HEADER LIGASE/DNA 21-NOV-23 8V1U TITLE HUMAN DNA LIGASE I F872A BOUND TO ADENYLATED NICKED DNA WITH A 5' TITLE 2 TERMINAL RIBONUCLEOTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA LIGASE 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DNA LIGASE I,POLYDEOXYRIBONUCLEOTIDE SYNTHASE [ATP] 1; COMPND 5 EC: 6.5.1.1; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*TP*C)-3'); COMPND 10 CHAIN: B; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: DNA/RNA (5'-R(P*G)-D(P*TP*CP*GP*GP*AP*C)-3'); COMPND 14 CHAIN: C; COMPND 15 ENGINEERED: YES; COMPND 16 MOL_ID: 4; COMPND 17 MOLECULE: DNA (5'- COMPND 18 D(*GP*TP*CP*CP*GP*AP*CP*GP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'); COMPND 19 CHAIN: D; COMPND 20 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: LIG1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 11 ORGANISM_TAXID: 32630; SOURCE 12 MOL_ID: 3; SOURCE 13 SYNTHETIC: YES; SOURCE 14 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 15 ORGANISM_TAXID: 32630; SOURCE 16 MOL_ID: 4; SOURCE 17 SYNTHETIC: YES; SOURCE 18 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 19 ORGANISM_TAXID: 32630 KEYWDS ADENYLATION DOMAIN, METALLOENZYME, LIGASE, LIGASE-DNA COMPLEX, DNA KEYWDS 2 BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR P.P.TUMBALE,R.S.WILLIAMS REVDAT 2 14-JAN-26 8V1U 1 JRNL REVDAT 1 02-JUL-25 8V1U 0 JRNL AUTH P.P.TUMBALE,T.J.JURKIW,J.M.KRAHN,N.V.BOKIL,S.J.ADMIRAAL, JRNL AUTH 2 L.C.PEDERSEN,J.S.WILLIAMS,T.A.KUNKEL,P.J.O'BRIEN, JRNL AUTH 3 R.S.WILLIAMS JRNL TITL MOLECULAR BASIS FOR RNA DISCRIMINATION BY HUMAN DNA LIGASE JRNL TITL 2 1. JRNL REF NUCLEIC ACIDS RES. V. 53 2025 JRNL REFN ESSN 1362-4962 JRNL PMID 40239996 JRNL DOI 10.1093/NAR/GKAF299 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2_4158 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.87 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 3 NUMBER OF REFLECTIONS : 54583 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.188 REMARK 3 R VALUE (WORKING SET) : 0.188 REMARK 3 FREE R VALUE : 0.210 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.650 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 40.8700 - 4.8200 0.98 4003 152 0.1883 0.1905 REMARK 3 2 4.8200 - 3.8300 0.98 3811 144 0.1435 0.1565 REMARK 3 3 3.8200 - 3.3400 0.98 3794 144 0.1558 0.1843 REMARK 3 4 3.3400 - 3.0400 0.98 3729 141 0.1746 0.2008 REMARK 3 5 3.0400 - 2.8200 0.97 3737 143 0.1855 0.2107 REMARK 3 6 2.8200 - 2.6500 0.97 3672 139 0.1962 0.2440 REMARK 3 7 2.6500 - 2.5200 0.98 3719 142 0.2016 0.2366 REMARK 3 8 2.5200 - 2.4100 0.97 3713 141 0.2018 0.2236 REMARK 3 9 2.4100 - 2.3200 0.98 3730 141 0.2057 0.2404 REMARK 3 10 2.3200 - 2.2400 0.98 3719 141 0.2183 0.2395 REMARK 3 11 2.2400 - 2.1700 0.99 3704 141 0.2332 0.2732 REMARK 3 12 2.1700 - 2.1100 0.99 3780 142 0.2500 0.2836 REMARK 3 13 2.1100 - 2.0500 0.99 3739 140 0.2707 0.2698 REMARK 3 14 2.0500 - 2.0000 0.99 3739 143 0.2724 0.2980 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.219 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.828 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 27.34 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.23 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 : 0.004 5931 REMARK 3 ANGLE : 0.619 8215 REMARK 3 CHIRALITY : 0.041 936 REMARK 3 PLANARITY : 0.004 937 REMARK 3 DIHEDRAL : 15.535 2275 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 7 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 258 THROUGH 509 ) REMARK 3 ORIGIN FOR THE GROUP (A): 36.7592 6.5266 -10.1566 REMARK 3 T TENSOR REMARK 3 T11: 0.1461 T22: 0.2252 REMARK 3 T33: 0.2210 T12: -0.0165 REMARK 3 T13: -0.0094 T23: 0.0138 REMARK 3 L TENSOR REMARK 3 L11: 1.5326 L22: 1.0862 REMARK 3 L33: 2.2185 L12: 0.0580 REMARK 3 L13: -0.6418 L23: 0.3684 REMARK 3 S TENSOR REMARK 3 S11: 0.0089 S12: -0.1315 S13: 0.1379 REMARK 3 S21: 0.0582 S22: -0.0190 S23: -0.0276 REMARK 3 S31: -0.0656 S32: 0.0157 S33: 0.0158 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 510 THROUGH 741 ) REMARK 3 ORIGIN FOR THE GROUP (A): 18.3881 -21.7265 -16.3606 REMARK 3 T TENSOR REMARK 3 T11: 0.1788 T22: 0.1599 REMARK 3 T33: 0.1893 T12: 0.0209 REMARK 3 T13: 0.0111 T23: -0.0009 REMARK 3 L TENSOR REMARK 3 L11: 2.0089 L22: 1.5517 REMARK 3 L33: 1.3073 L12: -0.1258 REMARK 3 L13: -0.3172 L23: 0.1978 REMARK 3 S TENSOR REMARK 3 S11: 0.0293 S12: 0.0732 S13: -0.0193 REMARK 3 S21: 0.0028 S22: -0.0281 S23: 0.0836 REMARK 3 S31: 0.0061 S32: -0.1093 S33: 0.0194 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 742 THROUGH 901 ) REMARK 3 ORIGIN FOR THE GROUP (A): -1.5536 4.2929 -5.3721 REMARK 3 T TENSOR REMARK 3 T11: 0.1473 T22: 0.2118 REMARK 3 T33: 0.2156 T12: -0.0036 REMARK 3 T13: -0.0133 T23: 0.0046 REMARK 3 L TENSOR REMARK 3 L11: 2.9971 L22: 1.5110 REMARK 3 L33: 1.6702 L12: -0.0979 REMARK 3 L13: -0.5118 L23: 0.4716 REMARK 3 S TENSOR REMARK 3 S11: 0.0441 S12: -0.1053 S13: 0.1080 REMARK 3 S21: 0.0304 S22: -0.0733 S23: 0.1628 REMARK 3 S31: 0.0183 S32: -0.2011 S33: 0.0318 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 3 THROUGH 13 ) REMARK 3 ORIGIN FOR THE GROUP (A): 15.9606 -5.3805 8.0821 REMARK 3 T TENSOR REMARK 3 T11: 0.3235 T22: 0.3181 REMARK 3 T33: 0.1751 T12: -0.0175 REMARK 3 T13: 0.0094 T23: -0.0256 REMARK 3 L TENSOR REMARK 3 L11: 1.0639 L22: 1.0771 REMARK 3 L33: 9.3770 L12: 0.3754 REMARK 3 L13: 2.8517 L23: -0.2257 REMARK 3 S TENSOR REMARK 3 S11: 0.0084 S12: -0.3813 S13: -0.0057 REMARK 3 S21: 0.4147 S22: 0.1622 S23: -0.1274 REMARK 3 S31: -0.7791 S32: -0.0824 S33: -0.2124 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 1 THROUGH 7 ) REMARK 3 ORIGIN FOR THE GROUP (A): 13.5264 3.1302 -20.0293 REMARK 3 T TENSOR REMARK 3 T11: 0.1593 T22: 0.1666 REMARK 3 T33: 0.1432 T12: 0.0063 REMARK 3 T13: -0.0017 T23: 0.0265 REMARK 3 L TENSOR REMARK 3 L11: -0.0054 L22: -0.0060 REMARK 3 L33: -0.0021 L12: 0.0134 REMARK 3 L13: 0.0066 L23: -0.0068 REMARK 3 S TENSOR REMARK 3 S11: 0.0800 S12: 0.2225 S13: 0.0047 REMARK 3 S21: 0.0249 S22: 0.0696 S23: 0.1332 REMARK 3 S31: 0.1149 S32: 0.1329 S33: 0.0000 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'D' AND (RESID 9 THROUGH 18 ) REMARK 3 ORIGIN FOR THE GROUP (A): 15.5745 0.5288 -14.0284 REMARK 3 T TENSOR REMARK 3 T11: 0.1683 T22: 0.2005 REMARK 3 T33: 0.1701 T12: 0.0237 REMARK 3 T13: -0.0346 T23: -0.0078 REMARK 3 L TENSOR REMARK 3 L11: 3.8492 L22: 2.1105 REMARK 3 L33: 5.4003 L12: 0.8709 REMARK 3 L13: -3.6518 L23: -1.4077 REMARK 3 S TENSOR REMARK 3 S11: 0.0065 S12: 0.2067 S13: 0.0293 REMARK 3 S21: -0.1412 S22: 0.0800 S23: 0.0695 REMARK 3 S31: 0.2184 S32: -0.0052 S33: -0.0926 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'D' AND (RESID 19 THROUGH 26 ) REMARK 3 ORIGIN FOR THE GROUP (A): 18.2651 -5.5979 12.7946 REMARK 3 T TENSOR REMARK 3 T11: 0.2947 T22: 0.3213 REMARK 3 T33: 0.1698 T12: -0.0111 REMARK 3 T13: 0.0177 T23: 0.0191 REMARK 3 L TENSOR REMARK 3 L11: 2.9293 L22: 3.3042 REMARK 3 L33: 7.1408 L12: 0.8735 REMARK 3 L13: 1.2742 L23: 2.9125 REMARK 3 S TENSOR REMARK 3 S11: 0.0032 S12: -0.2249 S13: 0.0174 REMARK 3 S21: 0.0051 S22: 0.2253 S23: -0.1635 REMARK 3 S31: -0.4407 S32: 0.4307 S33: -0.3401 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 8V1U COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-NOV-23. REMARK 100 THE DEPOSITION ID IS D_1000279348. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-JUN-21 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 : APS REMARK 200 BEAMLINE : 22-ID 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 EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 54724 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 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 (%) : 98.3 REMARK 200 DATA REDUNDANCY : 5.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.03 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.2 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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 (%): 52.46 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.59 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MES PH5.5 100MM, LITHIUM ACETATE REMARK 280 500MM, PEG 3350 10%, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 293K 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 36.49300 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 57.33050 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 48.41600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 57.33050 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 36.49300 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 48.41600 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: 8960 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 30280 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -78.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, 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 GLN A 902 REMARK 465 ILE A 903 REMARK 465 GLN A 904 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 LEU A 345 CD1 CD2 REMARK 470 LYS A 356 CE NZ REMARK 470 GLU A 375 CD OE1 OE2 REMARK 470 GLU A 384 CD OE1 OE2 REMARK 470 ASN A 385 CG OD1 ND2 REMARK 470 SER A 386 OG REMARK 470 GLN A 390 CG CD OE1 NE2 REMARK 470 ARG A 391 CG CD NE CZ NH1 NH2 REMARK 470 LEU A 392 CG CD1 CD2 REMARK 470 MET A 393 CG SD CE REMARK 470 LEU A 394 CG CD1 CD2 REMARK 470 GLU A 475 CG CD OE1 OE2 REMARK 470 LYS A 485 CG CD CE NZ REMARK 470 GLU A 490 CG CD OE1 OE2 REMARK 470 ARG A 527 NE CZ NH1 NH2 REMARK 470 LYS A 533 CE NZ REMARK 470 LYS A 556 CG CD CE NZ REMARK 470 GLU A 559 CG CD OE1 OE2 REMARK 470 GLU A 580 CD OE1 OE2 REMARK 470 LYS A 630 CE NZ REMARK 470 LYS A 642 CD CE NZ REMARK 470 ARG A 643 CD NE CZ NH1 NH2 REMARK 470 LYS A 644 CD CE NZ REMARK 470 GLU A 645 CG CD OE1 OE2 REMARK 470 VAL A 646 CG1 CG2 REMARK 470 ASP A 647 CG OD1 OD2 REMARK 470 SER A 649 OG REMARK 470 GLU A 650 CG CD OE1 OE2 REMARK 470 ARG A 672 CZ NH1 NH2 REMARK 470 GLU A 690 CG CD OE1 OE2 REMARK 470 LYS A 702 CG CD CE NZ REMARK 470 GLU A 705 CG CD OE1 OE2 REMARK 470 GLU A 709 CD OE1 OE2 REMARK 470 GLU A 712 CD OE1 OE2 REMARK 470 LYS A 747 CG CD CE NZ REMARK 470 ASP A 751 CG OD1 OD2 REMARK 470 GLU A 803 CD OE1 OE2 REMARK 470 GLU A 880 CD OE1 OE2 REMARK 470 LYS A 899 CD CE NZ 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 B 4 O3' DT B 5 P 0.088 REMARK 500 DG B 6 O3' DA B 7 P -0.098 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 378 114.79 -166.70 REMARK 500 MET A 393 43.74 -105.10 REMARK 500 LEU A 394 103.83 -171.48 REMARK 500 HIS A 436 -117.45 53.15 REMARK 500 ALA A 455 -150.20 -139.78 REMARK 500 GLU A 560 -48.76 76.51 REMARK 500 ASP A 570 78.21 -100.53 REMARK 500 GLU A 692 -52.68 -130.98 REMARK 500 SER A 718 41.00 71.38 REMARK 500 ASP A 728 -31.60 -138.12 REMARK 500 ARG A 738 116.52 -162.33 REMARK 500 HIS A 740 61.49 -107.30 REMARK 500 ASP A 748 1.64 -68.50 REMARK 500 ASP A 827 -110.92 51.18 REMARK 500 SER A 839 -55.34 -163.82 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 MES A 1003 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 B 202 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 594 OD1 REMARK 620 2 DG B 11 O3' 171.3 REMARK 620 3 DT B 12 OP1 120.1 65.0 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA C 102 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 311 O REMARK 620 2 DA C 6 OP2 160.1 REMARK 620 N 1 DBREF 8V1U A 262 904 UNP P18858 DNLI1_HUMAN 262 904 DBREF 8V1U B 3 13 PDB 8V1U 8V1U 3 13 DBREF 8V1U C 1 7 PDB 8V1U 8V1U 1 7 DBREF 8V1U D 9 26 PDB 8V1U 8V1U 9 26 SEQADV 8V1U SER A 258 UNP P18858 EXPRESSION TAG SEQADV 8V1U ASN A 259 UNP P18858 EXPRESSION TAG SEQADV 8V1U ASP A 260 UNP P18858 EXPRESSION TAG SEQADV 8V1U MET A 261 UNP P18858 EXPRESSION TAG SEQADV 8V1U ALA A 872 UNP P18858 PHE 872 ENGINEERED MUTATION SEQRES 1 A 647 SER ASN ASP MET ASP PRO SER GLY TYR ASN PRO ALA LYS SEQRES 2 A 647 ASN ASN TYR HIS PRO VAL GLU ASP ALA CYS TRP LYS PRO SEQRES 3 A 647 GLY GLN LYS VAL PRO TYR LEU ALA VAL ALA ARG THR PHE SEQRES 4 A 647 GLU LYS ILE GLU GLU VAL SER ALA ARG LEU ARG MET VAL SEQRES 5 A 647 GLU THR LEU SER ASN LEU LEU ARG SER VAL VAL ALA LEU SEQRES 6 A 647 SER PRO PRO ASP LEU LEU PRO VAL LEU TYR LEU SER LEU SEQRES 7 A 647 ASN HIS LEU GLY PRO PRO GLN GLN GLY LEU GLU LEU GLY SEQRES 8 A 647 VAL GLY ASP GLY VAL LEU LEU LYS ALA VAL ALA GLN ALA SEQRES 9 A 647 THR GLY ARG GLN LEU GLU SER VAL ARG ALA GLU ALA ALA SEQRES 10 A 647 GLU LYS GLY ASP VAL GLY LEU VAL ALA GLU ASN SER ARG SEQRES 11 A 647 SER THR GLN ARG LEU MET LEU PRO PRO PRO PRO LEU THR SEQRES 12 A 647 ALA SER GLY VAL PHE SER LYS PHE ARG ASP ILE ALA ARG SEQRES 13 A 647 LEU THR GLY SER ALA SER THR ALA LYS LYS ILE ASP ILE SEQRES 14 A 647 ILE LYS GLY LEU PHE VAL ALA CYS ARG HIS SER GLU ALA SEQRES 15 A 647 ARG PHE ILE ALA ARG SER LEU SER GLY ARG LEU ARG LEU SEQRES 16 A 647 GLY LEU ALA GLU GLN SER VAL LEU ALA ALA LEU SER GLN SEQRES 17 A 647 ALA VAL SER LEU THR PRO PRO GLY GLN GLU PHE PRO PRO SEQRES 18 A 647 ALA MET VAL ASP ALA GLY LYS GLY LYS THR ALA GLU ALA SEQRES 19 A 647 ARG LYS THR TRP LEU GLU GLU GLN GLY MET ILE LEU LYS SEQRES 20 A 647 GLN THR PHE CYS GLU VAL PRO ASP LEU ASP ARG ILE ILE SEQRES 21 A 647 PRO VAL LEU LEU GLU HIS GLY LEU GLU ARG LEU PRO GLU SEQRES 22 A 647 HIS CYS LYS LEU SER PRO GLY ILE PRO LEU LYS PRO MET SEQRES 23 A 647 LEU ALA HIS PRO THR ARG GLY ILE SER GLU VAL LEU LYS SEQRES 24 A 647 ARG PHE GLU GLU ALA ALA PHE THR CYS GLU TYR LYS TYR SEQRES 25 A 647 ASP GLY GLN ARG ALA GLN ILE HIS ALA LEU GLU GLY GLY SEQRES 26 A 647 GLU VAL LYS ILE PHE SER ARG ASN GLN GLU ASP ASN THR SEQRES 27 A 647 GLY LYS TYR PRO ASP ILE ILE SER ARG ILE PRO LYS ILE SEQRES 28 A 647 LYS LEU PRO SER VAL THR SER PHE ILE LEU ASP THR GLU SEQRES 29 A 647 ALA VAL ALA TRP ASP ARG GLU LYS LYS GLN ILE GLN PRO SEQRES 30 A 647 PHE GLN VAL LEU THR THR ARG LYS ARG LYS GLU VAL ASP SEQRES 31 A 647 ALA SER GLU ILE GLN VAL GLN VAL CYS LEU TYR ALA PHE SEQRES 32 A 647 ASP LEU ILE TYR LEU ASN GLY GLU SER LEU VAL ARG GLU SEQRES 33 A 647 PRO LEU SER ARG ARG ARG GLN LEU LEU ARG GLU ASN PHE SEQRES 34 A 647 VAL GLU THR GLU GLY GLU PHE VAL PHE ALA THR SER LEU SEQRES 35 A 647 ASP THR LYS ASP ILE GLU GLN ILE ALA GLU PHE LEU GLU SEQRES 36 A 647 GLN SER VAL LYS ASP SER CYS GLU GLY LEU MET VAL LYS SEQRES 37 A 647 THR LEU ASP VAL ASP ALA THR TYR GLU ILE ALA LYS ARG SEQRES 38 A 647 SER HIS ASN TRP LEU LYS LEU LYS LYS ASP TYR LEU ASP SEQRES 39 A 647 GLY VAL GLY ASP THR LEU ASP LEU VAL VAL ILE GLY ALA SEQRES 40 A 647 TYR LEU GLY ARG GLY LYS ARG ALA GLY ARG TYR GLY GLY SEQRES 41 A 647 PHE LEU LEU ALA SER TYR ASP GLU ASP SER GLU GLU LEU SEQRES 42 A 647 GLN ALA ILE CYS LYS LEU GLY THR GLY PHE SER ASP GLU SEQRES 43 A 647 GLU LEU GLU GLU HIS HIS GLN SER LEU LYS ALA LEU VAL SEQRES 44 A 647 LEU PRO SER PRO ARG PRO TYR VAL ARG ILE ASP GLY ALA SEQRES 45 A 647 VAL ILE PRO ASP HIS TRP LEU ASP PRO SER ALA VAL TRP SEQRES 46 A 647 GLU VAL LYS CYS ALA ASP LEU SER LEU SER PRO ILE TYR SEQRES 47 A 647 PRO ALA ALA ARG GLY LEU VAL ASP SER ASP LYS GLY ILE SEQRES 48 A 647 SER LEU ARG ALA PRO ARG PHE ILE ARG VAL ARG GLU ASP SEQRES 49 A 647 LYS GLN PRO GLU GLN ALA THR THR SER ALA GLN VAL ALA SEQRES 50 A 647 CYS LEU TYR ARG LYS GLN SER GLN ILE GLN SEQRES 1 B 11 DG DC DT DG DA DT DG DC DG DT DC SEQRES 1 C 7 G DT DC DG DG DA DC SEQRES 1 D 18 DG DT DC DC DG DA DC DG DA DC DG DC DA SEQRES 2 D 18 DT DC DA DG DC HET PEG A1001 17 HET MES A1002 25 HET MES A1003 5 HET CL A1004 1 HET GOL B 201 14 HET NA B 202 1 HET AMP C 101 35 HET NA C 102 1 HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID HETNAM CL CHLORIDE ION HETNAM GOL GLYCEROL HETNAM NA SODIUM ION HETNAM AMP ADENOSINE MONOPHOSPHATE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 5 PEG C4 H10 O3 FORMUL 6 MES 2(C6 H13 N O4 S) FORMUL 8 CL CL 1- FORMUL 9 GOL C3 H8 O3 FORMUL 10 NA 2(NA 1+) FORMUL 11 AMP C10 H14 N5 O7 P FORMUL 13 HOH *469(H2 O) HELIX 1 AA1 ASP A 262 TYR A 266 5 5 HELIX 2 AA2 PRO A 288 GLU A 301 1 14 HELIX 3 AA3 ALA A 304 SER A 323 1 20 HELIX 4 AA4 ASP A 326 ASN A 336 1 11 HELIX 5 AA5 PRO A 340 GLY A 344 5 5 HELIX 6 AA6 GLY A 350 GLY A 363 1 14 HELIX 7 AA7 GLN A 365 GLY A 377 1 13 HELIX 8 AA8 ASP A 378 SER A 386 1 9 HELIX 9 AA9 THR A 400 LEU A 414 1 15 HELIX 10 AB1 ALA A 418 ALA A 433 1 16 HELIX 11 AB2 SER A 437 GLY A 448 1 12 HELIX 12 AB3 ALA A 455 THR A 470 1 16 HELIX 13 AB4 THR A 488 VAL A 510 1 23 HELIX 14 AB5 ASP A 512 GLY A 524 1 13 HELIX 15 AB6 ARG A 527 CYS A 532 1 6 HELIX 16 AB7 GLY A 550 PHE A 558 1 9 HELIX 17 AB8 ASN A 594 LYS A 597 5 4 HELIX 18 AB9 TYR A 598 SER A 603 1 6 HELIX 19 AC1 ARG A 604 ILE A 608 5 5 HELIX 20 AC2 PRO A 634 THR A 639 1 6 HELIX 21 AC3 ASP A 647 ILE A 651 5 5 HELIX 22 AC4 PRO A 674 PHE A 686 1 13 HELIX 23 AC5 ASP A 703 ASP A 717 1 15 HELIX 24 AC6 ASP A 748 LEU A 750 5 3 HELIX 25 AC7 ARG A 768 ALA A 772 5 5 HELIX 26 AC8 SER A 801 LYS A 813 1 13 HELIX 27 AC9 GLN A 883 ALA A 887 5 5 HELIX 28 AD1 THR A 889 SER A 901 1 13 SHEET 1 AA1 5 ALA A 545 PRO A 547 0 SHEET 2 AA1 5 TRP A 742 LYS A 746 1 O TRP A 742 N HIS A 546 SHEET 3 AA1 5 CYS A 719 THR A 726 -1 N LEU A 722 O LEU A 745 SHEET 4 AA1 5 PHE A 563 TYR A 569 -1 N GLU A 566 O MET A 723 SHEET 5 AA1 5 SER A 698 ASP A 700 -1 O LEU A 699 N CYS A 565 SHEET 1 AA2 5 VAL A 584 PHE A 587 0 SHEET 2 AA2 5 GLN A 572 ALA A 578 -1 N HIS A 577 O LYS A 585 SHEET 3 AA2 5 PHE A 616 ASP A 626 -1 O ALA A 622 N GLN A 572 SHEET 4 AA2 5 GLN A 654 LEU A 665 -1 O CYS A 656 N VAL A 623 SHEET 5 AA2 5 GLU A 668 SER A 669 -1 O GLU A 668 N LEU A 665 SHEET 1 AA3 4 GLN A 631 ILE A 632 0 SHEET 2 AA3 4 PHE A 616 ASP A 626 -1 N ASP A 626 O GLN A 631 SHEET 3 AA3 4 GLN A 654 LEU A 665 -1 O CYS A 656 N VAL A 623 SHEET 4 AA3 4 PHE A 693 PHE A 695 1 O VAL A 694 N LEU A 657 SHEET 1 AA4 6 VAL A 816 LEU A 817 0 SHEET 2 AA4 6 HIS A 834 LEU A 836 -1 O TRP A 835 N LEU A 817 SHEET 3 AA4 6 ASP A 755 LEU A 766 -1 N ALA A 764 O HIS A 834 SHEET 4 AA4 6 TYR A 775 ASP A 784 -1 O GLY A 777 N TYR A 765 SHEET 5 AA4 6 GLU A 789 LEU A 796 -1 O GLU A 789 N ASP A 784 SHEET 6 AA4 6 VAL A 824 ARG A 825 1 O ARG A 825 N LEU A 790 SHEET 1 AA5 5 VAL A 816 LEU A 817 0 SHEET 2 AA5 5 HIS A 834 LEU A 836 -1 O TRP A 835 N LEU A 817 SHEET 3 AA5 5 ASP A 755 LEU A 766 -1 N ALA A 764 O HIS A 834 SHEET 4 AA5 5 VAL A 841 CYS A 846 -1 O VAL A 844 N LEU A 757 SHEET 5 AA5 5 ARG A 874 VAL A 878 -1 O ARG A 877 N GLU A 843 SHEET 1 AA6 2 ASP A 848 SER A 852 0 SHEET 2 AA6 2 GLY A 867 ARG A 871 -1 O ARG A 871 N ASP A 848 LINK P G C 1 O3P AMP C 101 1555 1555 1.56 LINK OD1 ASN A 594 NA NA B 202 1555 1555 3.19 LINK O3' DG B 11 NA NA B 202 1555 1555 2.47 LINK OP1 DT B 12 NA NA B 202 1555 1555 2.12 LINK O HOH B 311 NA NA C 102 2554 1555 2.55 LINK OP2 DA C 6 NA NA C 102 1555 1555 2.19 CISPEP 1 PHE A 476 PRO A 477 0 -2.84 CRYST1 72.986 96.832 114.661 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 0.013701 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010327 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008721 0.00000 CONECT 508311098 CONECT1015411098 CONECT1018011098 CONECT1024311102 CONECT1040711134 CONECT1103611037110381104311044 CONECT110371103611045 CONECT1103811036110391104611047 CONECT110391103811040 CONECT1104011039110411104811049 CONECT1104111040110421105011051 CONECT110421104111052 CONECT1104311036 CONECT1104411036 CONECT1104511037 CONECT1104611038 CONECT1104711038 CONECT1104811040 CONECT1104911040 CONECT1105011041 CONECT1105111041 CONECT1105211042 CONECT110531105411058 CONECT1105411053110551106511066 CONECT1105511054110561106711068 CONECT1105611055110571105911069 CONECT1105711056110581107011071 CONECT1105811053110571107211073 CONECT1105911056110601107411075 CONECT1106011059110611107611077 CONECT1106111060110621106311064 CONECT1106211061 CONECT1106311061 CONECT1106411061 CONECT1106511054 CONECT1106611054 CONECT1106711055 CONECT1106811055 CONECT1106911056 CONECT1107011057 CONECT1107111057 CONECT1107211058 CONECT1107311058 CONECT1107411059 CONECT1107511059 CONECT1107611060 CONECT1107711060 CONECT1107811079 CONECT1107911078110801108111082 CONECT1108011079 CONECT1108111079 CONECT1108211079 CONECT1108411085110861109011091 CONECT110851108411092 CONECT1108611084110871108811093 CONECT110871108611094 CONECT1108811086110891109511096 CONECT110891108811097 CONECT1109011084 CONECT1109111084 CONECT1109211085 CONECT1109311086 CONECT1109411087 CONECT1109511088 CONECT1109611088 CONECT1109711089 CONECT11098 50831015410180 CONECT1109911100111011110211103 CONECT1110011099 CONECT1110111099 CONECT111021024311099 CONECT111031109911104 CONECT1110411103111051112211123 CONECT1110511104111061110711124 CONECT111061110511111 CONECT1110711105111081110911125 CONECT111081110711126 CONECT1110911107111101111111127 CONECT111101110911128 CONECT1111111106111091111211129 CONECT11112111111111311121 CONECT11113111121111411130 CONECT111141111311115 CONECT11115111141111611121 CONECT11116111151111711118 CONECT11117111161113111132 CONECT111181111611119 CONECT11119111181112011133 CONECT111201111911121 CONECT11121111121111511120 CONECT1112211104 CONECT1112311104 CONECT1112411105 CONECT1112511107 CONECT1112611108 CONECT1112711109 CONECT1112811110 CONECT1112911111 CONECT1113011113 CONECT1113111117 CONECT1113211117 CONECT1113311119 CONECT1113410407 MASTER 444 0 8 28 27 0 0 6 6164 4 103 54 END