PDB Short entry for 5VU8 HEADER TRANSFERASE/DNA 18-MAY-17 5VU8 TITLE TNA POLYMERASE, CLOSED 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 5VU8 1 JRNL REVDAT 1 06-DEC-17 5VU8 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. 3.20 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) : 3.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.42 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 19544 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.261 REMARK 3 R VALUE (WORKING SET) : 0.258 REMARK 3 FREE R VALUE : 0.295 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.270 REMARK 3 FREE R VALUE TEST SET COUNT : 1616 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 43.4283 - 7.3155 1.00 1611 145 0.2292 0.2734 REMARK 3 2 7.3155 - 5.8109 1.00 1542 138 0.2808 0.2775 REMARK 3 3 5.8109 - 5.0777 1.00 1508 136 0.2319 0.2692 REMARK 3 4 5.0777 - 4.6140 1.00 1496 134 0.1999 0.2725 REMARK 3 5 4.6140 - 4.2836 1.00 1472 133 0.2134 0.2634 REMARK 3 6 4.2836 - 4.0312 0.99 1476 134 0.2333 0.2639 REMARK 3 7 4.0312 - 3.8295 1.00 1474 132 0.2986 0.3842 REMARK 3 8 3.8295 - 3.6629 1.00 1488 135 0.2966 0.3067 REMARK 3 9 3.6629 - 3.5219 0.99 1468 134 0.3288 0.3783 REMARK 3 10 3.5219 - 3.4004 0.99 1465 130 0.3324 0.3267 REMARK 3 11 3.4004 - 3.2941 1.00 1456 131 0.3442 0.3672 REMARK 3 12 3.2941 - 3.2000 1.00 1472 134 0.3656 0.3855 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) : 0.510 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 35.980 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 : 0.002 6880 REMARK 3 ANGLE : 0.540 9410 REMARK 3 CHIRALITY : 0.039 1019 REMARK 3 PLANARITY : 0.003 1108 REMARK 3 DIHEDRAL : 13.321 4056 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 5 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 214 ) REMARK 3 ORIGIN FOR THE GROUP (A): 101.3459 143.6048 483.5694 REMARK 3 T TENSOR REMARK 3 T11: 0.8711 T22: 0.7755 REMARK 3 T33: 0.8494 T12: -0.0765 REMARK 3 T13: 0.0027 T23: -0.0414 REMARK 3 L TENSOR REMARK 3 L11: 3.3297 L22: 2.0447 REMARK 3 L33: 0.8314 L12: -1.6776 REMARK 3 L13: 0.5963 L23: -0.0637 REMARK 3 S TENSOR REMARK 3 S11: -0.0172 S12: -0.0090 S13: 0.1208 REMARK 3 S21: 0.1733 S22: -0.0579 S23: -0.1305 REMARK 3 S31: 0.0815 S32: -0.0392 S33: 0.0000 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 215 THROUGH 588 ) REMARK 3 ORIGIN FOR THE GROUP (A): 88.9518 126.4301 468.5344 REMARK 3 T TENSOR REMARK 3 T11: 0.8089 T22: 0.8687 REMARK 3 T33: 0.8614 T12: -0.0386 REMARK 3 T13: 0.0558 T23: 0.0596 REMARK 3 L TENSOR REMARK 3 L11: 0.4117 L22: 1.4023 REMARK 3 L33: 1.1904 L12: -0.2256 REMARK 3 L13: 0.0915 L23: 0.7327 REMARK 3 S TENSOR REMARK 3 S11: 0.0648 S12: 0.0675 S13: 0.0874 REMARK 3 S21: -0.1769 S22: -0.0914 S23: 0.1076 REMARK 3 S31: 0.0951 S32: -0.1910 S33: -0.0000 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 589 THROUGH 758 ) REMARK 3 ORIGIN FOR THE GROUP (A): 78.2455 137.4132 443.3424 REMARK 3 T TENSOR REMARK 3 T11: 1.6120 T22: 1.2490 REMARK 3 T33: 1.2106 T12: 0.2254 REMARK 3 T13: -0.0451 T23: 0.1128 REMARK 3 L TENSOR REMARK 3 L11: 0.8290 L22: 1.2130 REMARK 3 L33: 1.4039 L12: -0.8331 REMARK 3 L13: -0.6362 L23: 0.0168 REMARK 3 S TENSOR REMARK 3 S11: 0.1161 S12: 0.4472 S13: 0.4819 REMARK 3 S21: -0.3707 S22: 0.1822 S23: 0.4877 REMARK 3 S31: -0.5770 S32: -0.5662 S33: 0.0001 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'T' AND (RESID 3 THROUGH 16 ) REMARK 3 ORIGIN FOR THE GROUP (A): 95.3501 131.1330 445.1907 REMARK 3 T TENSOR REMARK 3 T11: 1.6975 T22: 1.1681 REMARK 3 T33: 1.2435 T12: -0.0571 REMARK 3 T13: -0.0620 T23: 0.2696 REMARK 3 L TENSOR REMARK 3 L11: 0.5321 L22: 0.2310 REMARK 3 L33: 0.0626 L12: -0.3609 REMARK 3 L13: 0.1943 L23: -0.1238 REMARK 3 S TENSOR REMARK 3 S11: -0.3327 S12: 0.6253 S13: 0.9054 REMARK 3 S21: -0.8580 S22: -0.0309 S23: -0.4669 REMARK 3 S31: -0.7154 S32: 0.6000 S33: -0.0003 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'P' AND (RESID 1 THROUGH 11 ) REMARK 3 ORIGIN FOR THE GROUP (A): 93.9169 131.3241 441.4398 REMARK 3 T TENSOR REMARK 3 T11: 2.0844 T22: 1.4894 REMARK 3 T33: 0.9649 T12: 0.0067 REMARK 3 T13: -0.1040 T23: 0.1114 REMARK 3 L TENSOR REMARK 3 L11: 0.0096 L22: 0.0605 REMARK 3 L33: -0.0042 L12: 0.0366 REMARK 3 L13: -0.0032 L23: -0.0038 REMARK 3 S TENSOR REMARK 3 S11: 0.4038 S12: 0.3457 S13: 0.0619 REMARK 3 S21: -0.1185 S22: 0.0069 S23: -0.3386 REMARK 3 S31: 0.1882 S32: 0.1587 S33: 0.0002 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 5VU8 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_1000227877. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-OCT-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.2.1 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 : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19544 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.200 REMARK 200 RESOLUTION RANGE LOW (A) : 43.424 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : 0.27500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.29 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 1.10000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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 (%): 57.66 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM SULFATE, 0.1 M MES, PH REMARK 280 4.0, 3% W/V 1,6-HEXANEDIOL, 19% 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 53.68000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 73.86600 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 53.68000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 73.86600 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: 5100 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 37850 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -49.0 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 GLU A 658 REMARK 465 ARG A 689 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 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 150 CG CD OE1 OE2 REMARK 470 GLU A 154 CG CD OE1 OE2 REMARK 470 GLU A 200 CG CD OE1 OE2 REMARK 470 LYS A 221 CG CD CE NZ REMARK 470 GLN A 285 CG CD OE1 NE2 REMARK 470 ARG A 346 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 385 CG CD OE1 OE2 REMARK 470 ARG A 394 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 476 CG CD NE CZ NH1 NH2 REMARK 470 ILE A 528 CG1 CG2 CD1 REMARK 470 LYS A 531 CG CD CE NZ REMARK 470 LYS A 638 CG CD CE NZ REMARK 470 ARG A 668 CG CD NE CZ NH1 NH2 REMARK 470 LEU A 704 CG CD1 CD2 REMARK 470 LYS A 705 CG CD CE NZ REMARK 470 ILE A 710 CG1 CG2 CD1 REMARK 470 ARG A 713 CG CD NE CZ NH1 NH2 REMARK 470 HIS A 725 CG ND1 CD2 CE1 NE2 REMARK 470 LYS A 726 CG CD CE NZ REMARK 470 TYR A 727 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ASP A 728 CG OD1 OD2 REMARK 470 GLN A 736 CG CD OE1 NE2 REMARK 470 ARG A 751 CG CD NE CZ NH1 NH2 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 OE2 GLU A 580 MG MG A 803 1.26 REMARK 500 O2A 9O7 A 801 MG MG A 802 1.33 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 DG P 11 C3' - O3' - P ANGL. DEV. = 28.6 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 52 1.95 -66.38 REMARK 500 LYS A 66 -80.08 -65.33 REMARK 500 LYS A 124 -32.83 63.19 REMARK 500 ALA A 153 41.66 -104.15 REMARK 500 ASP A 164 -140.31 -124.56 REMARK 500 SER A 185 -70.34 -76.58 REMARK 500 PHE A 214 -71.41 -128.77 REMARK 500 ARG A 255 -166.33 -119.98 REMARK 500 ARG A 364 1.34 -67.71 REMARK 500 GLN A 436 -64.14 59.06 REMARK 500 ILE A 449 -51.55 109.12 REMARK 500 TRP A 504 48.68 -88.79 REMARK 500 TYR A 532 -30.71 67.46 REMARK 500 ASP A 540 -70.43 -110.54 REMARK 500 THR A 541 -43.67 -148.99 REMARK 500 TYR A 566 59.74 -103.18 REMARK 500 ILE A 567 -37.62 -168.62 REMARK 500 ASP A 614 49.88 -95.19 REMARK 500 ASP A 633 44.18 -158.54 REMARK 500 PRO A 656 109.92 -45.90 REMARK 500 ARG A 668 -127.65 56.41 REMARK 500 ASP A 669 103.72 -160.04 REMARK 500 LEU A 670 -76.32 50.15 REMARK 500 HIS A 679 -166.78 -79.84 REMARK 500 VAL A 680 -52.28 62.05 REMARK 500 LEU A 704 -151.25 -132.87 REMARK 500 LYS A 705 -117.63 59.47 REMARK 500 ILE A 710 -115.77 68.94 REMARK 500 ILE A 715 99.54 65.02 REMARK 500 PRO A 716 -142.42 -78.24 REMARK 500 GLU A 719 75.72 -112.82 REMARK 500 THR A 723 -63.25 -99.95 REMARK 500 TYR A 731 -56.36 59.88 REMARK 500 GLN A 736 -83.79 -97.55 REMARK 500 LEU A 738 -54.62 112.32 REMARK 500 ARG A 751 34.84 -80.12 REMARK 500 LYS A 752 14.95 48.46 REMARK 500 ASP A 754 -160.12 -75.40 REMARK 500 LEU A 755 109.66 60.31 REMARK 500 ARG A 756 178.08 70.76 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 803 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 580 OE1 REMARK 620 2 9O7 A 801 O2G 78.1 REMARK 620 3 9O7 A 801 O3G 109.5 53.5 REMARK 620 4 9O7 A 801 O1G 139.6 62.0 51.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG P 101 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 9O4 P 12 O1P REMARK 620 2 9O7 A 801 O1A 95.8 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 9O7 A 801 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 802 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 803 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG P 101 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: 5VU7 RELATED DB: PDB REMARK 900 RELATED ID: 5VU9 RELATED DB: PDB DBREF 5VU8 A 1 774 UNP D0VWU9 D0VWU9_THEKO 1 774 DBREF 5VU8 T 1 16 PDB 5VU8 5VU8 1 16 DBREF 5VU8 P 1 12 PDB 5VU8 5VU8 1 12 SEQADV 5VU8 ALA A 141 UNP D0VWU9 ASP 141 ENGINEERED MUTATION SEQADV 5VU8 ALA A 143 UNP D0VWU9 GLU 143 ENGINEERED MUTATION SEQADV 5VU8 HIS A 147 UNP D0VWU9 GLU 147 ENGINEERED MUTATION SEQADV 5VU8 ARG A 485 UNP D0VWU9 ALA 485 ENGINEERED MUTATION SEQADV 5VU8 LYS A 584 UNP D0VWU9 GLU 584 ENGINEERED MUTATION SEQADV 5VU8 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 9O7 A 801 29 HET MG A 802 1 HET MG A 803 1 HET MG P 101 1 HETNAM 9O4 (3R,5R)-5-(6-AMINO-9H-PURIN-9-YL)OXOLAN-3-YL DIHYDROGEN HETNAM 2 9O4 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 FORMUL 3 9O4 C9 H12 N5 O5 P FORMUL 4 9O7 C9 H14 N5 O12 P3 FORMUL 5 MG 3(MG 2+) FORMUL 8 HOH *(H2 O) HELIX 1 AA1 ASP A 44 ILE A 48 5 5 HELIX 2 AA2 GLN A 91 GLU A 102 1 12 HELIX 3 AA3 PRO A 115 ASP A 123 1 9 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 THR A 301 1 11 HELIX 9 AA9 ASN A 304 PHE A 326 1 23 HELIX 10 AB1 PHE A 326 GLY A 338 1 13 HELIX 11 AB2 SER A 340 SER A 347 1 8 HELIX 12 AB3 SER A 348 ARG A 364 1 17 HELIX 13 AB4 ASP A 373 ARG A 380 1 8 HELIX 14 AB5 SER A 407 ASN A 417 1 11 HELIX 15 AB6 ILE A 449 ALA A 469 1 21 HELIX 16 AB7 ASP A 472 TYR A 499 1 28 HELIX 17 AB8 CYS A 506 GLU A 530 1 25 HELIX 18 AB9 ASP A 552 ALA A 569 1 18 HELIX 19 AC1 SER A 616 GLY A 634 1 19 HELIX 20 AC2 ASP A 635 LYS A 652 1 18 HELIX 21 AC3 VAL A 680 ARG A 685 1 6 HELIX 22 AC4 LEU A 738 ARG A 746 1 9 HELIX 23 AC5 ALA A 747 GLY A 749 5 3 SHEET 1 AA1 3 ILE A 2 GLU A 10 0 SHEET 2 AA1 3 LYS A 13 GLU A 22 -1 O ARG A 17 N ASP A 6 SHEET 3 AA1 3 GLU A 25 ASP A 31 -1 O GLU A 29 N ILE A 18 SHEET 1 AA2 4 VAL A 68 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 ALA A 56 GLU A 57 0 SHEET 2 AA3 2 VAL A 62 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 ALA A 168 THR A 172 1 N VAL A 170 O ASP A 182 SHEET 3 AA4 6 ILE A 157 ALA A 163 -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 LEU A 158 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 GLU A 251 N LYS A 240 SHEET 1 AA6 6 TYR A 538 SER A 539 0 SHEET 2 AA6 6 GLY A 543 ALA A 546 -1 O PHE A 545 N TYR A 538 SHEET 3 AA6 6 GLY A 395 PHE A 405 -1 N VAL A 401 O ALA A 546 SHEET 4 AA6 6 LEU A 577 THR A 590 -1 O LYS A 584 N ASN A 399 SHEET 5 AA6 6 LYS A 593 ILE A 597 -1 O ALA A 595 N PHE A 587 SHEET 6 AA6 6 ILE A 603 ARG A 606 -1 O THR A 604 N VAL A 596 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 2 ILE A 662 ILE A 666 0 SHEET 2 AA8 2 THR A 697 TYR A 701 -1 O THR A 697 N ILE A 666 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 OE1 GLU A 580 MG MG A 803 1555 1555 2.89 LINK O3' DG P 11 P 9O4 P 12 1555 1555 1.60 LINK O1P 9O4 P 12 MG MG P 101 1555 1555 2.74 LINK O1A 9O7 A 801 MG MG A 802 1555 1555 2.43 LINK O1A 9O7 A 801 MG MG P 101 1555 1555 2.46 LINK O2G 9O7 A 801 MG MG A 803 1555 1555 2.02 LINK O3G 9O7 A 801 MG MG A 803 1555 1555 2.84 LINK O1G 9O7 A 801 MG MG A 803 1555 1555 2.42 CISPEP 1 ARG A 709 ILE A 710 0 20.99 CISPEP 2 ALA A 714 ILE A 715 0 12.12 CISPEP 3 ARG A 756 TYR A 757 0 12.85 CISPEP 4 GLN A 758 LYS A 759 0 0.97 SITE 1 AC1 16 ASP A 404 PHE A 405 SER A 407 ARG A 460 SITE 2 AC1 16 LYS A 487 ASN A 491 THR A 541 ASP A 542 SITE 3 AC1 16 GLU A 578 GLU A 580 MG A 802 MG A 803 SITE 4 AC1 16 9O4 P 12 MG P 101 DT T 4 DT T 5 SITE 1 AC2 3 TYR A 402 ASP A 542 9O7 A 801 SITE 1 AC3 3 GLU A 578 GLU A 580 9O7 A 801 SITE 1 AC4 3 LYS A 487 9O7 A 801 9O4 P 12 CRYST1 72.288 107.360 147.732 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 0.013834 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009314 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006769 0.00000