S11: 0.0257 S12: 0.1804 S13: 0.0598 REMARK 3 S21: -0.0511 S22: 0.0469 S23: -0.0501 REMARK 3 S31: 0.0103 S32: 0.0963 S33: 0.0000 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 305 THROUGH 532 ) REMARK 3 ORIGIN FOR THE GROUP (A): 18.0552 16.0635 317.5585 REMARK 3 T TENSOR REMARK 3 T11: 0.3680 T22: 0.3831 REMARK 3 T33: 0.3717 T12: -0.0207 REMARK 3 T13: -0.0757 T23: 0.0025 REMARK 3 L TENSOR REMARK 3 L11: 0.3869 L22: 1.3264 REMARK 3 L33: 0.6197 L12: 0.0225 REMARK 3 L13: 0.0959 L23: -0.2540 REMARK 3 S TENSOR REMARK 3 S11: -0.0471 S12: 0.0041 S13: -0.0559 REMARK 3 S21: -0.0961 S22: 0.0844 S23: -0.0190 REMARK 3 S31: 0.2348 S32: -0.0440 S33: -0.0002 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 533 THROUGH 756 ) REMARK 3 ORIGIN FOR THE GROUP (A): 1.9169 22.1577 295.2364 REMARK 3 T TENSOR REMARK 3 T11: 0.6294 T22: 0.4678 REMARK 3 T33: 0.5029 T12: -0.0984 REMARK 3 T13: -0.2487 T23: 0.0712 REMARK 3 L TENSOR REMARK 3 L11: 0.4586 L22: 3.6751 REMARK 3 L33: 1.8600 L12: -0.1507 REMARK 3 L13: -0.2360 L23: -1.2257 REMARK 3 S TENSOR REMARK 3 S11: -0.0208 S12: 0.0703 S13: 0.0069 REMARK 3 S21: -0.8384 S22: 0.2972 S23: 0.6877 REMARK 3 S31: 0.3910 S32: -0.2373 S33: 0.0201 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'T' AND (RESID 3 THROUGH 15 ) REMARK 3 ORIGIN FOR THE GROUP (A): 18.0199 22.6562 293.4303 REMARK 3 T TENSOR REMARK 3 T11: 0.8614 T22: 0.6023 REMARK 3 T33: 0.3796 T12: -0.0175 REMARK 3 T13: -0.0483 T23: 0.0094 REMARK 3 L TENSOR REMARK 3 L11: 0.6248 L22: 0.8045 REMARK 3 L33: 0.5765 L12: -0.6361 REMARK 3 L13: -0.0948 L23: -0.2297 REMARK 3 S TENSOR REMARK 3 S11: 0.3056 S12: 0.3133 S13: 0.0573 REMARK 3 S21: -0.6323 S22: -0.1939 S23: -0.5915 REMARK 3 S31: 0.0297 S32: 0.1100 S33: -0.0034 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'P' AND (RESID 1 THROUGH 11 ) REMARK 3 ORIGIN FOR THE GROUP (A): 17.6407 22.8727 287.8117 REMARK 3 T TENSOR REMARK 3 T11: 1.1142 T22: 0.8516 REMARK 3 T33: 0.4985 T12: 0.0855 REMARK 3 T13: -0.0483 T23: 0.0127 REMARK 3 L TENSOR REMARK 3 L11: 0.3469 L22: 0.2119 REMARK 3 L33: 0.0037 L12: 0.2596 REMARK 3 L13: -0.0306 L23: -0.0157 REMARK 3 S TENSOR REMARK 3 S11: 0.1963 S12: 0.4517 S13: 0.1525 REMARK 3 S21: -0.9653 S22: 0.1274 S23: -0.2543 REMARK 3 S31: 1.4461 S32: 0.7162 S33: 0.0129 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 5VU7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-MAY-17. REMARK 100 THE DEPOSITION ID IS D_1000227862. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-JUL-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL14-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 325 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29340 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.720 REMARK 200 RESOLUTION RANGE LOW (A) : 49.100 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.07380 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.72 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.79 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.57500 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: NULL 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 (%): 55.46 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.76 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM SULFATE, 0.1 M MES, PH REMARK 280 5.5, 3% W/V 1,6-HEXANEDIOL, 22% PEG3350, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 X,-Y,-Z REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 -X,-Y+1/2,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 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 56.30500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 72.73000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 56.30500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 72.73000 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 TOTAL BURIED SURFACE AREA: 5790 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 36020 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -44.0 KCAL/MOL 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 TYR A 757 REMARK 465 GLN A 758 REMARK 465 LYS A 759 REMARK 465 THR A 760 REMARK 465 ARG A 761 REMARK 465 GLN A 762 REMARK 465 VAL A 763 REMARK 465 GLY A 764 REMARK 465 LEU A 765 REMARK 465 SER A 766 REMARK 465 ALA A 767 REMARK 465 TRP A 768 REMARK 465 LEU A 769 REMARK 465 LYS A 770 REMARK 465 PRO A 771 REMARK 465 LYS A 772 REMARK 465 GLY A 773 REMARK 465 THR A 774 REMARK 465 DA T 1 REMARK 465 DA T 2 REMARK 465 DG T 16 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 OG SER A 419 OD1 ASP A 421 2.13 REMARK 500 NH1 ARG A 58 OD1 ASP A 92 2.15 REMARK 500 NH2 ARG A 689 OE2 GLU A 719 2.16 REMARK 500 NH2 ARG A 265 OE1 GLN A 665 2.16 REMARK 500 OE1 GLU A 354 OH TYR A 496 2.18 REMARK 500 NH2 ARG A 685 O GLY A 711 2.19 REMARK 500 OE1 GLU A 580 OH TYR A 583 2.19 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 DC P 7 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 DC P 10 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DG P 11 C3' - O3' - P ANGL. DEV. = -7.7 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASP A 6 -159.45 -157.94 REMARK 500 LYS A 53 33.45 -91.56 REMARK 500 ARG A 58 -76.07 -121.12 REMARK 500 HIS A 59 76.58 -116.21 REMARK 500 GLU A 148 -59.69 -29.38 REMARK 500 GLU A 151 151.61 75.97 REMARK 500 ASP A 164 -158.66 -156.64 REMARK 500 PHE A 214 -64.33 -126.06 REMARK 500 ARG A 247 -178.40 -69.72 REMARK 500 GLN A 436 -61.84 66.85 REMARK 500 TRP A 504 37.33 -86.97 REMARK 500 SER A 539 120.37 -171.74 REMARK 500 THR A 541 -58.82 74.04 REMARK 500 THR A 590 -179.57 -170.71 REMARK 500 GLU A 600 -9.41 -52.26 REMARK 500 ASP A 614 30.68 -90.74 REMARK 500 ALA A 629 -70.44 -58.95 REMARK 500 TYR A 653 18.57 56.44 REMARK 500 TYR A 673 111.90 -19.78 REMARK 500 ARG A 689 -159.82 -76.65 REMARK 500 GLN A 736 -66.89 -103.51 REMARK 500 VAL A 737 -71.65 -70.13 REMARK 500 ARG A 746 42.15 -73.39 REMARK 500 LYS A 752 -35.33 -37.90 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 FA2 A 803 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 801 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 802 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FA2 A 803 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5VU5 RELATED DB: PDB REMARK 900 RELATED ID: 5VU6 RELATED DB: PDB REMARK 900 RELATED ID: 5VU8 RELATED DB: PDB REMARK 900 RELATED ID: 5VU9 RELATED DB: PDB DBREF 5VU7 A 1 774 UNP D0VWU9 D0VWU9_THEKO 1 774 DBREF 5VU7 T 1 16 PDB 5VU7 5VU7 1 16 DBREF 5VU7 P 1 12 PDB 5VU7 5VU7 1 12 SEQADV 5VU7 ALA A 141 UNP D0VWU9 ASP 141 ENGINEERED MUTATION SEQADV 5VU7 ALA A 143 UNP D0VWU9 GLU 143 ENGINEERED MUTATION SEQADV 5VU7 HIS A 147 UNP D0VWU9 GLU 147 ENGINEERED MUTATION SEQADV 5VU7 ARG A 485 UNP D0VWU9 ALA 485 ENGINEERED MUTATION SEQADV 5VU7 LYS A 584 UNP D0VWU9 GLU 584 ENGINEERED MUTATION SEQADV 5VU7 ILE A 664 UNP D0VWU9 GLU 664 ENGINEERED MUTATION SEQRES 1 A 774 MET ILE LEU ASP THR ASP TYR ILE THR GLU ASP GLY LYS SEQRES 2 A 774 PRO VAL ILE ARG ILE PHE LYS LYS GLU ASN GLY GLU PHE SEQRES 3 A 774 LYS ILE GLU TYR ASP ARG THR PHE GLU PRO TYR PHE TYR SEQRES 4 A 774 ALA LEU LEU LYS ASP ASP SER ALA ILE GLU GLU VAL LYS SEQRES 5 A 774 LYS ILE THR ALA GLU ARG HIS GLY THR VAL VAL THR VAL SEQRES 6 A 774 LYS ARG VAL GLU LYS VAL GLN LYS LYS PHE LEU GLY ARG SEQRES 7 A 774 PRO VAL GLU VAL TRP LYS LEU TYR PHE THR HIS PRO GLN SEQRES 8 A 774 ASP VAL PRO ALA ILE ARG ASP LYS ILE ARG GLU HIS PRO SEQRES 9 A 774 ALA VAL ILE ASP ILE TYR GLU TYR ASP ILE PRO PHE ALA SEQRES 10 A 774 LYS ARG TYR LEU ILE ASP LYS GLY LEU VAL PRO MET GLU SEQRES 11 A 774 GLY ASP GLU GLU LEU LYS MET LEU ALA PHE ALA ILE ALA SEQRES 12 A 774 THR LEU TYR HIS GLU GLY GLU GLU PHE ALA GLU GLY PRO SEQRES 13 A 774 ILE LEU MET ILE SER TYR ALA ASP GLU GLU GLY ALA ARG SEQRES 14 A 774 VAL ILE THR TRP LYS ASN VAL ASP LEU PRO TYR VAL ASP SEQRES 15 A 774 VAL VAL SER THR GLU ARG GLU MET ILE LYS ARG PHE LEU SEQRES 16 A 774 ARG VAL VAL LYS GLU LYS ASP PRO ASP VAL LEU ILE THR SEQRES 17 A 774 TYR ASN GLY ASP ASN PHE ASP PHE ALA TYR LEU LYS LYS SEQRES 18 A 774 ARG CYS GLU LYS LEU GLY ILE ASN PHE ALA LEU GLY ARG SEQRES 19 A 774 ASP GLY SER GLU PRO LYS ILE GLN ARG MET GLY ASP ARG SEQRES 20 A 774 PHE ALA VAL GLU VAL LYS GLY ARG ILE HIS PHE ASP LEU SEQRES 21 A 774 TYR PRO VAL ILE ARG ARG THR ILE ASN LEU PRO THR TYR SEQRES 22 A 774 THR LEU GLU ALA VAL TYR GLU ALA VAL PHE GLY GLN PRO SEQRES 23 A 774 LYS GLU LYS VAL TYR ALA GLU GLU ILE THR THR ALA TRP SEQRES 24 A 774 GLU THR GLY GLU ASN LEU GLU ARG VAL ALA ARG TYR SER SEQRES 25 A 774 MET GLU ASP ALA LYS VAL THR TYR GLU LEU GLY LYS GLU SEQRES 26 A 774 PHE LEU PRO MET GLU ALA GLN LEU SER ARG LEU ILE GLY SEQRES 27 A 774 GLN SER LEU TRP ASP VAL SER ARG SER SER THR GLY ASN SEQRES 28 A 774 LEU VAL GLU TRP PHE LEU LEU ARG LYS ALA TYR GLU ARG SEQRES 29 A 774 ASN GLU LEU ALA PRO ASN LYS PRO ASP GLU LYS GLU LEU SEQRES 30 A 774 ALA ARG ARG ARG GLN SER TYR GLU GLY GLY TYR VAL LYS SEQRES 31 A 774 GLU PRO GLU ARG GLY LEU TRP GLU ASN ILE VAL TYR LEU SEQRES 32 A 774 ASP PHE ARG SER LEU TYR PRO SER ILE ILE ILE THR HIS SEQRES 33 A 774 ASN VAL SER PRO ASP THR LEU ASN ARG GLU GLY CYS LYS SEQRES 34 A 774 GLU TYR ASP VAL ALA PRO GLN VAL GLY HIS ARG PHE CYS SEQRES 35 A 774 LYS ASP PHE PRO GLY PHE ILE PRO SER LEU LEU GLY ASP SEQRES 36 A 774 LEU LEU GLU GLU ARG GLN LYS ILE LYS LYS LYS MET LYS SEQRES 37 A 774 ALA THR ILE ASP PRO ILE GLU ARG LYS LEU LEU ASP TYR SEQRES 38 A 774 ARG GLN ARG ARG ILE LYS ILE LEU ALA ASN SER TYR TYR SEQRES 39 A 774 GLY TYR TYR GLY TYR ALA ARG ALA ARG TRP TYR CYS LYS SEQRES 40 A 774 GLU CYS ALA GLU SER VAL THR ALA TRP GLY ARG GLU TYR SEQRES 41 A 774 ILE THR MET THR ILE LYS GLU ILE GLU GLU LYS TYR GLY SEQRES 42 A 774 PHE LYS VAL ILE TYR SER ASP THR ASP GLY PHE PHE ALA SEQRES 43 A 774 THR ILE PRO GLY ALA ASP ALA GLU THR VAL LYS LYS LYS SEQRES 44 A 774 ALA MET GLU PHE LEU LYS TYR ILE ASN ALA LYS LEU PRO SEQRES 45 A 774 GLY ALA LEU GLU LEU GLU TYR GLU GLY PHE TYR LYS ARG SEQRES 46 A 774 GLY PHE PHE VAL THR LYS LYS LYS TYR ALA VAL ILE ASP SEQRES 47 A 774 GLU GLU GLY LYS ILE THR THR ARG GLY LEU GLU ILE VAL SEQRES 48 A 774 ARG ARG ASP TRP SER GLU ILE ALA LYS GLU THR GLN ALA SEQRES 49 A 774 ARG VAL LEU GLU ALA LEU LEU LYS ASP GLY ASP VAL GLU SEQRES 50 A 774 LYS ALA VAL ARG ILE VAL LYS GLU VAL THR GLU LYS LEU SEQRES 51 A 774 SER LYS TYR GLU VAL PRO PRO GLU LYS LEU VAL ILE HIS SEQRES 52 A 774 ILE GLN ILE THR ARG ASP LEU LYS ASP TYR LYS ALA THR SEQRES 53 A 774 GLY PRO HIS VAL ALA VAL ALA LYS ARG LEU ALA ALA ARG SEQRES 54 A 774 GLY VAL LYS ILE ARG PRO GLY THR VAL ILE SER TYR ILE SEQRES 55 A 774 VAL LEU LYS GLY SER GLY ARG ILE GLY ASP ARG ALA ILE SEQRES 56 A 774 PRO PHE ASP GLU PHE ASP PRO THR LYS HIS LYS TYR ASP SEQRES 57 A 774 ALA GLU TYR TYR ILE GLU ASN GLN VAL LEU PRO ALA VAL SEQRES 58 A 774 GLU ARG ILE LEU ARG ALA PHE GLY TYR ARG LYS GLU ASP SEQRES 59 A 774 LEU ARG TYR GLN LYS THR ARG GLN VAL GLY LEU SER ALA SEQRES 60 A 774 TRP LEU LYS PRO LYS GLY THR SEQRES 1 T 16 DA DA DA DT DT DC DG DC DA DG DT DT DC SEQRES 2 T 16 DG DC DG SEQRES 1 P 12 DC DG DC DG DA DA DC DT DG DC DG 9O4 HET 9O4 P 12 19 HET MG A 801 1 HET SO4 A 802 5 HET FA2 A 803 20 HETNAM 9O4 (3R,5R)-5-(6-AMINO-9H-PURIN-9-YL)OXOLAN-3-YL DIHYDROGEN HETNAM 2 9O4 PHOSPHATE HETNAM MG MAGNESIUM ION HETNAM SO4 SULFATE ION HETNAM FA2 5-(6-AMINO-9H-PURIN-9-YL)-4-HYDROXYTETRAHYDROFURAN-3-YL HETNAM 2 FA2 DIHYDROGEN PHOSPHATE FORMUL 3 9O4 C9 H12 N5 O5 P FORMUL 4 MG MG 2+ FORMUL 5 SO4 O4 S 2- FORMUL 6 FA2 C9 H12 N5 O6 P HELIX 1 AA1 SER A 46 LYS A 53 1 8 HELIX 2 AA2 GLN A 91 HIS A 103 1 13 HELIX 3 AA3 PRO A 115 LYS A 124 1 10 HELIX 4 AA4 THR A 186 ASP A 202 1 17 HELIX 5 AA5 PHE A 214 GLY A 227 1 14 HELIX 6 AA6 LEU A 260 ILE A 268 1 9 HELIX 7 AA7 THR A 274 GLY A 284 1 11 HELIX 8 AA8 TYR A 291 GLY A 302 1 12 HELIX 9 AA9 ASN A 304 GLY A 338 1 35 HELIX 10 AB1 SER A 340 SER A 345 1 6 HELIX 11 AB2 SER A 348 ARG A 364 1 17 HELIX 12 AB3 ASP A 373 ARG A 380 1 8 HELIX 13 AB4 SER A 407 HIS A 416 1 10 HELIX 14 AB5 GLY A 447 THR A 470 1 24 HELIX 15 AB6 ASP A 472 ASN A 491 1 20 HELIX 16 AB7 SER A 492 GLY A 498 1 7 HELIX 17 AB8 CYS A 506 LYS A 531 1 26 HELIX 18 AB9 ASP A 552 LEU A 571 1 20 HELIX 19 AC1 SER A 616 ASP A 633 1 18 HELIX 20 AC2 ASP A 635 LYS A 652 1 18 HELIX 21 AC3 PRO A 656 LEU A 660 5 5 HELIX 22 AC4 GLY A 677 ARG A 689 1 13 HELIX 23 AC5 ARG A 709 ASP A 712 5 4 HELIX 24 AC6 ASP A 718 PHE A 720 5 3 HELIX 25 AC7 ASP A 728 ASN A 735 1 8 HELIX 26 AC8 GLN A 736 ARG A 746 1 11 HELIX 27 AC9 ARG A 751 LEU A 755 5 5 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 ASP A 31 N ILE A 16 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 ALA A 40 O TRP A 83 SHEET 4 AA2 4 VAL A 106 TYR A 110 -1 O ILE A 107 N LEU A 41 SHEET 1 AA3 2 THR A 55 GLU A 57 0 SHEET 2 AA3 2 VAL A 62 THR A 64 -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 TYR A 162 O ARG A 169 SHEET 4 AA4 6 MET A 137 THR A 144 -1 N ALA A 143 O MET A 159 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 THR A 208 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 535 SER A 539 0 SHEET 2 AA6 6 GLY A 543 THR A 547 -1 O THR A 547 N LYS A 535 SHEET 3 AA6 6 GLY A 395 PHE A 405 -1 N LEU A 403 O PHE A 544 SHEET 4 AA6 6 LEU A 577 THR A 590 -1 O TYR A 583 N ILE A 400 SHEET 5 AA6 6 LYS A 593 ASP A 598 -1 O ALA A 595 N PHE A 587 SHEET 6 AA6 6 ILE A 603 ARG A 606 -1 O ARG A 606 N TYR A 594 SHEET 1 AA7 2 TYR A 431 VAL A 433 0 SHEET 2 AA7 2 ARG A 440 CYS A 442 -1 O PHE A 441 N ASP A 432 SHEET 1 AA8 3 ILE A 662 GLN A 665 0 SHEET 2 AA8 3 VAL A 698 VAL A 703 -1 O TYR A 701 N ILE A 662 SHEET 3 AA8 3 ALA A 714 PRO A 716 -1 O ILE A 715 N ILE A 702 SSBOND 1 CYS A 428 CYS A 442 1555 1555 2.03 SSBOND 2 CYS A 506 CYS A 509 1555 1555 2.03 LINK O3' DG P 11 P 9O4 P 12 1555 1555 1.60 SITE 1 AC1 1 TYR A 583 SITE 1 AC2 1 ARG A 460 SITE 1 AC3 9 PHE A 405 SER A 407 LEU A 408 TYR A 409 SITE 2 AC3 9 TYR A 494 ASP A 542 9O4 P 12 DT T 4 SITE 3 AC3 9 DT T 5 CRYST1 66.550 112.610 145.460 90.00 90.00 90.00 P 2 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 0.015026 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008880 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006875 0.00000