HEADER RNA BINDING PROTEIN/RNA 16-MAR-20 6M6R TITLE CRYSTAL STRUCTURE OF CAENORHABDITIS ELEGANS DICER-RELATED HELICASE 3 TITLE 2 (DRH-3) C-TERMINAL DOMAIN WITH 5'-PPP 8-MER SSRNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (5'-R(*(GTP)P*GP*CP*CP*GP*CP*CP*C)-3'); COMPND 3 CHAIN: B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DICER RELATED HELICASE; COMPND 7 CHAIN: A; COMPND 8 FRAGMENT: C-TERMINAL DOMAIN; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630; SOURCE 5 MOL_ID: 2; SOURCE 6 ORGANISM_SCIENTIFIC: CAENORHABDITIS ELEGANS; SOURCE 7 ORGANISM_TAXID: 6239; SOURCE 8 GENE: DRH-3, CELE_D2005.5, D2005.5; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 562 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 2 10-AUG-22 6M6R 1 JRNL REVDAT 1 17-MAR-21 6M6R 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. 1.89 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.14_3260: ???) 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) : 1.89 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.04 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.6 REMARK 3 NUMBER OF REFLECTIONS : 17265 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.180 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.221 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.780 REMARK 3 FREE R VALUE TEST SET COUNT : 825 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 43.0300 - 3.4334 0.98 3006 143 0.1622 0.2071 REMARK 3 2 3.4334 - 2.7253 0.97 2790 146 0.1789 0.2139 REMARK 3 3 2.7253 - 2.3808 0.96 2730 146 0.1818 0.2219 REMARK 3 4 2.3808 - 2.1632 0.96 2701 131 0.1784 0.2689 REMARK 3 5 2.1632 - 2.0081 0.95 2658 132 0.1976 0.2190 REMARK 3 6 2.0081 - 1.8900 0.92 2555 127 0.2444 0.2621 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) : 20.980 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 26.70 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 : 0.008 1598 REMARK 3 ANGLE : 0.991 2185 REMARK 3 CHIRALITY : 0.058 243 REMARK 3 PLANARITY : 0.005 244 REMARK 3 DIHEDRAL : 9.831 1307 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 7 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 2 THROUGH 8 ) REMARK 3 ORIGIN FOR THE GROUP (A): 27.3468 29.3839 3.5067 REMARK 3 T TENSOR REMARK 3 T11: 0.5990 T22: 0.4283 REMARK 3 T33: 0.6550 T12: 0.1697 REMARK 3 T13: -0.2547 T23: -0.0663 REMARK 3 L TENSOR REMARK 3 L11: 0.5810 L22: 0.3745 REMARK 3 L33: 1.0390 L12: -0.1444 REMARK 3 L13: -0.7315 L23: 0.1686 REMARK 3 S TENSOR REMARK 3 S11: -0.6620 S12: -0.1252 S13: 0.7734 REMARK 3 S21: 0.4294 S22: -0.2347 S23: 0.0437 REMARK 3 S31: -0.4573 S32: 0.1041 S33: -0.1911 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 940 THROUGH 948 ) REMARK 3 ORIGIN FOR THE GROUP (A): 28.6970 20.7972 26.8874 REMARK 3 T TENSOR REMARK 3 T11: 0.2210 T22: 0.2461 REMARK 3 T33: 0.2462 T12: -0.0002 REMARK 3 T13: -0.0289 T23: -0.0560 REMARK 3 L TENSOR REMARK 3 L11: 0.2404 L22: 0.0721 REMARK 3 L33: 0.1213 L12: -0.1417 REMARK 3 L13: 0.1136 L23: -0.0720 REMARK 3 S TENSOR REMARK 3 S11: -0.0920 S12: -0.3101 S13: 0.2752 REMARK 3 S21: 0.5078 S22: 0.0803 S23: -0.0867 REMARK 3 S31: -0.0281 S32: -0.0661 S33: 0.0033 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 949 THROUGH 986 ) REMARK 3 ORIGIN FOR THE GROUP (A): 23.0307 7.8069 12.1807 REMARK 3 T TENSOR REMARK 3 T11: 0.1541 T22: 0.1856 REMARK 3 T33: 0.1521 T12: 0.0111 REMARK 3 T13: -0.0362 T23: 0.0211 REMARK 3 L TENSOR REMARK 3 L11: 0.8697 L22: 0.2617 REMARK 3 L33: 0.4339 L12: -0.1125 REMARK 3 L13: -0.2868 L23: -0.0549 REMARK 3 S TENSOR REMARK 3 S11: 0.0995 S12: -0.0505 S13: -0.0821 REMARK 3 S21: 0.0542 S22: -0.0308 S23: 0.0173 REMARK 3 S31: 0.0415 S32: -0.0841 S33: 0.0000 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 987 THROUGH 998 ) REMARK 3 ORIGIN FOR THE GROUP (A): 29.1815 9.7378 -7.8729 REMARK 3 T TENSOR REMARK 3 T11: 0.2390 T22: 0.4419 REMARK 3 T33: 0.1733 T12: -0.0665 REMARK 3 T13: 0.0395 T23: 0.0030 REMARK 3 L TENSOR REMARK 3 L11: 0.1418 L22: 1.7441 REMARK 3 L33: 0.2326 L12: -0.0925 REMARK 3 L13: -0.2007 L23: 0.0920 REMARK 3 S TENSOR REMARK 3 S11: 0.3435 S12: -0.4106 S13: 0.2156 REMARK 3 S21: -0.2452 S22: -0.3784 S23: 0.0290 REMARK 3 S31: -0.0447 S32: 0.4883 S33: -0.0369 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 999 THROUGH 1029 ) REMARK 3 ORIGIN FOR THE GROUP (A): 24.0304 7.2557 3.2020 REMARK 3 T TENSOR REMARK 3 T11: 0.1608 T22: 0.2557 REMARK 3 T33: 0.1960 T12: 0.0112 REMARK 3 T13: -0.0234 T23: 0.0022 REMARK 3 L TENSOR REMARK 3 L11: 0.3091 L22: 0.4169 REMARK 3 L33: 1.2183 L12: 0.2436 REMARK 3 L13: -0.4569 L23: 0.1479 REMARK 3 S TENSOR REMARK 3 S11: 0.1064 S12: 0.2427 S13: -0.0681 REMARK 3 S21: 0.0747 S22: 0.0549 S23: 0.0112 REMARK 3 S31: 0.0846 S32: -0.0560 S33: 0.0005 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1030 THROUGH 1077 ) REMARK 3 ORIGIN FOR THE GROUP (A): 26.3462 12.3591 16.2076 REMARK 3 T TENSOR REMARK 3 T11: 0.0976 T22: 0.1506 REMARK 3 T33: 0.1611 T12: 0.0025 REMARK 3 T13: 0.0087 T23: 0.0382 REMARK 3 L TENSOR REMARK 3 L11: 1.6245 L22: 0.4652 REMARK 3 L33: 1.9899 L12: 0.0260 REMARK 3 L13: 0.7469 L23: 0.4829 REMARK 3 S TENSOR REMARK 3 S11: 0.0606 S12: -0.0607 S13: 0.0744 REMARK 3 S21: 0.0874 S22: 0.0295 S23: -0.0181 REMARK 3 S31: 0.1129 S32: -0.0524 S33: 0.0386 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1078 THROUGH 1105 ) REMARK 3 ORIGIN FOR THE GROUP (A): 29.9741 1.5368 -8.3506 REMARK 3 T TENSOR REMARK 3 T11: 0.2292 T22: 0.3594 REMARK 3 T33: 0.2229 T12: 0.0466 REMARK 3 T13: -0.0216 T23: -0.0635 REMARK 3 L TENSOR REMARK 3 L11: 2.5630 L22: 2.1122 REMARK 3 L33: 2.4376 L12: -0.0175 REMARK 3 L13: 0.2710 L23: 0.9426 REMARK 3 S TENSOR REMARK 3 S11: 0.1256 S12: 0.4323 S13: -0.3117 REMARK 3 S21: -0.1200 S22: -0.0558 S23: -0.3661 REMARK 3 S31: 0.5085 S32: 0.3559 S33: 0.6197 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 6M6R 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_1300016187. 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 : 8.5 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) : 1.2819 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 : 17289 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.890 REMARK 200 RESOLUTION RANGE LOW (A) : 43.040 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.3 REMARK 200 DATA REDUNDANCY : 9.200 REMARK 200 R MERGE (I) : 0.14200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.89 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.93 REMARK 200 COMPLETENESS FOR SHELL (%) : 88.4 REMARK 200 DATA REDUNDANCY IN SHELL : 7.50 REMARK 200 R MERGE FOR SHELL (I) : 1.71500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.79 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.31 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS PH 8.5, 25% W/V REMARK 280 POLYETHYLENE GLYCOL 3350, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 291.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 65.87500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 28.42150 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 28.42150 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 98.81250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 28.42150 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 28.42150 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 32.93750 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 28.42150 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 28.42150 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 98.81250 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 28.42150 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 28.42150 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 32.93750 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 65.87500 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: 4770 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19590 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, A 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 350 BIOMT1 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A1326 LIES ON A SPECIAL POSITION. 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 GLN A 1106 REMARK 465 GLN A 1107 REMARK 465 GLU A 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 ASP A1004 CG OD1 OD2 REMARK 470 GLU A1064 CG CD OE1 OE2 REMARK 470 GLU A1078 CG CD OE1 OE2 REMARK 470 GLU A1082 CG CD OE1 OE2 REMARK 470 HIS A1104 CG ND1 CD2 CE1 NE2 REMARK 470 ILE A1105 CG1 CG2 CD1 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 NE2 GLN A 1027 O HOH A 1301 2.02 REMARK 500 NH1 ARG A 1021 O HOH A 1302 2.08 REMARK 500 OP1 G B 2 O HOH B 101 2.12 REMARK 500 ND2 ASN A 971 OE1 GLN A 1027 2.17 REMARK 500 OD1 ASP A 1013 O HOH A 1303 2.17 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 O3A GTP B 1 NZ LYS A 1031 7555 1.19 REMARK 500 PB GTP B 1 NZ LYS A 1031 7555 1.65 REMARK 500 O1B GTP B 1 NZ LYS A 1031 7555 2.12 REMARK 500 O3B GTP B 1 NZ LYS A 1031 7555 2.16 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 GTP B 1 C3' - O3' - P ANGL. DEV. = 7.8 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 SER A 970 -0.73 68.99 REMARK 500 ASN A 999 73.63 -153.21 REMARK 500 LEU A1002 -125.75 -122.15 REMARK 500 SER A1075 73.45 -117.14 REMARK 500 ASP A1076 -16.80 -153.59 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 113.9 REMARK 620 3 CYS A1007 SG 111.6 102.9 REMARK 620 4 CYS A1010 SG 103.3 116.3 108.8 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 DBREF 6M6R B 1 8 PDB 6M6R 6M6R 1 8 DBREF 6M6R A 940 1108 UNP Q93413 Q93413_CAEEL 940 1108 SEQADV 6M6R MET A 939 UNP Q93413 INITIATING METHIONINE SEQRES 1 B 8 GTP G C C G C C C 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 HET GTP B 1 32 HET ZN A1201 1 HETNAM GTP GUANOSINE-5'-TRIPHOSPHATE HETNAM ZN ZINC ION FORMUL 1 GTP C10 H16 N5 O14 P3 FORMUL 3 ZN ZN 2+ FORMUL 4 HOH *124(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 PHE A 1103 1 27 SHEET 1 AA1 4 GLU A 958 LYS A 961 0 SHEET 2 AA1 4 LYS A 949 CYS A 952 -1 N LEU A 950 O PHE A 959 SHEET 3 AA1 4 LEU A1033 GLN A1037 -1 O VAL A1036 N LYS A 949 SHEET 4 AA1 4 SER A1042 MET A1044 -1 O MET A1044 N PHE A1035 SHEET 1 AA2 2 ILE A 965 VAL A 968 0 SHEET 2 AA2 2 ASN A 971 VAL A 974 -1 O ASN A 971 N VAL A 968 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 LEU A1002 SHEET 4 AA3 4 THR A1023 LEU A1028 -1 O LEU A1025 N TYR A1018 LINK O3' GTP B 1 P G B 2 1555 1555 1.59 LINK SG CYS A 952 ZN ZN A1201 1555 1555 2.33 LINK SG CYS A 955 ZN ZN A1201 1555 1555 2.30 LINK SG CYS A1007 ZN ZN A1201 1555 1555 2.41 LINK SG CYS A1010 ZN ZN A1201 1555 1555 2.31 SITE 1 AC1 4 CYS A 952 CYS A 955 CYS A1007 CYS A1010 CRYST1 56.843 56.843 131.750 90.00 90.00 90.00 P 43 21 2 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 0.017592 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017592 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007590 0.00000 HETATM 1 PG GTP B 1 25.815 14.811 -7.150 1.00 44.09 P HETATM 2 O1G GTP B 1 24.728 13.974 -7.769 1.00 56.51 O HETATM 3 O2G GTP B 1 26.839 15.210 -8.183 1.00 41.11 O HETATM 4 O3G GTP B 1 26.516 14.038 -6.059 1.00 45.94 O HETATM 5 O3B GTP B 1 25.118 16.113 -6.535 1.00 70.01 O HETATM 6 PB GTP B 1 23.711 15.910 -5.767 1.00 84.09 P HETATM 7 O1B GTP B 1 22.613 15.752 -6.792 1.00 79.96 O HETATM 8 O2B GTP B 1 23.761 14.691 -4.863 1.00 86.50 O HETATM 9 O3A GTP B 1 23.544 17.268 -4.921 1.00 89.80 O HETATM 10 PA GTP B 1 22.458 17.420 -3.739 1.00102.15 P HETATM 11 O1A GTP B 1 22.160 18.889 -3.456 1.00 91.08 O HETATM 12 O2A GTP B 1 21.209 16.608 -4.036 1.00 97.21 O HETATM 13 O5' GTP B 1 23.243 16.781 -2.488 1.00 90.32 O HETATM 14 C5' GTP B 1 22.917 15.489 -2.031 1.00 74.74 C HETATM 15 C4' GTP B 1 24.121 14.984 -1.259 1.00 64.59 C HETATM 16 O4' GTP B 1 25.112 14.429 -2.108 1.00 51.22 O HETATM 17 C3' GTP B 1 24.877 16.099 -0.576 1.00 60.85 C HETATM 18 O3' GTP B 1 24.182 16.612 0.540 1.00 54.00 O HETATM 19 C2' GTP B 1 26.136 15.327 -0.240 1.00 63.14 C HETATM 20 O2' GTP B 1 25.882 14.402 0.799 1.00 47.73 O HETATM 21 C1' GTP B 1 26.393 14.531 -1.500 1.00 56.06 C HETATM 22 N9 GTP B 1 27.347 15.315 -2.314 1.00 60.77 N HETATM 23 C8 GTP B 1 27.073 15.911 -3.520 1.00 57.26 C HETATM 24 N7 GTP B 1 28.190 16.542 -3.951 1.00 60.43 N HETATM 25 C5 GTP B 1 29.178 16.352 -3.046 1.00 60.36 C HETATM 26 C6 GTP B 1 30.504 16.786 -3.008 1.00 62.37 C HETATM 27 O6 GTP B 1 30.951 17.479 -3.931 1.00 52.81 O HETATM 28 N1 GTP B 1 31.306 16.437 -1.932 1.00 48.88 N HETATM 29 C2 GTP B 1 30.780 15.668 -0.902 1.00 53.79 C HETATM 30 N2 GTP B 1 31.542 15.328 0.140 1.00 55.99 N HETATM 31 N3 GTP B 1 29.458 15.253 -0.949 1.00 57.41 N HETATM 32 C4 GTP B 1 28.665 15.584 -2.006 1.00 55.00 C