HEADER TRANSFERASE/DNA 20-MAY-19 6P1S TITLE POST-CATALYTIC NICKED COMPLEX OF HUMAN DNA POLYMERASE MU WITH 1-NT TITLE 2 GAPPED SUBSTRATE CONTAINING TEMPLATE 8OG AND NEWLY INCORPORATED AMP COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA-DIRECTED DNA/RNA POLYMERASE MU; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 134-494; COMPND 5 SYNONYM: POL MU,TERMINAL TRANSFERASE; COMPND 6 EC: 2.7.7.7; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: DNA (5'-D(*CP*GP*GP*CP*(8OG)P*TP*AP*CP*G)-3'); COMPND 10 CHAIN: T; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: DNA/RNA (5'-D(*CP*GP*TP*A)-R(P*A)-3'); COMPND 14 CHAIN: P; COMPND 15 ENGINEERED: YES; COMPND 16 MOL_ID: 4; COMPND 17 MOLECULE: DNA (5'-D(P*GP*CP*CP*G)-3'); COMPND 18 CHAIN: D; COMPND 19 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: POLM, POLMU; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: ROSETTA2 (DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEXM; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 14 ORGANISM_COMMON: HUMAN; SOURCE 15 ORGANISM_TAXID: 9606; SOURCE 16 MOL_ID: 3; SOURCE 17 SYNTHETIC: YES; SOURCE 18 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 19 ORGANISM_COMMON: HUMAN; SOURCE 20 ORGANISM_TAXID: 9606; SOURCE 21 MOL_ID: 4; SOURCE 22 SYNTHETIC: YES; SOURCE 23 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 24 ORGANISM_COMMON: HUMAN; SOURCE 25 ORGANISM_TAXID: 9606 KEYWDS FAMILY X POLYMERASE, NHEJ, TRANSFERASE, TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.M.KAMINSKI,L.C.PEDERSEN,K.BEBENEK,K.K.CHIRUVELLA,D.A.RAMSDEN, AUTHOR 2 T.A.KUNKEL REVDAT 4 11-OCT-23 6P1S 1 LINK REVDAT 3 18-DEC-19 6P1S 1 REMARK REVDAT 2 09-OCT-19 6P1S 1 JRNL REVDAT 1 04-SEP-19 6P1S 0 JRNL AUTH A.M.KAMINSKI,K.K.CHIRUVELLA,D.A.RAMSDEN,T.A.KUNKEL, JRNL AUTH 2 K.BEBENEK,L.C.PEDERSEN JRNL TITL UNEXPECTED BEHAVIOR OF DNA POLYMERASE MU OPPOSITE TEMPLATE JRNL TITL 2 8-OXO-7,8-DIHYDRO-2'-GUANOSINE. JRNL REF NUCLEIC ACIDS RES. V. 47 9410 2019 JRNL REFN ESSN 1362-4962 JRNL PMID 31435651 JRNL DOI 10.1093/NAR/GKZ680 REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.39 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 46541 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.173 REMARK 3 R VALUE (WORKING SET) : 0.172 REMARK 3 FREE R VALUE : 0.196 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.980 REMARK 3 FREE R VALUE TEST SET COUNT : 2320 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 31.3909 - 4.4937 1.00 2811 149 0.1716 0.1929 REMARK 3 2 4.4937 - 3.5684 1.00 2683 141 0.1429 0.1533 REMARK 3 3 3.5684 - 3.1178 1.00 2660 140 0.1664 0.1806 REMARK 3 4 3.1178 - 2.8329 1.00 2628 140 0.1926 0.2028 REMARK 3 5 2.8329 - 2.6300 1.00 2627 134 0.1919 0.2203 REMARK 3 6 2.6300 - 2.4750 1.00 2614 138 0.1851 0.2149 REMARK 3 7 2.4750 - 2.3511 1.00 2617 139 0.1758 0.2011 REMARK 3 8 2.3511 - 2.2488 1.00 2604 140 0.1734 0.2151 REMARK 3 9 2.2488 - 2.1622 1.00 2612 134 0.1719 0.2173 REMARK 3 10 2.1622 - 2.0876 1.00 2580 137 0.1705 0.1959 REMARK 3 11 2.0876 - 2.0224 1.00 2592 139 0.1713 0.2037 REMARK 3 12 2.0224 - 1.9646 1.00 2581 131 0.1720 0.2260 REMARK 3 13 1.9646 - 1.9128 1.00 2584 137 0.1822 0.2281 REMARK 3 14 1.9128 - 1.8662 0.98 2528 132 0.1737 0.2045 REMARK 3 15 1.8662 - 1.8238 0.97 2530 132 0.1861 0.2228 REMARK 3 16 1.8238 - 1.7850 0.97 2515 133 0.1989 0.2274 REMARK 3 17 1.7850 - 1.7493 0.96 2455 124 0.2289 0.2547 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) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.380 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 : 0.009 3188 REMARK 3 ANGLE : 1.087 4415 REMARK 3 CHIRALITY : 0.058 478 REMARK 3 PLANARITY : 0.007 517 REMARK 3 DIHEDRAL : 9.710 1661 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 2.9262 -4.3784 -11.4618 REMARK 3 T TENSOR REMARK 3 T11: 0.1678 T22: 0.1696 REMARK 3 T33: 0.1461 T12: 0.0043 REMARK 3 T13: 0.0041 T23: 0.0123 REMARK 3 L TENSOR REMARK 3 L11: 0.9894 L22: 0.6454 REMARK 3 L33: 0.5160 L12: -0.2336 REMARK 3 L13: -0.1327 L23: 0.0998 REMARK 3 S TENSOR REMARK 3 S11: 0.0543 S12: 0.1004 S13: 0.0678 REMARK 3 S21: -0.0357 S22: -0.0386 S23: -0.0297 REMARK 3 S31: 0.0164 S32: 0.0030 S33: 0.0000 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 6P1S COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-MAY-19. REMARK 100 THE DEPOSITION ID IS D_1000241732. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-MAR-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : MIRRORS REMARK 200 OPTICS : VARIMAX HF REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 46614 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 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 (%) : 99.3 REMARK 200 DATA REDUNDANCY : 12.00 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 42.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.78 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.8 REMARK 200 DATA REDUNDANCY IN SHELL : 7.80 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.45200 REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.260 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: 4M04 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.86 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM HEPES PH 7.5, 100MM NACL, 10% REMARK 280 PEG4000, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K 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 29.94000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 55.28100 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.41900 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 55.28100 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.94000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.41900 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6450 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15620 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -67.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, T, P, D 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 GLY A 129 REMARK 465 SER A 130 REMARK 465 ALA A 131 REMARK 465 ALA A 132 REMARK 465 ALA A 133 REMARK 465 SER A 134 REMARK 465 PRO A 135 REMARK 465 ALA A 136 REMARK 465 TRP A 137 REMARK 465 HIS A 365 REMARK 465 GLN A 366 REMARK 465 HIS A 367 REMARK 465 SER A 368 REMARK 465 CYS A 369 REMARK 465 CYS A 370 REMARK 465 GLU A 371 REMARK 465 SER A 372 REMARK 465 PRO A 373 REMARK 465 THR A 374 REMARK 465 ARG A 375 REMARK 465 LEU A 376 REMARK 465 ALA A 377 REMARK 465 GLN A 378 REMARK 465 GLN A 379 REMARK 465 SER A 380 REMARK 465 HIS A 381 REMARK 465 MET A 382 REMARK 465 ASP A 383 REMARK 465 ALA A 384 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 173 CD OE1 OE2 REMARK 470 LEU A 196 CD1 CD2 REMARK 470 GLN A 200 CD OE1 NE2 REMARK 470 GLU A 207 CD OE1 OE2 REMARK 470 GLU A 223 CD OE1 OE2 REMARK 470 LYS A 249 CE NZ REMARK 470 GLU A 267 CG CD OE1 OE2 REMARK 470 GLN A 268 CG CD OE1 NE2 REMARK 470 GLN A 270 CG CD OE1 NE2 REMARK 470 LYS A 271 CG CD CE NZ REMARK 470 GLN A 274 CG CD OE1 NE2 REMARK 470 LEU A 280 CD1 CD2 REMARK 470 GLN A 300 CD OE1 NE2 REMARK 470 GLU A 304 CD OE1 OE2 REMARK 470 LYS A 339 CD CE NZ REMARK 470 GLN A 355 CD OE1 NE2 REMARK 470 GLN A 357 OE1 NE2 REMARK 470 HIS A 363 ND1 CD2 CE1 NE2 REMARK 470 GLN A 364 CG CD OE1 NE2 REMARK 470 GLU A 465 OE1 OE2 REMARK 470 LYS A 467 CE NZ REMARK 470 GLN A 471 OE1 NE2 REMARK 470 GLU A 485 CD OE1 OE2 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 NH2 ARG A 145 O HOH A 601 2.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 DC T 1 O3' DC T 1 C3' -0.054 REMARK 500 DT T 6 O3' DT T 6 C3' -0.038 REMARK 500 DG D 1 P DG D 1 OP3 -0.126 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 ARG A 393 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 DC T 4 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 DT T 6 O4' - C1' - N1 ANGL. DEV. = 2.9 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 ASN A 153 40.34 -142.34 REMARK 500 LEU A 310 94.88 -161.29 REMARK 500 THR A 318 -151.83 -123.93 REMARK 500 SER A 411 -146.51 -169.22 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 874 DISTANCE = 5.81 ANGSTROMS REMARK 525 HOH T 133 DISTANCE = 6.43 ANGSTROMS REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 THE AUTHORS STATE THAT ANOMALOUS SIGNAL IS OBSERVED FOR THE METAL A REMARK 600 SITE (PEAK GREATER THAN 10 SIGMA), THOUGH NO ANOMALOUS SCATTERERS REMARK 600 WERE ADDED TO THE CRYSTALLIZATION OR SOAKING SOLUTIONS. THEREFORE, REMARK 600 THIS METAL HAS BEEN MODELED AS MANGANESE, BASED ON THE COORDINATION REMARK 600 GEOMETRY AND INTERATOMIC DISTANCES. 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 ATP A 501 REMARK 610 EPE A 507 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 NA A 504 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 241 O REMARK 620 2 ILE A 243 O 98.4 REMARK 620 3 VAL A 246 O 88.8 93.2 REMARK 620 4 HOH A 817 O 85.5 88.3 174.2 REMARK 620 5 DT P 3 OP1 171.2 90.4 90.7 94.8 REMARK 620 6 HOH P 111 O 85.4 176.2 87.0 91.8 85.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 502 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 330 OD2 REMARK 620 2 ASP A 332 OD1 119.9 REMARK 620 3 ASP A 418 OD2 96.1 103.2 REMARK 620 4 A P 5 OP1 101.8 105.8 131.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 503 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 330 OD1 REMARK 620 2 ASP A 332 OD2 93.8 REMARK 620 3 ATP A 501 O2G 165.8 99.8 REMARK 620 4 ATP A 501 O2G 168.3 97.5 2.6 REMARK 620 5 ATP A 501 O2B 88.7 169.6 78.6 80.7 REMARK 620 6 ATP A 501 O2B 88.5 167.9 79.0 81.1 1.8 REMARK 620 7 HOH A 735 O 85.1 88.7 91.1 92.1 101.5 103.3 REMARK 620 8 A P 5 OP1 83.7 82.5 102.0 100.7 87.8 86.0 165.3 REMARK 620 N 1 2 3 4 5 6 7 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ATP A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EPE A 507 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 508 DBREF 6P1S A 134 494 UNP Q9NP87 DPOLM_HUMAN 134 494 DBREF 6P1S T 1 9 PDB 6P1S 6P1S 1 9 DBREF 6P1S P 1 5 PDB 6P1S 6P1S 1 5 DBREF 6P1S D 1 4 PDB 6P1S 6P1S 1 4 SEQADV 6P1S GLY A 129 UNP Q9NP87 EXPRESSION TAG SEQADV 6P1S SER A 130 UNP Q9NP87 EXPRESSION TAG SEQADV 6P1S ALA A 131 UNP Q9NP87 EXPRESSION TAG SEQADV 6P1S ALA A 132 UNP Q9NP87 EXPRESSION TAG SEQADV 6P1S ALA A 133 UNP Q9NP87 EXPRESSION TAG SEQADV 6P1S A UNP Q9NP87 PRO 398 DELETION SEQADV 6P1S A UNP Q9NP87 GLY 399 DELETION SEQADV 6P1S A UNP Q9NP87 ALA 400 DELETION SEQADV 6P1S A UNP Q9NP87 ALA 401 DELETION SEQADV 6P1S A UNP Q9NP87 VAL 402 DELETION SEQADV 6P1S A UNP Q9NP87 GLY 403 DELETION SEQADV 6P1S A UNP Q9NP87 GLY 404 DELETION SEQADV 6P1S A UNP Q9NP87 SER 405 DELETION SEQADV 6P1S A UNP Q9NP87 THR 406 DELETION SEQADV 6P1S A UNP Q9NP87 ARG 407 DELETION SEQADV 6P1S A UNP Q9NP87 PRO 408 DELETION SEQADV 6P1S A UNP Q9NP87 CYS 409 DELETION SEQADV 6P1S GLY A 410 UNP Q9NP87 PRO 410 LINKER SEQRES 1 A 354 GLY SER ALA ALA ALA SER PRO ALA TRP MET PRO ALA TYR SEQRES 2 A 354 ALA CYS GLN ARG PRO THR PRO LEU THR HIS HIS ASN THR SEQRES 3 A 354 GLY LEU SER GLU ALA LEU GLU ILE LEU ALA GLU ALA ALA SEQRES 4 A 354 GLY PHE GLU GLY SER GLU GLY ARG LEU LEU THR PHE CYS SEQRES 5 A 354 ARG ALA ALA SER VAL LEU LYS ALA LEU PRO SER PRO VAL SEQRES 6 A 354 THR THR LEU SER GLN LEU GLN GLY LEU PRO HIS PHE GLY SEQRES 7 A 354 GLU HIS SER SER ARG VAL VAL GLN GLU LEU LEU GLU HIS SEQRES 8 A 354 GLY VAL CYS GLU GLU VAL GLU ARG VAL ARG ARG SER GLU SEQRES 9 A 354 ARG TYR GLN THR MET LYS LEU PHE THR GLN ILE PHE GLY SEQRES 10 A 354 VAL GLY VAL LYS THR ALA ASP ARG TRP TYR ARG GLU GLY SEQRES 11 A 354 LEU ARG THR LEU ASP ASP LEU ARG GLU GLN PRO GLN LYS SEQRES 12 A 354 LEU THR GLN GLN GLN LYS ALA GLY LEU GLN HIS HIS GLN SEQRES 13 A 354 ASP LEU SER THR PRO VAL LEU ARG SER ASP VAL ASP ALA SEQRES 14 A 354 LEU GLN GLN VAL VAL GLU GLU ALA VAL GLY GLN ALA LEU SEQRES 15 A 354 PRO GLY ALA THR VAL THR LEU THR GLY GLY PHE ARG ARG SEQRES 16 A 354 GLY LYS LEU GLN GLY HIS ASP VAL ASP PHE LEU ILE THR SEQRES 17 A 354 HIS PRO LYS GLU GLY GLN GLU ALA GLY LEU LEU PRO ARG SEQRES 18 A 354 VAL MET CYS ARG LEU GLN ASP GLN GLY LEU ILE LEU TYR SEQRES 19 A 354 HIS GLN HIS GLN HIS SER CYS CYS GLU SER PRO THR ARG SEQRES 20 A 354 LEU ALA GLN GLN SER HIS MET ASP ALA PHE GLU ARG SER SEQRES 21 A 354 PHE CYS ILE PHE ARG LEU PRO GLN PRO GLY SER TRP LYS SEQRES 22 A 354 ALA VAL ARG VAL ASP LEU VAL VAL ALA PRO VAL SER GLN SEQRES 23 A 354 PHE PRO PHE ALA LEU LEU GLY TRP THR GLY SER LYS LEU SEQRES 24 A 354 PHE GLN ARG GLU LEU ARG ARG PHE SER ARG LYS GLU LYS SEQRES 25 A 354 GLY LEU TRP LEU ASN SER HIS GLY LEU PHE ASP PRO GLU SEQRES 26 A 354 GLN LYS THR PHE PHE GLN ALA ALA SER GLU GLU ASP ILE SEQRES 27 A 354 PHE ARG HIS LEU GLY LEU GLU TYR LEU PRO PRO GLU GLN SEQRES 28 A 354 ARG ASN ALA SEQRES 1 T 9 DC DG DG DC 8OG DT DA DC DG SEQRES 1 P 5 DC DG DT DA A SEQRES 1 D 4 DG DC DC DG HET 8OG T 5 23 HET ATP A 501 24 HET MN A 502 1 HET NA A 503 1 HET NA A 504 1 HET CL A 505 1 HET CL A 506 1 HET EPE A 507 5 HET EDO A 508 4 HETNAM 8OG 8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE HETNAM ATP ADENOSINE-5'-TRIPHOSPHATE HETNAM MN MANGANESE (II) ION HETNAM NA SODIUM ION HETNAM CL CHLORIDE ION HETNAM EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HETNAM EDO 1,2-ETHANEDIOL HETSYN 8OG 8-OXO-7,8-DIHYDRO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE HETSYN EPE HEPES HETSYN EDO ETHYLENE GLYCOL FORMUL 2 8OG C10 H14 N5 O8 P FORMUL 5 ATP C10 H16 N5 O13 P3 FORMUL 6 MN MN 2+ FORMUL 7 NA 2(NA 1+) FORMUL 9 CL 2(CL 1-) FORMUL 11 EPE C8 H18 N2 O4 S FORMUL 12 EDO C2 H6 O2 FORMUL 13 HOH *335(H2 O) HELIX 1 AA1 TYR A 141 ARG A 145 5 5 HELIX 2 AA2 ASN A 153 GLU A 170 1 18 HELIX 3 AA3 SER A 172 LEU A 189 1 18 HELIX 4 AA4 THR A 195 GLN A 200 5 6 HELIX 5 AA5 GLY A 206 GLY A 220 1 15 HELIX 6 AA6 CYS A 222 SER A 231 1 10 HELIX 7 AA7 SER A 231 GLN A 242 1 12 HELIX 8 AA8 GLY A 247 GLU A 257 1 11 HELIX 9 AA9 THR A 261 GLU A 267 1 7 HELIX 10 AB1 GLN A 268 LEU A 272 5 5 HELIX 11 AB2 THR A 273 HIS A 282 1 10 HELIX 12 AB3 HIS A 282 SER A 287 1 6 HELIX 13 AB4 ARG A 292 LEU A 310 1 19 HELIX 14 AB5 THR A 318 ARG A 323 1 6 HELIX 15 AB6 GLY A 345 GLN A 357 1 13 HELIX 16 AB7 PRO A 423 SER A 425 5 3 HELIX 17 AB8 GLN A 426 GLY A 436 1 11 HELIX 18 AB9 SER A 437 GLY A 453 1 17 HELIX 19 AC1 SER A 474 LEU A 482 1 9 HELIX 20 AC2 PRO A 488 ARG A 492 5 5 SHEET 1 AA1 2 VAL A 290 LEU A 291 0 SHEET 2 AA1 2 GLN A 327 GLY A 328 -1 O GLY A 328 N VAL A 290 SHEET 1 AA2 5 THR A 314 LEU A 317 0 SHEET 2 AA2 5 ASP A 330 THR A 336 -1 O LEU A 334 N THR A 316 SHEET 3 AA2 5 SER A 411 VAL A 421 1 O VAL A 420 N ILE A 335 SHEET 4 AA2 5 ARG A 387 GLN A 396 -1 N PHE A 392 O VAL A 415 SHEET 5 AA2 5 ILE A 360 TYR A 362 -1 N LEU A 361 O ILE A 391 SHEET 1 AA3 3 TRP A 455 LEU A 456 0 SHEET 2 AA3 3 LEU A 461 ASP A 463 -1 O PHE A 462 N TRP A 455 SHEET 3 AA3 3 THR A 468 PHE A 469 -1 O THR A 468 N ASP A 463 LINK O3' DC T 4 P 8OG T 5 1555 1555 1.61 LINK O3' 8OG T 5 P DT T 6 1555 1555 1.59 LINK O THR A 241 NA NA A 504 1555 1555 2.36 LINK O ILE A 243 NA NA A 504 1555 1555 2.32 LINK O VAL A 246 NA NA A 504 1555 1555 2.35 LINK OD2 ASP A 330 MN MN A 502 1555 1555 1.89 LINK OD1 ASP A 330 NA NA A 503 1555 1555 2.17 LINK OD1 ASP A 332 MN MN A 502 1555 1555 1.91 LINK OD2 ASP A 332 NA NA A 503 1555 1555 2.22 LINK OD2 ASP A 418 MN MN A 502 1555 1555 1.99 LINK O2GAATP A 501 NA NA A 503 1555 1555 2.19 LINK O2GBATP A 501 NA NA A 503 1555 1555 2.20 LINK O2BAATP A 501 NA NA A 503 1555 1555 2.53 LINK O2BBATP A 501 NA NA A 503 1555 1555 2.46 LINK MN MN A 502 OP1 A P 5 1555 1555 2.06 LINK NA NA A 503 O HOH A 735 1555 1555 2.32 LINK NA NA A 503 OP1 A P 5 1555 1555 2.56 LINK NA NA A 504 O HOH A 817 1555 1555 2.41 LINK NA NA A 504 OP1 DT P 3 1555 1555 2.61 LINK NA NA A 504 O HOH P 111 1555 1555 2.39 CISPEP 1 GLY A 436 SER A 437 0 -9.05 SITE 1 AC1 12 GLY A 319 GLY A 320 ARG A 323 HIS A 329 SITE 2 AC1 12 ASP A 330 ASP A 332 NA A 503 HOH A 607 SITE 3 AC1 12 HOH A 608 HOH A 681 HOH A 739 A P 5 SITE 1 AC2 6 ASP A 330 ASP A 332 ASP A 418 NA A 503 SITE 2 AC2 6 DA P 4 A P 5 SITE 1 AC3 6 ASP A 330 ASP A 332 ATP A 501 MN A 502 SITE 2 AC3 6 HOH A 735 A P 5 SITE 1 AC4 6 THR A 241 ILE A 243 VAL A 246 HOH A 817 SITE 2 AC4 6 DT P 3 HOH P 111 SITE 1 AC5 2 SER A 458 DA T 7 SITE 1 AC6 4 SER A 172 GLY A 174 ARG A 175 HOH A 746 SITE 1 AC7 4 LYS A 325 LEU A 326 GLN A 327 HOH A 622 SITE 1 AC8 6 ARG A 387 GLY A 433 TRP A 434 ARG A 445 SITE 2 AC8 6 SER A 458 DA P 4 CRYST1 59.880 68.838 110.562 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 0.016700 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014527 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009045 0.00000