HEADER TRANSFERASE/DNA 13-DEC-13 4O0I TITLE CRYSTAL STRUCTURE OF FRAGMENT DNA POLYMERASE I FROM BACILLUS TITLE 2 STEAROTHERMOPHILUS WITH 2'-MESE-ARABINO-GUANOSINE DERIVATIZED DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE I; COMPND 3 CHAIN: A; COMPND 4 EC: 2.7.7.7; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: 5'-D(*C*(1TW)P*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3'; COMPND 8 CHAIN: B, C; COMPND 9 ENGINEERED: YES; COMPND 10 OTHER_DETAILS: 2'-MESE-ARABINO-GUANOSINE DERIVATIZED DNA SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GEOBACILLUS STEAROTHERMOPHILUS; SOURCE 3 ORGANISM_TAXID: 1422; SOURCE 4 GENE: DPO1; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES KEYWDS TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR S.JIANG,J.GAN,H.SUN,Z.HUANG REVDAT 3 20-SEP-23 4O0I 1 REMARK SEQADV LINK REVDAT 2 22-NOV-17 4O0I 1 REMARK REVDAT 1 17-DEC-14 4O0I 0 JRNL AUTH S.JIANG,J.GAN,H.SUN,Z.HUANG JRNL TITL CRYSTAL STRUCTURE OF FRAGMENT DNA POLYMERASE I FROM BACILLUS JRNL TITL 2 STEAROTHERMOPHILUS WITH 2'-MESE-ARABINO-GUANOSINE JRNL TITL 3 DERIVATIZED DNA JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.4_1496 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.04 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.440 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.8 REMARK 3 NUMBER OF REFLECTIONS : 42200 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.176 REMARK 3 FREE R VALUE : 0.228 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.040 REMARK 3 FREE R VALUE TEST SET COUNT : 2125 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 30.0421 - 5.4231 1.00 2991 158 0.1608 0.1945 REMARK 3 2 5.4231 - 4.3086 0.99 2861 150 0.1338 0.1734 REMARK 3 3 4.3086 - 3.7651 1.00 2817 172 0.1435 0.1786 REMARK 3 4 3.7651 - 3.4214 0.99 2823 149 0.1579 0.1926 REMARK 3 5 3.4214 - 3.1764 0.99 2800 142 0.1674 0.2445 REMARK 3 6 3.1764 - 2.9893 0.99 2759 156 0.1946 0.2735 REMARK 3 7 2.9893 - 2.8398 0.99 2777 140 0.2019 0.2924 REMARK 3 8 2.8398 - 2.7162 0.98 2736 163 0.2032 0.2708 REMARK 3 9 2.7162 - 2.6117 0.98 2720 143 0.2093 0.2862 REMARK 3 10 2.6117 - 2.5216 0.97 2706 151 0.2139 0.2966 REMARK 3 11 2.5216 - 2.4428 0.97 2702 140 0.2214 0.2650 REMARK 3 12 2.4428 - 2.3730 0.93 2583 126 0.2274 0.3145 REMARK 3 13 2.3730 - 2.3106 0.88 2463 127 0.2471 0.2687 REMARK 3 14 2.3106 - 2.2542 0.82 2279 111 0.2508 0.2965 REMARK 3 15 2.2542 - 2.2030 0.73 2058 97 0.2749 0.4039 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) : 0.280 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.680 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 48.84 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 : 0.011 5277 REMARK 3 ANGLE : 1.258 7228 REMARK 3 CHIRALITY : 0.048 800 REMARK 3 PLANARITY : 0.006 857 REMARK 3 DIHEDRAL : 20.114 2070 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 8 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 297 THROUGH 467 ) REMARK 3 ORIGIN FOR THE GROUP (A): -9.9820 -21.1962 47.1959 REMARK 3 T TENSOR REMARK 3 T11: 0.3660 T22: 0.2637 REMARK 3 T33: 0.2513 T12: 0.0253 REMARK 3 T13: 0.0417 T23: 0.0023 REMARK 3 L TENSOR REMARK 3 L11: 2.0942 L22: 1.7712 REMARK 3 L33: 1.7185 L12: -0.2986 REMARK 3 L13: -0.4077 L23: -0.0843 REMARK 3 S TENSOR REMARK 3 S11: -0.0316 S12: -0.1641 S13: -0.1105 REMARK 3 S21: 0.2109 S22: 0.0310 S23: 0.0070 REMARK 3 S31: 0.1617 S32: 0.0513 S33: 0.0014 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 468 THROUGH 521 ) REMARK 3 ORIGIN FOR THE GROUP (A): -23.8005 -2.8801 27.8402 REMARK 3 T TENSOR REMARK 3 T11: 0.3870 T22: 0.1535 REMARK 3 T33: 0.2424 T12: -0.0549 REMARK 3 T13: 0.0592 T23: 0.0695 REMARK 3 L TENSOR REMARK 3 L11: 1.0014 L22: 1.0180 REMARK 3 L33: 2.0031 L12: -0.3111 REMARK 3 L13: 0.0396 L23: 0.8190 REMARK 3 S TENSOR REMARK 3 S11: -0.0441 S12: -0.3313 S13: 0.3579 REMARK 3 S21: -0.0868 S22: -0.0643 S23: -0.0094 REMARK 3 S31: -0.0997 S32: -0.4035 S33: 0.1423 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 522 THROUGH 604 ) REMARK 3 ORIGIN FOR THE GROUP (A): -35.7461 -9.3175 12.7620 REMARK 3 T TENSOR REMARK 3 T11: 0.5510 T22: 0.3525 REMARK 3 T33: 0.3576 T12: -0.0791 REMARK 3 T13: 0.0559 T23: -0.0191 REMARK 3 L TENSOR REMARK 3 L11: 0.8379 L22: 1.7780 REMARK 3 L33: 3.9902 L12: 0.4150 REMARK 3 L13: 1.9933 L23: 1.1228 REMARK 3 S TENSOR REMARK 3 S11: 0.0413 S12: 0.0634 S13: -0.0040 REMARK 3 S21: -0.5147 S22: 0.0694 S23: 0.0208 REMARK 3 S31: -0.0625 S32: -0.1289 S33: -0.0580 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 605 THROUGH 676 ) REMARK 3 ORIGIN FOR THE GROUP (A): -12.6036 0.3775 22.2772 REMARK 3 T TENSOR REMARK 3 T11: 0.3599 T22: 0.2240 REMARK 3 T33: 0.3044 T12: -0.0143 REMARK 3 T13: 0.0053 T23: -0.0304 REMARK 3 L TENSOR REMARK 3 L11: 1.2826 L22: 1.1930 REMARK 3 L33: 1.5919 L12: 0.2386 REMARK 3 L13: -0.6546 L23: -0.2294 REMARK 3 S TENSOR REMARK 3 S11: 0.1137 S12: 0.0196 S13: 0.1350 REMARK 3 S21: -0.0610 S22: -0.0516 S23: 0.2250 REMARK 3 S31: -0.0931 S32: -0.0902 S33: -0.0094 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 677 THROUGH 743 ) REMARK 3 ORIGIN FOR THE GROUP (A): -8.3382 -2.2487 -0.2624 REMARK 3 T TENSOR REMARK 3 T11: 0.5638 T22: 0.3688 REMARK 3 T33: 0.4183 T12: 0.0786 REMARK 3 T13: -0.1594 T23: -0.0702 REMARK 3 L TENSOR REMARK 3 L11: 5.7340 L22: 3.3969 REMARK 3 L33: 3.9861 L12: 0.4706 REMARK 3 L13: 1.1059 L23: -1.1154 REMARK 3 S TENSOR REMARK 3 S11: 0.5267 S12: 0.3709 S13: -0.7164 REMARK 3 S21: -0.5306 S22: -0.1097 S23: 0.4454 REMARK 3 S31: 0.2820 S32: 0.0151 S33: -0.4184 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 744 THROUGH 876 ) REMARK 3 ORIGIN FOR THE GROUP (A): -4.5301 -3.5663 22.5212 REMARK 3 T TENSOR REMARK 3 T11: 0.3097 T22: 0.2267 REMARK 3 T33: 0.2206 T12: -0.0022 REMARK 3 T13: -0.0163 T23: 0.0144 REMARK 3 L TENSOR REMARK 3 L11: 1.2404 L22: 2.4456 REMARK 3 L33: 1.6022 L12: -0.7828 REMARK 3 L13: -0.8172 L23: 0.9534 REMARK 3 S TENSOR REMARK 3 S11: 0.0706 S12: 0.0065 S13: -0.0246 REMARK 3 S21: -0.1696 S22: -0.0578 S23: 0.0499 REMARK 3 S31: -0.0142 S32: 0.0673 S33: -0.0275 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 5 THROUGH 14 ) REMARK 3 ORIGIN FOR THE GROUP (A): -26.8979 -15.7873 18.4765 REMARK 3 T TENSOR REMARK 3 T11: 0.7894 T22: 0.6627 REMARK 3 T33: 0.6830 T12: 0.0208 REMARK 3 T13: -0.0254 T23: 0.0313 REMARK 3 L TENSOR REMARK 3 L11: 2.9454 L22: 3.8422 REMARK 3 L33: 2.4697 L12: 1.1985 REMARK 3 L13: -0.6648 L23: -1.2337 REMARK 3 S TENSOR REMARK 3 S11: 0.0789 S12: -0.5828 S13: -0.1476 REMARK 3 S21: -0.6443 S22: -0.0842 S23: -0.5415 REMARK 3 S31: 0.7446 S32: 0.0342 S33: 0.1068 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 4 THROUGH 14 ) REMARK 3 ORIGIN FOR THE GROUP (A): -28.4422 -17.4438 20.4110 REMARK 3 T TENSOR REMARK 3 T11: 0.9895 T22: 0.5778 REMARK 3 T33: 0.6022 T12: -0.1044 REMARK 3 T13: -0.0027 T23: 0.0503 REMARK 3 L TENSOR REMARK 3 L11: 5.7529 L22: 2.9225 REMARK 3 L33: 2.5676 L12: -0.5837 REMARK 3 L13: 1.2577 L23: 0.8329 REMARK 3 S TENSOR REMARK 3 S11: 0.4662 S12: -0.0541 S13: -0.6276 REMARK 3 S21: -0.1744 S22: -0.2161 S23: 0.1587 REMARK 3 S31: 1.0866 S32: -0.1835 S33: -0.1802 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 4O0I COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-JAN-14. REMARK 100 THE DEPOSITION ID IS D_1000083887. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-OCT-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.2.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 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 : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 42234 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.203 REMARK 200 RESOLUTION RANGE LOW (A) : 70.328 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.0 REMARK 200 DATA REDUNDANCY : 5.600 REMARK 200 R MERGE (I) : 0.08100 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 77.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.10 REMARK 200 R MERGE FOR SHELL (I) : 0.37000 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 4DWI REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.06 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.93 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG3350, 0.2 M AMMONIUM SULFATE, REMARK 280 0.1 M BIS-TRIS, PH 6.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 43.38500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 53.02050 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 46.98350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 53.02050 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 43.38500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 46.98350 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6050 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27820 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -118.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 DC B 3 REMARK 465 DG C 15 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 1TW B 4 P OP1 OP2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 1179 O HOH A 1183 1.84 REMARK 500 NZ LYS A 366 O HOH A 1194 2.01 REMARK 500 O5' 1TW B 4 O HOH B 109 2.06 REMARK 500 O PHE A 539 O HOH A 1163 2.14 REMARK 500 O HOH A 1183 O HOH A 1197 2.14 REMARK 500 O HOH A 1157 O HOH A 1195 2.15 REMARK 500 O HOH A 1151 O HOH A 1168 2.19 REMARK 500 OP1 DT B 10 O HOH B 105 2.19 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 298 112.36 22.59 REMARK 500 ASP A 402 95.75 -166.93 REMARK 500 ALA A 421 37.33 -81.87 REMARK 500 ASP A 439 158.13 -49.39 REMARK 500 GLN A 524 148.58 -177.13 REMARK 500 GLN A 543 42.28 19.80 REMARK 500 ILE A 588 -68.17 -91.71 REMARK 500 ILE A 628 -23.80 -145.91 REMARK 500 ILE A 716 -145.30 38.05 REMARK 500 SER A 717 -10.93 170.19 REMARK 500 ASP A 718 -63.18 59.14 REMARK 500 ASN A 726 82.07 -1.45 REMARK 500 HIS A 829 -58.18 69.72 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 LEU A 725 ASN A 726 -144.99 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 NA A 908 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 308 OG1 REMARK 620 2 GLU A 310 OE2 106.5 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 909 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 372 O REMARK 620 2 GOL A 907 O1 101.3 REMARK 620 3 HOH A1060 O 141.2 90.0 REMARK 620 4 HOH A1061 O 115.0 105.0 97.1 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 902 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 903 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 904 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 905 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 906 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 907 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 908 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 909 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1KW0 RELATED DB: PDB REMARK 900 2'-MESE-ARABINO-GUANOSINE DERIVATIZED DNA DBREF 4O0I A 298 876 UNP D9N168 D9N168_GEOSE 1 579 DBREF 4O0I B 3 14 PDB 4O0I 4O0I 3 14 DBREF 4O0I C 4 15 PDB 4O0I 4O0I 4 15 SEQADV 4O0I SER A 297 UNP D9N168 EXPRESSION TAG SEQADV 4O0I ASP A 598 UNP D9N168 ALA 301 CONFLICT SEQADV 4O0I VAL A 713 UNP D9N168 PRO 416 CONFLICT SEQRES 1 A 580 SER LYS MET ALA PHE THR LEU ALA ASP ARG VAL THR GLU SEQRES 2 A 580 GLU MET LEU ALA ASP LYS ALA ALA LEU VAL VAL GLU VAL SEQRES 3 A 580 VAL GLU GLU ASN TYR HIS ASP ALA PRO ILE VAL GLY ILE SEQRES 4 A 580 ALA VAL VAL ASN GLU HIS GLY ARG PHE PHE LEU ARG PRO SEQRES 5 A 580 GLU THR ALA LEU ALA ASP PRO GLN PHE VAL ALA TRP LEU SEQRES 6 A 580 GLY ASP GLU THR LYS LYS LYS SER MET PHE ASP SER LYS SEQRES 7 A 580 ARG ALA ALA VAL ALA LEU LYS TRP LYS GLY ILE GLU LEU SEQRES 8 A 580 CYS GLY VAL SER PHE ASP LEU LEU LEU ALA ALA TYR LEU SEQRES 9 A 580 LEU ASP PRO ALA GLN GLY VAL ASP ASP VAL ALA ALA ALA SEQRES 10 A 580 ALA LYS MET LYS GLN TYR GLU ALA VAL ARG PRO ASP GLU SEQRES 11 A 580 ALA VAL TYR GLY LYS GLY ALA LYS ARG ALA VAL PRO ASP SEQRES 12 A 580 GLU PRO VAL LEU ALA GLU HIS LEU VAL ARG LYS ALA ALA SEQRES 13 A 580 ALA ILE TRP GLU LEU GLU ARG PRO PHE LEU ASP GLU LEU SEQRES 14 A 580 ARG ARG ASN GLU GLN ASP ARG LEU LEU VAL GLU LEU GLU SEQRES 15 A 580 GLN PRO LEU SER SER ILE LEU ALA GLU MET GLU PHE ALA SEQRES 16 A 580 GLY VAL LYS VAL ASP THR LYS ARG LEU GLU GLN MET GLY SEQRES 17 A 580 LYS GLU LEU ALA GLU GLN LEU GLY THR VAL GLU GLN ARG SEQRES 18 A 580 ILE TYR GLU LEU ALA GLY GLN GLU PHE ASN ILE ASN SER SEQRES 19 A 580 PRO LYS GLN LEU GLY VAL ILE LEU PHE GLU LYS LEU GLN SEQRES 20 A 580 LEU PRO VAL LEU LYS LYS THR LYS THR GLY TYR SER THR SEQRES 21 A 580 SER ALA ASP VAL LEU GLU LYS LEU ALA PRO TYR HIS GLU SEQRES 22 A 580 ILE VAL GLU ASN ILE LEU HIS TYR ARG GLN LEU GLY LYS SEQRES 23 A 580 LEU GLN SER THR TYR ILE GLU GLY LEU LEU LYS VAL VAL SEQRES 24 A 580 ARG PRO ASP THR LYS LYS VAL HIS THR ILE PHE ASN GLN SEQRES 25 A 580 ALA LEU THR GLN THR GLY ARG LEU SER SER THR GLU PRO SEQRES 26 A 580 ASN LEU GLN ASN ILE PRO ILE ARG LEU GLU GLU GLY ARG SEQRES 27 A 580 LYS ILE ARG GLN ALA PHE VAL PRO SER GLU SER ASP TRP SEQRES 28 A 580 LEU ILE PHE ALA ALA ASP TYR SER GLN ILE GLU LEU ARG SEQRES 29 A 580 VAL LEU ALA HIS ILE ALA GLU ASP ASP ASN LEU MET GLU SEQRES 30 A 580 ALA PHE ARG ARG ASP LEU ASP ILE HIS THR LYS THR ALA SEQRES 31 A 580 MET ASP ILE PHE GLN VAL SER GLU ASP GLU VAL THR PRO SEQRES 32 A 580 ASN MET ARG ARG GLN ALA LYS ALA VAL ASN PHE GLY ILE SEQRES 33 A 580 VAL TYR GLY ILE SER ASP TYR GLY LEU ALA GLN ASN LEU SEQRES 34 A 580 ASN ILE SER ARG LYS GLU ALA ALA GLU PHE ILE GLU ARG SEQRES 35 A 580 TYR PHE GLU SER PHE PRO GLY VAL LYS ARG TYR MET GLU SEQRES 36 A 580 ASN ILE VAL GLN GLU ALA LYS GLN LYS GLY TYR VAL THR SEQRES 37 A 580 THR LEU LEU HIS ARG ARG ARG TYR LEU PRO ASP ILE THR SEQRES 38 A 580 SER ARG ASN PHE ASN VAL ARG SER PHE ALA GLU ARG MET SEQRES 39 A 580 ALA MET ASN THR PRO ILE GLN GLY SER ALA ALA ASP ILE SEQRES 40 A 580 ILE LYS LYS ALA MET ILE ASP LEU ASN ALA ARG LEU LYS SEQRES 41 A 580 GLU GLU ARG LEU GLN ALA HIS LEU LEU LEU GLN VAL HIS SEQRES 42 A 580 ASP GLU LEU ILE LEU GLU ALA PRO LYS GLU GLU MET GLU SEQRES 43 A 580 ARG LEU CYS ARG LEU VAL PRO GLU VAL MET GLU GLN ALA SEQRES 44 A 580 VAL THR LEU ARG VAL PRO LEU LYS VAL ASP TYR HIS TYR SEQRES 45 A 580 GLY SER THR TRP TYR ASP ALA LYS SEQRES 1 B 12 DC 1TW DC DG DA DA DT DT DC DG DC DG SEQRES 1 C 12 DC 1TW DC DG DA DA DT DT DC DG DC DG HET 1TW B 4 21 HET 1TW C 5 24 HET SO4 A 901 5 HET SO4 A 902 5 HET SO4 A 903 5 HET SO4 A 904 5 HET SO4 A 905 5 HET SO4 A 906 5 HET GOL A 907 6 HET NA A 908 1 HET NA A 909 1 HETNAM 1TW 2-AMINO-9-(2-SE-METHYL-5-O-PHOSPHONO-2-SELENO-BETA-D- HETNAM 2 1TW ARABINOFURANOSYL)-1,9-DIHYDRO-6H-PURIN-6-ONE HETNAM SO4 SULFATE ION HETNAM GOL GLYCEROL HETNAM NA SODIUM ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 1TW 2(C11 H16 N5 O7 P SE) FORMUL 4 SO4 6(O4 S 2-) FORMUL 10 GOL C3 H8 O3 FORMUL 11 NA 2(NA 1+) FORMUL 13 HOH *238(H2 O) HELIX 1 1 THR A 308 ALA A 313 5 6 HELIX 2 2 ARG A 347 LEU A 352 1 6 HELIX 3 3 ASP A 354 ASP A 363 1 10 HELIX 4 4 ASP A 372 TRP A 382 1 11 HELIX 5 5 LEU A 394 ASP A 402 1 9 HELIX 6 6 PRO A 403 GLY A 406 5 4 HELIX 7 7 ASP A 409 MET A 416 1 8 HELIX 8 8 PRO A 424 GLY A 430 1 7 HELIX 9 9 LYS A 431 ARG A 435 5 5 HELIX 10 10 ASP A 439 ASN A 468 1 30 HELIX 11 11 GLN A 470 LEU A 477 1 8 HELIX 12 12 LEU A 477 GLY A 492 1 16 HELIX 13 13 ASP A 496 GLY A 523 1 28 HELIX 14 14 SER A 530 GLU A 540 1 11 HELIX 15 15 SER A 557 ALA A 565 1 9 HELIX 16 16 GLU A 569 TYR A 587 1 19 HELIX 17 17 ILE A 588 VAL A 595 1 8 HELIX 18 18 LEU A 630 LYS A 635 1 6 HELIX 19 19 ILE A 636 GLN A 638 5 3 HELIX 20 20 GLN A 656 GLU A 667 1 12 HELIX 21 21 ASP A 668 ARG A 677 1 10 HELIX 22 22 ASP A 680 GLN A 691 1 12 HELIX 23 23 SER A 693 VAL A 697 5 5 HELIX 24 24 THR A 698 VAL A 713 1 16 HELIX 25 25 ASP A 718 LEU A 725 1 8 HELIX 26 26 SER A 728 PHE A 743 1 16 HELIX 27 27 PHE A 743 GLY A 761 1 19 HELIX 28 28 PRO A 774 SER A 778 5 5 HELIX 29 29 ASN A 780 GLU A 818 1 39 HELIX 30 30 GLU A 840 ALA A 855 1 16 SHEET 1 A 6 THR A 302 LEU A 303 0 SHEET 2 A 6 GLY A 342 LEU A 346 1 O ARG A 343 N THR A 302 SHEET 3 A 6 ILE A 335 ASN A 339 -1 N VAL A 337 O PHE A 344 SHEET 4 A 6 LYS A 315 VAL A 320 -1 N ALA A 317 O VAL A 338 SHEET 5 A 6 LYS A 367 MET A 370 1 O SER A 369 N LEU A 318 SHEET 6 A 6 VAL A 390 ASP A 393 1 O PHE A 392 N MET A 370 SHEET 1 B 3 LYS A 601 VAL A 602 0 SHEET 2 B 3 VAL A 493 VAL A 495 -1 N VAL A 493 O VAL A 602 SHEET 3 B 3 PHE A 640 VAL A 641 -1 O VAL A 641 N LYS A 494 SHEET 1 C 2 ILE A 605 ASN A 607 0 SHEET 2 C 2 SER A 617 THR A 619 -1 O SER A 617 N ASN A 607 SHEET 1 D 4 HIS A 823 GLN A 827 0 SHEET 2 D 4 GLU A 831 PRO A 837 -1 O ILE A 833 N LEU A 825 SHEET 3 D 4 TRP A 647 TYR A 654 -1 N PHE A 650 O LEU A 834 SHEET 4 D 4 VAL A 864 GLY A 869 -1 O ASP A 865 N ASP A 653 SHEET 1 E 2 TYR A 762 THR A 764 0 SHEET 2 E 2 ARG A 770 TYR A 772 -1 O ARG A 771 N VAL A 763 LINK O3' 1TW B 4 P DC B 5 1555 1555 1.62 LINK O3' DC C 4 P 1TW C 5 1555 1555 1.61 LINK O3' 1TW C 5 P DC C 6 1555 1555 1.61 LINK OG1 THR A 308 NA NA A 908 1555 1555 2.89 LINK OE2 GLU A 310 NA NA A 908 1555 1555 2.75 LINK O ASP A 372 NA NA A 909 1555 1555 2.98 LINK O1 GOL A 907 NA NA A 909 1555 1555 3.09 LINK NA NA A 909 O HOH A1060 1555 1555 2.65 LINK NA NA A 909 O HOH A1061 1555 1555 2.98 CISPEP 1 GLU A 620 PRO A 621 0 2.86 SITE 1 AC1 5 MET A 299 ALA A 300 ARG A 343 ARG A 677 SITE 2 AC1 5 LYS A 684 SITE 1 AC2 4 HIS A 682 ARG A 702 LYS A 706 HOH A1016 SITE 1 AC3 3 THR A 308 GLU A 309 HOH A1030 SITE 1 AC4 5 GLU A 364 LYS A 367 GLY A 389 VAL A 390 SITE 2 AC4 5 SER A 391 SITE 1 AC5 7 GLU A 515 TYR A 519 PHE A 526 ASN A 527 SITE 2 AC5 7 ILE A 528 ASN A 529 TYR A 577 SITE 1 AC6 6 GLU A 667 ASP A 668 ASP A 669 GLY A 745 SITE 2 AC6 6 ARG A 748 HOH A1052 SITE 1 AC7 11 GLU A 321 PHE A 371 ASP A 372 ARG A 375 SITE 2 AC7 11 ASP A 409 VAL A 410 ASP A 425 LYS A 450 SITE 3 AC7 11 NA A 909 HOH A1062 HOH A1079 SITE 1 AC8 2 THR A 308 GLU A 310 SITE 1 AC9 6 PHE A 371 ASP A 372 ARG A 375 GOL A 907 SITE 2 AC9 6 HOH A1060 HOH A1061 CRYST1 86.770 93.967 106.041 90.00 90.00 90.00 P 21 21 21 8 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 0.011525 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010642 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009430 0.00000