HEADER RNA BINDING PROTEIN/RNA 16-MAR-20 6M6S TITLE CRYSTAL STRUCTURE OF CAENORHABDITIS ELEGANS DICER-RELATED HELICASE 3 TITLE 2 (DRH-3) C-TERMINAL DOMAIN WITH 5'-PPP 12-MER DSRNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: DICER RELATED HELICASE; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: C-TERMINAL DOMAIN; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: RNA (5'-R(*(GTP)P*GP*CP*GP*CP*GP*CP*GP*CP*GP*CP*C)-3'); COMPND 8 CHAIN: C, D; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CAENORHABDITIS ELEGANS; SOURCE 3 ORGANISM_TAXID: 6239; SOURCE 4 GENE: DRH-3, CELE_D2005.5, D2005.5; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 SYNTHETIC: YES; SOURCE 9 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 10 ORGANISM_TAXID: 32630 KEYWDS RNA INTERFERENCE (RNAI), RNA HELICASE, HYDROLASE, RNA BINDING KEYWDS 2 PROTEIN, RNA BINDING PROTEIN-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR K.LI,J.ZHENG,M.WIRAWAN,Z.XIONG,O.FEDOROVA,P.GRIFFIN,A.PLYLE,D.LUO REVDAT 3 29-NOV-23 6M6S 1 REMARK REVDAT 2 10-AUG-22 6M6S 1 JRNL REVDAT 1 17-MAR-21 6M6S 0 JRNL AUTH K.LI,J.ZHENG,M.WIRAWAN,N.M.TRINH,O.FEDOROVA,P.R.GRIFFIN, JRNL AUTH 2 A.M.PYLE,D.LUO JRNL TITL INSIGHTS INTO THE STRUCTURE AND RNA-BINDING SPECIFICITY OF JRNL TITL 2 CAENORHABDITIS ELEGANS DICER-RELATED HELICASE 3 (DRH-3). JRNL REF NUCLEIC ACIDS RES. V. 49 9978 2021 JRNL REFN ESSN 1362-4962 JRNL PMID 34403472 JRNL DOI 10.1093/NAR/GKAB712 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX DEV_1137 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.03 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.910 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 56281 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.171 REMARK 3 R VALUE (WORKING SET) : 0.169 REMARK 3 FREE R VALUE : 0.199 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.080 REMARK 3 FREE R VALUE TEST SET COUNT : 2858 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 23.0300 - 4.3339 0.92 2699 153 0.1588 0.1848 REMARK 3 2 4.3339 - 3.4436 0.97 2683 146 0.1389 0.1652 REMARK 3 3 3.4436 - 3.0094 0.98 2708 133 0.1549 0.1597 REMARK 3 4 3.0094 - 2.7347 0.99 2714 147 0.1780 0.2187 REMARK 3 5 2.7347 - 2.5390 0.99 2704 133 0.1774 0.2125 REMARK 3 6 2.5390 - 2.3895 0.99 2678 131 0.1659 0.1917 REMARK 3 7 2.3895 - 2.2699 1.00 2660 158 0.1671 0.1975 REMARK 3 8 2.2699 - 2.1712 1.00 2701 152 0.1638 0.1995 REMARK 3 9 2.1712 - 2.0876 1.00 2655 144 0.1667 0.2046 REMARK 3 10 2.0876 - 2.0157 1.00 2658 154 0.1727 0.2112 REMARK 3 11 2.0157 - 1.9527 1.00 2691 141 0.1741 0.1996 REMARK 3 12 1.9527 - 1.8969 1.00 2655 133 0.1796 0.2232 REMARK 3 13 1.8969 - 1.8470 1.00 2698 130 0.1825 0.2233 REMARK 3 14 1.8470 - 1.8019 1.00 2631 157 0.1879 0.2196 REMARK 3 15 1.8019 - 1.7610 1.00 2640 145 0.1999 0.2273 REMARK 3 16 1.7610 - 1.7235 1.00 2663 147 0.2037 0.2603 REMARK 3 17 1.7235 - 1.6890 1.00 2632 134 0.2195 0.2526 REMARK 3 18 1.6890 - 1.6572 1.00 2678 145 0.2266 0.2739 REMARK 3 19 1.6572 - 1.6276 1.00 2636 139 0.2403 0.2744 REMARK 3 20 1.6276 - 1.6000 1.00 2639 136 0.2607 0.2940 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) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.740 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.10 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 : 0.017 3452 REMARK 3 ANGLE : 1.881 4775 REMARK 3 CHIRALITY : 0.125 532 REMARK 3 PLANARITY : 0.009 499 REMARK 3 DIHEDRAL : 20.001 1399 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' REMARK 3 ORIGIN FOR THE GROUP (A): -11.9244 -14.7492 -1.2914 REMARK 3 T TENSOR REMARK 3 T11: 0.1304 T22: 0.0862 REMARK 3 T33: 0.0720 T12: 0.0002 REMARK 3 T13: -0.0078 T23: -0.0006 REMARK 3 L TENSOR REMARK 3 L11: 1.7957 L22: 1.8271 REMARK 3 L33: 1.9842 L12: 0.5947 REMARK 3 L13: -0.0564 L23: -0.3894 REMARK 3 S TENSOR REMARK 3 S11: -0.0422 S12: 0.2065 S13: -0.0858 REMARK 3 S21: -0.1357 S22: 0.0904 S23: -0.0002 REMARK 3 S31: 0.0437 S32: -0.0776 S33: -0.0453 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'B' REMARK 3 ORIGIN FOR THE GROUP (A): -7.6694 -33.6456 32.6755 REMARK 3 T TENSOR REMARK 3 T11: 0.1626 T22: 0.2064 REMARK 3 T33: 0.1212 T12: -0.0140 REMARK 3 T13: -0.0394 T23: 0.0661 REMARK 3 L TENSOR REMARK 3 L11: 1.4405 L22: 2.1788 REMARK 3 L33: 2.5555 L12: 0.1691 REMARK 3 L13: -0.2369 L23: -0.5831 REMARK 3 S TENSOR REMARK 3 S11: -0.0254 S12: -0.0897 S13: -0.1585 REMARK 3 S21: -0.0560 S22: -0.0239 S23: 0.0536 REMARK 3 S31: 0.1286 S32: 0.2416 S33: 0.0231 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'C' REMARK 3 ORIGIN FOR THE GROUP (A): -8.3833 -37.3567 8.1379 REMARK 3 T TENSOR REMARK 3 T11: 0.5458 T22: 0.2913 REMARK 3 T33: 0.2546 T12: 0.1069 REMARK 3 T13: 0.0193 T23: 0.0631 REMARK 3 L TENSOR REMARK 3 L11: 0.3320 L22: 1.0338 REMARK 3 L33: 0.5337 L12: -0.5895 REMARK 3 L13: 0.4236 L23: -0.7683 REMARK 3 S TENSOR REMARK 3 S11: -0.0025 S12: -0.2722 S13: -0.2982 REMARK 3 S21: -0.2107 S22: 0.0626 S23: 0.0941 REMARK 3 S31: 0.9098 S32: 0.1667 S33: -0.0864 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'D' REMARK 3 ORIGIN FOR THE GROUP (A): -9.6433 -39.0314 10.3231 REMARK 3 T TENSOR REMARK 3 T11: 0.6305 T22: 0.3825 REMARK 3 T33: 0.2454 T12: -0.0486 REMARK 3 T13: -0.0255 T23: 0.0244 REMARK 3 L TENSOR REMARK 3 L11: 1.5383 L22: 0.2817 REMARK 3 L33: 5.0269 L12: -0.1622 REMARK 3 L13: -0.9139 L23: -1.0028 REMARK 3 S TENSOR REMARK 3 S11: -0.0332 S12: -0.2563 S13: -0.2735 REMARK 3 S21: -0.6842 S22: -0.1284 S23: 0.0928 REMARK 3 S31: 1.1262 S32: 1.0041 S33: -0.0776 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 6M6S COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-MAR-20. REMARK 100 THE DEPOSITION ID IS D_1300016186. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-APR-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 56358 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 43.960 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 3.100 REMARK 200 R MERGE (I) : 0.04200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.63 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : 0.76100 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: 6M6R REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.02 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS PH 7.5, 30% W/V REMARK 280 POLYETHYLENE GLYCOL 6000, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 291.15K 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 46.54500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 66.91150 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 46.54500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 66.91150 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: 5260 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19680 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -16.0 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 MET A 939 REMARK 465 ARG A 940 REMARK 465 LEU A 941 REMARK 465 ARG A 942 REMARK 465 HIS A 943 REMARK 465 GLU A 944 REMARK 465 ILE A 1105 REMARK 465 GLN A 1106 REMARK 465 GLN A 1107 REMARK 465 GLU A 1108 REMARK 465 MET B 939 REMARK 465 ARG B 940 REMARK 465 LEU B 941 REMARK 465 ARG B 942 REMARK 465 HIS B 943 REMARK 465 GLU B 944 REMARK 465 GLN B 1107 REMARK 465 GLU B 1108 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 ASN A 945 CG OD1 ND2 REMARK 470 LYS A 946 CG CD CE NZ REMARK 470 GLU A1078 CG CD OE1 OE2 REMARK 470 LYS A1101 CG CD CE NZ REMARK 470 HIS A1104 CG ND1 CD2 CE1 NE2 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 1361 O HOH A 1446 1.82 REMARK 500 O HOH A 1310 O HOH A 1334 1.94 REMARK 500 O HOH C 110 O HOH C 126 1.97 REMARK 500 NZ LYS A 990 O HOH A 1301 1.97 REMARK 500 O HOH C 113 O HOH C 125 1.98 REMARK 500 O ASN B 945 O HOH B 1301 1.99 REMARK 500 OE2 GLU B 1082 O HOH B 1302 2.03 REMARK 500 O HOH A 1412 O HOH A 1435 2.03 REMARK 500 O HOH A 1437 O HOH B 1387 2.04 REMARK 500 O6 G D 2 O HOH D 101 2.04 REMARK 500 NZ LYS A 961 O HOH A 1302 2.07 REMARK 500 SD MET B 951 O HOH B 1405 2.07 REMARK 500 NH1 ARG B 1021 O HOH B 1303 2.11 REMARK 500 O HOH C 125 O HOH C 129 2.12 REMARK 500 O HOH A 1430 O HOH A 1432 2.12 REMARK 500 O HOH A 1456 O HOH C 128 2.13 REMARK 500 OP1 C D 3 O HOH D 102 2.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 1466 O HOH A 1466 2555 1.72 REMARK 500 O HOH A 1311 O HOH A 1446 2555 1.99 REMARK 500 O HOH A 1446 O HOH A 1449 2555 2.10 REMARK 500 O HOH A 1426 O HOH A 1426 2555 2.13 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 MET A 951 CG - SD - CE ANGL. DEV. = -25.8 DEGREES REMARK 500 C D 3 OP1 - P - OP2 ANGL. DEV. = 9.5 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 990 114.86 -164.06 REMARK 500 LEU A1002 -128.74 -125.91 REMARK 500 ASP A1076 -45.01 79.09 REMARK 500 LYS B 990 119.35 -162.22 REMARK 500 ASN B 999 86.62 -153.84 REMARK 500 LEU B1002 -122.44 -122.74 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 ZN A1201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 952 SG REMARK 620 2 CYS A 955 SG 109.0 REMARK 620 3 CYS A1007 SG 113.9 103.4 REMARK 620 4 CYS A1010 SG 102.0 118.8 110.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B1201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 952 SG REMARK 620 2 CYS B 955 SG 111.7 REMARK 620 3 CYS B1007 SG 111.4 102.8 REMARK 620 4 CYS B1010 SG 105.0 115.1 111.0 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 ZN A 1201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 1201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-nucleotide GTP C 1 and G C 2 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-nucleotide GTP C 1 and G C 2 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-nucleotide GTP D 1 and G D 2 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-nucleotide GTP D 1 and G D 2 DBREF 6M6S A 940 1108 UNP Q93413 Q93413_CAEEL 940 1108 DBREF 6M6S B 940 1108 UNP Q93413 Q93413_CAEEL 940 1108 DBREF 6M6S C 1 12 PDB 6M6S 6M6S 1 12 DBREF 6M6S D 1 12 PDB 6M6S 6M6S 1 12 SEQADV 6M6S MET A 939 UNP Q93413 INITIATING METHIONINE SEQADV 6M6S MET B 939 UNP Q93413 INITIATING METHIONINE SEQRES 1 A 170 MET ARG LEU ARG HIS GLU ASN LYS ILE TYR LYS LEU MET SEQRES 2 A 170 CYS SER ASN CYS SER LYS GLU PHE CYS LYS SER ILE TYR SEQRES 3 A 170 ILE LYS LYS VAL PHE SER ASN TYR MET VAL PHE ASP PRO SEQRES 4 A 170 SER VAL TRP ARG PHE LEU HIS VAL GLU SER LYS ARG LYS SEQRES 5 A 170 VAL SER LYS TYR LEU SER GLU ASP ASN GLN PRO LEU SER SEQRES 6 A 170 ASP ILE LYS CYS PHE HIS CYS LYS LEU ASP VAL GLY ARG SEQRES 7 A 170 ALA TYR LYS ILE ARG GLY THR TYR LEU PRO GLN LEU SER SEQRES 8 A 170 VAL LYS ALA LEU THR PHE VAL GLN GLU SER ASP TYR SER SEQRES 9 A 170 SER MET THR LYS ALA LYS TRP SER ASP VAL GLU GLN ASP SEQRES 10 A 170 LEU PHE TYR ILE SER GLU ALA ILE GLU ASP ASP PHE ARG SEQRES 11 A 170 ILE MET LEU ASN ALA LEU SER ASP THR GLU GLU ASN ILE SEQRES 12 A 170 GLU LYS LYS ILE VAL LEU ASP LEU ASP SER ARG GLN HIS SEQRES 13 A 170 ASN LYS GLN LEU GLU MET LYS ARG PHE HIS ILE GLN GLN SEQRES 14 A 170 GLU SEQRES 1 B 170 MET ARG LEU ARG HIS GLU ASN LYS ILE TYR LYS LEU MET SEQRES 2 B 170 CYS SER ASN CYS SER LYS GLU PHE CYS LYS SER ILE TYR SEQRES 3 B 170 ILE LYS LYS VAL PHE SER ASN TYR MET VAL PHE ASP PRO SEQRES 4 B 170 SER VAL TRP ARG PHE LEU HIS VAL GLU SER LYS ARG LYS SEQRES 5 B 170 VAL SER LYS TYR LEU SER GLU ASP ASN GLN PRO LEU SER SEQRES 6 B 170 ASP ILE LYS CYS PHE HIS CYS LYS LEU ASP VAL GLY ARG SEQRES 7 B 170 ALA TYR LYS ILE ARG GLY THR TYR LEU PRO GLN LEU SER SEQRES 8 B 170 VAL LYS ALA LEU THR PHE VAL GLN GLU SER ASP TYR SER SEQRES 9 B 170 SER MET THR LYS ALA LYS TRP SER ASP VAL GLU GLN ASP SEQRES 10 B 170 LEU PHE TYR ILE SER GLU ALA ILE GLU ASP ASP PHE ARG SEQRES 11 B 170 ILE MET LEU ASN ALA LEU SER ASP THR GLU GLU ASN ILE SEQRES 12 B 170 GLU LYS LYS ILE VAL LEU ASP LEU ASP SER ARG GLN HIS SEQRES 13 B 170 ASN LYS GLN LEU GLU MET LYS ARG PHE HIS ILE GLN GLN SEQRES 14 B 170 GLU SEQRES 1 C 12 GTP G C G C G C G C G C C SEQRES 1 D 12 GTP G C G C G C G C G C C HET GTP C 1 64 HET GTP D 1 64 HET ZN A1201 1 HET ZN B1201 1 HETNAM GTP GUANOSINE-5'-TRIPHOSPHATE HETNAM ZN ZINC ION FORMUL 3 GTP 2(C10 H16 N5 O14 P3) FORMUL 5 ZN 2(ZN 2+) FORMUL 7 HOH *332(H2 O) HELIX 1 AA1 ASP A 976 ARG A 981 5 6 HELIX 2 AA2 LYS A 1048 LEU A 1056 1 9 HELIX 3 AA3 ILE A 1063 LEU A 1071 1 9 HELIX 4 AA4 THR A 1077 ARG A 1102 1 26 HELIX 5 AA5 ASP B 976 ARG B 981 5 6 HELIX 6 AA6 LYS B 1048 LEU B 1056 1 9 HELIX 7 AA7 ILE B 1063 LEU B 1071 1 9 HELIX 8 AA8 THR B 1077 GLN B 1106 1 30 SHEET 1 AA1 8 GLU A 958 LYS A 961 0 SHEET 2 AA1 8 TYR A 948 CYS A 952 -1 N LEU A 950 O PHE A 959 SHEET 3 AA1 8 LEU A1033 GLN A1037 -1 O VAL A1036 N LYS A 949 SHEET 4 AA1 8 SER A1043 THR A1045 -1 O MET A1044 N PHE A1035 SHEET 5 AA1 8 SER B1042 MET B1044 1 O SER B1043 N THR A1045 SHEET 6 AA1 8 LEU B1033 GLN B1037 -1 N PHE B1035 O MET B1044 SHEET 7 AA1 8 LYS B 949 CYS B 952 -1 N LYS B 949 O VAL B1036 SHEET 8 AA1 8 GLU B 958 LYS B 961 -1 O PHE B 959 N LEU B 950 SHEET 1 AA2 2 ILE A 965 VAL A 968 0 SHEET 2 AA2 2 ASN A 971 VAL A 974 -1 O MET A 973 N LYS A 966 SHEET 1 AA3 4 LEU A 983 GLU A 986 0 SHEET 2 AA3 4 ASN A 999 CYS A1007 -1 O LYS A1006 N HIS A 984 SHEET 3 AA3 4 ASP A1013 ILE A1020 -1 O ALA A1017 N SER A1003 SHEET 4 AA3 4 THR A1023 LEU A1028 -1 O LEU A1025 N TYR A1018 SHEET 1 AA4 3 ASN B 971 VAL B 974 0 SHEET 2 AA4 3 ILE B 965 VAL B 968 -1 N LYS B 966 O MET B 973 SHEET 3 AA4 3 SER B1060 GLU B1061 1 O SER B1060 N LYS B 967 SHEET 1 AA5 4 LEU B 983 GLU B 986 0 SHEET 2 AA5 4 ASN B 999 CYS B1007 -1 O LYS B1006 N HIS B 984 SHEET 3 AA5 4 ASP B1013 ILE B1020 -1 O ALA B1017 N LEU B1002 SHEET 4 AA5 4 THR B1023 LEU B1028 -1 O THR B1023 N ILE B1020 LINK O3'AGTP C 1 P G C 2 1555 1555 1.59 LINK O3'BGTP C 1 P G C 2 1555 1555 1.59 LINK O3'AGTP D 1 P G D 2 1555 1555 1.59 LINK O3'BGTP D 1 P G D 2 1555 1555 1.59 LINK SG CYS A 952 ZN ZN A1201 1555 1555 2.38 LINK SG CYS A 955 ZN ZN A1201 1555 1555 2.26 LINK SG CYS A1007 ZN ZN A1201 1555 1555 2.29 LINK SG CYS A1010 ZN ZN A1201 1555 1555 2.34 LINK SG CYS B 952 ZN ZN B1201 1555 1555 2.41 LINK SG CYS B 955 ZN ZN B1201 1555 1555 2.23 LINK SG CYS B1007 ZN ZN B1201 1555 1555 2.33 LINK SG CYS B1010 ZN ZN B1201 1555 1555 2.30 SITE 1 AC1 4 CYS A 952 CYS A 955 CYS A1007 CYS A1010 SITE 1 AC2 4 CYS B 952 CYS B 955 CYS B1007 CYS B1010 SITE 1 AC3 23 PHE A 969 SER A 970 ASN A 971 LYS A 988 SITE 2 AC3 23 LYS A 990 SER A 992 LYS A 993 TYR A 994 SITE 3 AC3 23 ARG A1016 TYR A1018 GLN A1027 HOH A1301 SITE 4 AC3 23 C C 3 HOH C 102 HOH C 104 HOH C 107 SITE 5 AC3 23 HOH C 109 HOH C 112 HOH C 113 HOH C 117 SITE 6 AC3 23 G D 10 C D 11 C D 12 SITE 1 AC4 23 PHE A 969 SER A 970 ASN A 971 LYS A 988 SITE 2 AC4 23 LYS A 990 SER A 992 LYS A 993 TYR A 994 SITE 3 AC4 23 ARG A1016 TYR A1018 GLN A1027 HOH A1301 SITE 4 AC4 23 C C 3 HOH C 102 HOH C 104 HOH C 107 SITE 5 AC4 23 HOH C 109 HOH C 112 HOH C 113 HOH C 117 SITE 6 AC4 23 G D 10 C D 11 C D 12 SITE 1 AC5 22 PHE B 969 SER B 970 ASN B 971 LYS B 988 SITE 2 AC5 22 SER B 992 LYS B 993 TYR B 994 ARG B1016 SITE 3 AC5 22 TYR B1018 GLN B1027 HOH B1315 G C 10 SITE 4 AC5 22 C C 11 C C 12 C D 3 HOH D 101 SITE 5 AC5 22 HOH D 108 HOH D 109 HOH D 110 HOH D 111 SITE 6 AC5 22 HOH D 120 HOH D 124 SITE 1 AC6 22 PHE B 969 SER B 970 ASN B 971 LYS B 988 SITE 2 AC6 22 SER B 992 LYS B 993 TYR B 994 ARG B1016 SITE 3 AC6 22 TYR B1018 GLN B1027 HOH B1315 G C 10 SITE 4 AC6 22 C C 11 C C 12 C D 3 HOH D 101 SITE 5 AC6 22 HOH D 108 HOH D 109 HOH D 110 HOH D 111 SITE 6 AC6 22 HOH D 120 HOH D 124 CRYST1 33.775 93.090 133.823 90.00 90.00 90.00 P 2 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 0.029608 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010742 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007473 0.00000