HEADER HYDROLASE/RNA 18-MAY-23 8SWB TITLE RNASE H COMPLEX WITH STREOPURE ASO AND RNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBONUCLEASE H1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RNASE H1,RIBONUCLEASE H TYPE II; COMPND 5 EC: 3.1.26.4; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: RNA (5'- COMPND 9 R(*UP*GP*GP*CP*GP*AP*GP*UP*GP*GP*GP*UP*GP*AP*GP*UP*GP*AP*GP*G)-3'); COMPND 10 CHAIN: B; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: DNA (5'-R(*(OMC)P*(N7X)P*(T39)P*(C5L)P*(A2M))-D(P*(SC) COMPND 14 P*(PST)P*(SC)P*AP*(SC)P*(SC)P*(RC)P*(AS)P*(SC)P*(PST))-R(P*(6OO) COMPND 15 P*(RFJ)P*(6OO)P*(6OO)P*(6NW))-3'); COMPND 16 CHAIN: D; COMPND 17 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: RNASEH1, RNH1; 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: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606; SOURCE 13 MOL_ID: 3; SOURCE 14 SYNTHETIC: YES; SOURCE 15 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 16 ORGANISM_COMMON: HUMAN; SOURCE 17 ORGANISM_TAXID: 9606 KEYWDS COMPLEX OF DNA(ASO) AND RNA OSS STEREOCHEMISTRY (PS-BACKBONE) RNASE KEYWDS 2 H, HYDROLASE-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Y.-J.CHO,N.IWAMOTO REVDAT 2 25-DEC-24 8SWB 1 REMARK LINK REVDAT 1 22-MAY-24 8SWB 0 JRNL AUTH N.IWAMOTO,Y.-J.CHO JRNL TITL CRYSTAL STRUCTURE OF RNASE H/RNA/PS-ASO COMPLEX AT AN ATOMIC JRNL TITL 2 LEVEL JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.20.1_4487: ???) 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.62 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 18307 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.224 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 915 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 10.0000 - 3.8300 1.00 2629 142 0.1494 0.1692 REMARK 3 2 3.8300 - 3.0400 1.00 2514 131 0.1629 0.1955 REMARK 3 3 3.0400 - 2.6500 1.00 2453 144 0.2124 0.2809 REMARK 3 4 2.6500 - 2.4100 1.00 2470 114 0.2273 0.2725 REMARK 3 5 2.4100 - 2.2400 1.00 2438 133 0.2318 0.3256 REMARK 3 6 2.2400 - 2.1100 1.00 2439 129 0.2500 0.3201 REMARK 3 7 2.1100 - 2.0000 0.99 2449 122 0.2795 0.3434 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.260 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.450 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.008 2229 REMARK 3 ANGLE : 0.986 3145 REMARK 3 CHIRALITY : 0.048 343 REMARK 3 PLANARITY : 0.005 275 REMARK 3 DIHEDRAL : 21.502 550 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 10 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 137 THROUGH 149 ) REMARK 3 ORIGIN FOR THE GROUP (A): 11.0348 10.8680 20.7163 REMARK 3 T TENSOR REMARK 3 T11: 0.1329 T22: 0.2752 REMARK 3 T33: 0.1832 T12: 0.0697 REMARK 3 T13: -0.0131 T23: -0.0708 REMARK 3 L TENSOR REMARK 3 L11: 4.4860 L22: 5.8033 REMARK 3 L33: 5.4085 L12: 2.1220 REMARK 3 L13: -2.2303 L23: -2.3504 REMARK 3 S TENSOR REMARK 3 S11: 0.1980 S12: -0.6459 S13: 0.2569 REMARK 3 S21: 0.2866 S22: -0.4548 S23: 0.1393 REMARK 3 S31: -0.2685 S32: 0.2658 S33: 0.0748 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 150 THROUGH 171 ) REMARK 3 ORIGIN FOR THE GROUP (A): 19.6451 15.4910 20.2473 REMARK 3 T TENSOR REMARK 3 T11: 0.1796 T22: 0.3681 REMARK 3 T33: 0.2996 T12: 0.0237 REMARK 3 T13: -0.0361 T23: -0.0717 REMARK 3 L TENSOR REMARK 3 L11: 3.6765 L22: 5.0334 REMARK 3 L33: 4.0617 L12: -0.1249 REMARK 3 L13: 0.2452 L23: -1.6320 REMARK 3 S TENSOR REMARK 3 S11: 0.1801 S12: -0.4196 S13: -0.0812 REMARK 3 S21: 0.0685 S22: -0.2378 S23: -0.3073 REMARK 3 S31: 0.1133 S32: 0.6117 S33: 0.1998 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 172 THROUGH 181 ) REMARK 3 ORIGIN FOR THE GROUP (A): 23.5480 14.8557 13.0520 REMARK 3 T TENSOR REMARK 3 T11: 0.2933 T22: 0.2487 REMARK 3 T33: 0.4421 T12: 0.0370 REMARK 3 T13: 0.0682 T23: 0.0199 REMARK 3 L TENSOR REMARK 3 L11: 4.0542 L22: 3.6601 REMARK 3 L33: 1.6671 L12: 0.2251 REMARK 3 L13: -0.1402 L23: -2.3041 REMARK 3 S TENSOR REMARK 3 S11: -0.1456 S12: -0.1329 S13: 0.0298 REMARK 3 S21: -0.3259 S22: -0.0411 S23: -0.7081 REMARK 3 S31: 0.0785 S32: -0.1864 S33: 0.3394 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 182 THROUGH 219 ) REMARK 3 ORIGIN FOR THE GROUP (A): 11.5873 7.3204 15.0630 REMARK 3 T TENSOR REMARK 3 T11: 0.2328 T22: 0.2043 REMARK 3 T33: 0.3360 T12: 0.0025 REMARK 3 T13: 0.0411 T23: -0.0033 REMARK 3 L TENSOR REMARK 3 L11: 1.3058 L22: 3.2311 REMARK 3 L33: 3.5811 L12: 0.6826 REMARK 3 L13: -1.1157 L23: -2.1635 REMARK 3 S TENSOR REMARK 3 S11: -0.1379 S12: -0.0946 S13: -0.2134 REMARK 3 S21: -0.0887 S22: 0.0050 S23: -0.2684 REMARK 3 S31: 0.2393 S32: 0.0929 S33: 0.1058 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 220 THROUGH 228 ) REMARK 3 ORIGIN FOR THE GROUP (A): 5.2479 7.1821 -0.5488 REMARK 3 T TENSOR REMARK 3 T11: 0.3964 T22: 0.3387 REMARK 3 T33: 0.3389 T12: -0.0368 REMARK 3 T13: -0.0505 T23: 0.0202 REMARK 3 L TENSOR REMARK 3 L11: 6.3824 L22: 9.7359 REMARK 3 L33: 4.4937 L12: 1.5983 REMARK 3 L13: 2.3883 L23: 5.7825 REMARK 3 S TENSOR REMARK 3 S11: 0.0573 S12: -0.2937 S13: -0.9995 REMARK 3 S21: 0.7388 S22: -0.0702 S23: -0.1780 REMARK 3 S31: 1.3259 S32: -0.1380 S33: -0.2230 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 229 THROUGH 240 ) REMARK 3 ORIGIN FOR THE GROUP (A): 11.9569 13.4695 -4.5554 REMARK 3 T TENSOR REMARK 3 T11: 0.3072 T22: 0.2653 REMARK 3 T33: 0.2707 T12: 0.0074 REMARK 3 T13: 0.0853 T23: -0.0281 REMARK 3 L TENSOR REMARK 3 L11: 7.8478 L22: 8.6010 REMARK 3 L33: 8.6498 L12: -1.9629 REMARK 3 L13: 7.4875 L23: -3.0553 REMARK 3 S TENSOR REMARK 3 S11: 0.1944 S12: 0.8090 S13: -0.1820 REMARK 3 S21: -0.7533 S22: -0.2067 S23: -0.4322 REMARK 3 S31: 0.0302 S32: 1.1741 S33: -0.1460 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 241 THROUGH 250 ) REMARK 3 ORIGIN FOR THE GROUP (A): 14.7748 3.9983 5.3688 REMARK 3 T TENSOR REMARK 3 T11: 0.2970 T22: 0.2829 REMARK 3 T33: 0.4305 T12: 0.0271 REMARK 3 T13: -0.0029 T23: -0.0403 REMARK 3 L TENSOR REMARK 3 L11: 1.3381 L22: 6.5009 REMARK 3 L33: 5.5923 L12: 0.2932 REMARK 3 L13: -1.8373 L23: -4.8449 REMARK 3 S TENSOR REMARK 3 S11: -0.0706 S12: -0.0676 S13: 0.1341 REMARK 3 S21: -0.3720 S22: -0.4347 S23: -0.3700 REMARK 3 S31: 0.7485 S32: 0.4883 S33: 0.4352 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 251 THROUGH 260 ) REMARK 3 ORIGIN FOR THE GROUP (A): 4.8904 3.8077 14.6758 REMARK 3 T TENSOR REMARK 3 T11: 0.3683 T22: 0.3801 REMARK 3 T33: 0.4281 T12: -0.0942 REMARK 3 T13: 0.0638 T23: 0.0003 REMARK 3 L TENSOR REMARK 3 L11: 5.6857 L22: 5.9689 REMARK 3 L33: 5.5918 L12: -1.9674 REMARK 3 L13: -0.6813 L23: 0.9808 REMARK 3 S TENSOR REMARK 3 S11: 0.0522 S12: 0.0026 S13: -0.2413 REMARK 3 S21: -0.3802 S22: -0.2189 S23: 0.0412 REMARK 3 S31: 0.5838 S32: -0.6170 S33: 0.2021 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 261 THROUGH 267 ) REMARK 3 ORIGIN FOR THE GROUP (A): 3.5346 20.6643 23.2688 REMARK 3 T TENSOR REMARK 3 T11: 0.8565 T22: 0.5460 REMARK 3 T33: 0.5386 T12: -0.0599 REMARK 3 T13: -0.0584 T23: -0.0940 REMARK 3 L TENSOR REMARK 3 L11: 4.0198 L22: 2.3630 REMARK 3 L33: 4.4321 L12: -1.4103 REMARK 3 L13: -1.6438 L23: 3.2273 REMARK 3 S TENSOR REMARK 3 S11: 0.0426 S12: 0.8644 S13: 1.9835 REMARK 3 S21: -0.3492 S22: 0.2925 S23: -0.1796 REMARK 3 S31: -3.4351 S32: 0.3104 S33: -0.0243 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 268 THROUGH 285 ) REMARK 3 ORIGIN FOR THE GROUP (A): 19.2540 17.9876 23.4203 REMARK 3 T TENSOR REMARK 3 T11: 0.3783 T22: 0.5177 REMARK 3 T33: 0.3726 T12: -0.0603 REMARK 3 T13: -0.0327 T23: -0.0211 REMARK 3 L TENSOR REMARK 3 L11: 4.7990 L22: 6.6716 REMARK 3 L33: 4.7951 L12: 1.5579 REMARK 3 L13: -4.6525 L23: -1.6546 REMARK 3 S TENSOR REMARK 3 S11: 0.5185 S12: -0.2403 S13: 0.8646 REMARK 3 S21: 0.2535 S22: -0.3380 S23: -0.1234 REMARK 3 S31: -0.7748 S32: 0.7344 S33: -0.0560 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 8SWB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-MAY-23. REMARK 100 THE DEPOSITION ID IS D_1000274009. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-JAN-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SOLEIL REMARK 200 BEAMLINE : PROXIMA 1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97856 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 : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18366 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 47.360 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 9.300 REMARK 200 R MERGE (I) : 0.14500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.0000 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) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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 <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 2QK9 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.85 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1:1 COMPLEX : PRECIPITANT (0.8 M REMARK 280 AMMONIUM SULFATE, 0.1 M CITRATE, PH 4.0), CRYOPROTECTION: MOTHER REMARK 280 LIQUOR + 1.75 M AMMONIUM SULFATE, 1 MINUTE, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 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 23.27250 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 53.00400 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.46950 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 53.00400 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.27250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.46950 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: 9660 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12480 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 12.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, 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 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 OE2 GLU A 195 SP PST D 15 4555 1.47 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 OMC D 1 C3' - O3' - P ANGL. DEV. = -16.5 DEGREES REMARK 500 N7X D 2 O3' - P - OP2 ANGL. DEV. = 19.6 DEGREES REMARK 500 N7X D 2 C3' - O3' - P ANGL. DEV. = -8.8 DEGREES REMARK 500 T39 D 3 O3' - P - OP2 ANGL. DEV. = 23.1 DEGREES REMARK 500 T39 D 3 O3' - P - OP1 ANGL. DEV. = -17.3 DEGREES REMARK 500 SC D 6 O3' - P - OP1 ANGL. DEV. = 15.7 DEGREES REMARK 500 DA D 9 O3' - P - OP2 ANGL. DEV. = 6.7 DEGREES REMARK 500 DA D 9 O4' - C1' - N9 ANGL. DEV. = 4.0 DEGREES REMARK 500 SC D 10 O3' - P - OP1 ANGL. DEV. = 6.6 DEGREES REMARK 500 SC D 11 O3' - P - OP1 ANGL. DEV. = 14.9 DEGREES REMARK 500 C7R D 12 C3' - O3' - P ANGL. DEV. = -11.6 DEGREES REMARK 500 AS D 13 O3' - P - O5' ANGL. DEV. = -14.3 DEGREES REMARK 500 AS D 13 O3' - P - OP1 ANGL. DEV. = 14.4 DEGREES REMARK 500 AS D 13 C3' - O3' - P ANGL. DEV. = -9.0 DEGREES REMARK 500 SC D 14 O3' - P - OP1 ANGL. DEV. = 13.1 DEGREES REMARK 500 SC D 14 C3' - O3' - P ANGL. DEV. = -9.1 DEGREES REMARK 500 PST D 15 O3' - P - OP2 ANGL. DEV. = 10.8 DEGREES REMARK 500 OKQ D 16 C3' - O3' - P ANGL. DEV. = -10.7 DEGREES REMARK 500 RFJ D 17 O3' - P - O5' ANGL. DEV. = -18.5 DEGREES REMARK 500 RFJ D 17 O3' - P - OP2 ANGL. DEV. = 27.4 DEGREES REMARK 500 OKQ D 19 C3' - O3' - P ANGL. DEV. = -9.5 DEGREES REMARK 500 6NW D 20 O3' - P - O5' ANGL. DEV. = -13.7 DEGREES REMARK 500 6NW D 20 O3' - P - OP2 ANGL. DEV. = 26.9 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASN A 220 -62.85 -133.37 REMARK 500 ASN A 220 -59.01 -137.75 REMARK 500 PRO A 262 -6.00 -55.53 REMARK 500 HIS A 264 80.61 42.72 REMARK 500 SER A 265 31.60 -157.79 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6VRD RELATED DB: PDB REMARK 900 SIMILAR COMPLEX BUT DIFFERENT ASO (PS-CONFIGURATION) DBREF 8SWB A 137 285 UNP O60930 RNH1_HUMAN 137 285 DBREF 8SWB B 1 20 PDB 8SWB 8SWB 1 20 DBREF 8SWB D 1 20 PDB 8SWB 8SWB 1 20 SEQADV 8SWB ASN A 210 UNP O60930 ASP 210 CONFLICT SEQRES 1 A 149 GLY ASP PHE VAL VAL VAL TYR THR ASP GLY CYS CYS SER SEQRES 2 A 149 SER ASN GLY ARG ARG ARG PRO ARG ALA GLY ILE GLY VAL SEQRES 3 A 149 TYR TRP GLY PRO GLY HIS PRO LEU ASN VAL GLY ILE ARG SEQRES 4 A 149 LEU PRO GLY ARG GLN THR ASN GLN ARG ALA GLU ILE HIS SEQRES 5 A 149 ALA ALA CYS LYS ALA ILE GLU GLN ALA LYS THR GLN ASN SEQRES 6 A 149 ILE ASN LYS LEU VAL LEU TYR THR ASN SER MET PHE THR SEQRES 7 A 149 ILE ASN GLY ILE THR ASN TRP VAL GLN GLY TRP LYS LYS SEQRES 8 A 149 ASN GLY TRP LYS THR SER ALA GLY LYS GLU VAL ILE ASN SEQRES 9 A 149 LYS GLU ASP PHE VAL ALA LEU GLU ARG LEU THR GLN GLY SEQRES 10 A 149 MET ASP ILE GLN TRP MET HIS VAL PRO GLY HIS SER GLY SEQRES 11 A 149 PHE ILE GLY ASN GLU GLU ALA ASP ARG LEU ALA ARG GLU SEQRES 12 A 149 GLY ALA LYS GLN SER GLU SEQRES 1 B 20 U G G C G A G U G G G U G SEQRES 2 B 20 A G U G A G G SEQRES 1 D 20 OMC N7X T39 C5L A2M SC PST SC DA SC SC C7R AS SEQRES 2 D 20 SC PST OKQ RFJ OKQ OKQ 6NW HET OMC D 1 18 HET N7X D 2 25 HET T39 D 3 25 HET C5L D 4 25 HET A2M D 5 23 HET SC D 6 19 HET PST D 7 20 HET SC D 8 19 HET SC D 10 19 HET SC D 11 19 HET C7R D 12 19 HET AS D 13 21 HET SC D 14 19 HET PST D 15 20 HET OKQ D 16 21 HET RFJ D 17 24 HET OKQ D 18 21 HET OKQ D 19 21 HET 6NW D 20 23 HET GOL A 301 6 HET PO4 A 302 5 HET PEG D 201 7 HETNAM OMC O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE HETNAM N7X 5'-O-[(R)-HYDROXY(SULFANYLIDENE)-LAMBDA~5~-PHOSPHANYL]- HETNAM 2 N7X 2'-O-(2-METHOXYETHYL)-5-METHYLCYTIDINE HETNAM T39 2'-O-METHOXYETHYLENE THYMIDINE 5'-MONOPHOSPHATE HETNAM C5L 2'-O-(2-METHOXYETHYL)-5-METHYLCYTIDINE 5'-(DIHYDROGEN HETNAM 2 C5L PHOSPHATE) HETNAM A2M 2'-O-METHYLADENOSINE 5'-(DIHYDROGEN PHOSPHATE) HETNAM SC 2-DEOXY-CYTIDINE-5'-THIOPHOSPHORATE HETNAM PST THYMIDINE-5'-THIOPHOSPHATE HETNAM C7R 2'-DEOXY-5'-O-THIOPHOSPHONOCYTIDINE HETNAM AS 2-DEOXY-ADENOSINE -5'-THIO-MONOPHOSPHATE HETNAM OKQ 2'-O-METHYLCYTIDINE-5'-PHOSPHOROTHIOATE HETNAM RFJ 2'-O-METHYL-5'-O-THIOPHOSPHONOGUANOSINE HETNAM 6NW 2'-O-METHYL-5'-O-THIOPHOSPHONOADENOSINE HETNAM GOL GLYCEROL HETNAM PO4 PHOSPHATE ION HETNAM PEG DI(HYDROXYETHYL)ETHER HETSYN C7R 2'-DEOXY-5'-O-THIOPHOSPHONOCYTIDINE (THIOPHOSPHO HETSYN 2 C7R CONNECTION ISOFORM 1) HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 OMC C10 H16 N3 O8 P FORMUL 3 N7X C13 H22 N3 O8 P S FORMUL 3 T39 C13 H21 N2 O10 P FORMUL 3 C5L C13 H22 N3 O9 P FORMUL 3 A2M C11 H16 N5 O7 P FORMUL 3 SC 5(C9 H14 N3 O6 P S) FORMUL 3 PST 2(C10 H15 N2 O7 P S) FORMUL 3 C7R C9 H14 N3 O6 P S FORMUL 3 AS C10 H14 N5 O5 P S FORMUL 3 OKQ 3(C10 H16 N3 O7 P S) FORMUL 3 RFJ C11 H16 N5 O7 P S FORMUL 3 6NW C11 H16 N5 O6 P S FORMUL 4 GOL C3 H8 O3 FORMUL 5 PO4 O4 P 3- FORMUL 6 PEG C4 H10 O3 FORMUL 7 HOH *110(H2 O) HELIX 1 AA1 THR A 181 GLN A 200 1 20 HELIX 2 AA2 SER A 211 ASN A 220 1 10 HELIX 3 AA3 ASN A 220 GLY A 229 1 10 HELIX 4 AA4 ASN A 240 THR A 251 1 12 HELIX 5 AA5 PHE A 267 LYS A 282 1 16 SHEET 1 AA1 5 VAL A 172 ARG A 175 0 SHEET 2 AA1 5 ARG A 157 TYR A 163 -1 N ILE A 160 O ILE A 174 SHEET 3 AA1 5 VAL A 140 SER A 149 -1 N TYR A 143 O TYR A 163 SHEET 4 AA1 5 LYS A 204 THR A 209 1 O VAL A 206 N VAL A 140 SHEET 5 AA1 5 ASP A 255 HIS A 260 1 O GLN A 257 N LEU A 205 LINK O3' OMC D 1 P N7X D 2 1555 1555 1.56 LINK O3' N7X D 2 P T39 D 3 1555 1555 1.56 LINK O3' T39 D 3 P C5L D 4 1555 1555 1.61 LINK O3' C5L D 4 P A2M D 5 1555 1555 1.61 LINK O3' A2M D 5 P SC D 6 1555 1555 1.56 LINK O3' SC D 6 P PST D 7 1555 1555 1.56 LINK O3' PST D 7 P SC D 8 1555 1555 1.56 LINK O3' SC D 8 P DA D 9 1555 1555 1.57 LINK O3' DA D 9 P SC D 10 1555 1555 1.56 LINK O3' SC D 10 P SC D 11 1555 1555 1.56 LINK O3' SC D 11 P C7R D 12 1555 1555 1.56 LINK O3' C7R D 12 P AS D 13 1555 1555 1.56 LINK O3' AS D 13 P SC D 14 1555 1555 1.56 LINK O3' SC D 14 P PST D 15 1555 1555 1.56 LINK O3' PST D 15 P1 OKQ D 16 1555 1555 1.56 LINK O3' OKQ D 16 P RFJ D 17 1555 1555 1.56 LINK O3' RFJ D 17 P1 OKQ D 18 1555 1555 1.56 LINK O3' OKQ D 18 P1 OKQ D 19 1555 1555 1.56 LINK O3' OKQ D 19 P 6NW D 20 1555 1555 1.56 CRYST1 46.545 52.939 106.008 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 0.021485 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018890 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009433 0.00000