HEADER HYDROLASE/DNA/RNA 09-JUN-18 6DOD TITLE CRYSTAL STRUCTURE OF BACILLUS HALODURANS RIBONUCLEASE H1 IN COMPLEX TITLE 2 WITH AN RNA/DNA HYBRID: REACTION IN 2 MM MG2+ AND 200 MM K+ FOR 360 S TITLE 3 AT 21 C COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBONUCLEASE H; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CATALYTIC DOMAIN; COMPND 5 SYNONYM: RNASE H; COMPND 6 EC: 3.1.26.4; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: RNA (5'-R(*AP*CP*AP*U)-3'); COMPND 10 CHAIN: B; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: RNA (5'-R(P*CP*G)-3'); COMPND 14 CHAIN: b; COMPND 15 ENGINEERED: YES; COMPND 16 MOL_ID: 4; COMPND 17 MOLECULE: DNA (5'-D(*CP*GP*AP*TP*GP*T)-3'); COMPND 18 CHAIN: C; COMPND 19 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS HALODURANS; SOURCE 3 ORGANISM_TAXID: 272558; SOURCE 4 STRAIN: ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125; SOURCE 5 GENE: RNHA, BH0863; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET15B; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 14 ORGANISM_TAXID: 32630; SOURCE 15 MOL_ID: 3; SOURCE 16 SYNTHETIC: YES; SOURCE 17 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 18 ORGANISM_TAXID: 32630; SOURCE 19 MOL_ID: 4; SOURCE 20 SYNTHETIC: YES; SOURCE 21 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 22 ORGANISM_TAXID: 32630 KEYWDS PROTEIN-RNA-DNA COMPLEX, DOUBLE HELIX, RNA HYDROLYSIS, IN CRYSTALLO KEYWDS 2 CATALYSIS, METAL DEPENDENT CATALYSIS, MONOVALENT CATIONS, DIVALENT KEYWDS 3 CATIONS, HYDROLASE, HYDROLASE-DNA-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR N.L.SAMARA,W.YANG REVDAT 2 13-MAR-24 6DOD 1 LINK REVDAT 1 15-AUG-18 6DOD 0 JRNL AUTH N.L.SAMARA,W.YANG JRNL TITL CATION TRAFFICKING PROPELS RNA HYDROLYSIS. JRNL REF NAT. STRUCT. MOL. BIOL. V. 25 715 2018 JRNL REFN ESSN 1545-9985 JRNL PMID 30076410 JRNL DOI 10.1038/S41594-018-0099-4 REMARK 2 REMARK 2 RESOLUTION. 1.54 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.10.1_2155 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) : 1.54 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.09 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 3 NUMBER OF REFLECTIONS : 28054 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.162 REMARK 3 R VALUE (WORKING SET) : 0.160 REMARK 3 FREE R VALUE : 0.195 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.870 REMARK 3 FREE R VALUE TEST SET COUNT : 1367 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 31.0975 - 3.3061 0.98 2766 149 0.1295 0.1679 REMARK 3 2 3.3061 - 2.6246 1.00 2736 139 0.1528 0.1838 REMARK 3 3 2.6246 - 2.2929 1.00 2728 158 0.1561 0.1897 REMARK 3 4 2.2929 - 2.0833 1.00 2723 118 0.1569 0.2085 REMARK 3 5 2.0833 - 1.9340 1.00 2707 132 0.1730 0.1943 REMARK 3 6 1.9340 - 1.8200 0.99 2720 132 0.2065 0.2253 REMARK 3 7 1.8200 - 1.7289 1.00 2681 136 0.1959 0.2367 REMARK 3 8 1.7289 - 1.6536 0.99 2697 138 0.2123 0.2440 REMARK 3 9 1.6536 - 1.5900 0.97 2612 140 0.2345 0.2929 REMARK 3 10 1.5900 - 1.5351 0.85 2317 125 0.2515 0.2576 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) : 20.600 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.27 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.78 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 : 0.010 1514 REMARK 3 ANGLE : 1.149 2062 REMARK 3 CHIRALITY : 0.064 225 REMARK 3 PLANARITY : 0.007 213 REMARK 3 DIHEDRAL : 20.076 851 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 9 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ( CHAIN A AND RESID 61:87 ) REMARK 3 ORIGIN FOR THE GROUP (A): 25.281 -5.607 17.592 REMARK 3 T TENSOR REMARK 3 T11: 0.1535 T22: 0.0796 REMARK 3 T33: 0.1282 T12: 0.0186 REMARK 3 T13: 0.0153 T23: 0.0064 REMARK 3 L TENSOR REMARK 3 L11: 7.3493 L22: 1.7131 REMARK 3 L33: 3.8800 L12: -1.5839 REMARK 3 L13: 2.0481 L23: -0.2295 REMARK 3 S TENSOR REMARK 3 S11: 0.3004 S12: 0.2205 S13: -0.2273 REMARK 3 S21: -0.1214 S22: -0.1809 S23: -0.1077 REMARK 3 S31: 0.3502 S32: 0.1736 S33: -0.0536 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: ( CHAIN A AND RESID 88:96 ) REMARK 3 ORIGIN FOR THE GROUP (A): 27.899 -11.567 24.196 REMARK 3 T TENSOR REMARK 3 T11: 0.2368 T22: 0.1733 REMARK 3 T33: 0.2866 T12: 0.0728 REMARK 3 T13: -0.0173 T23: 0.0471 REMARK 3 L TENSOR REMARK 3 L11: 6.5004 L22: 5.7721 REMARK 3 L33: 7.3069 L12: -1.2839 REMARK 3 L13: -5.8753 L23: 0.3679 REMARK 3 S TENSOR REMARK 3 S11: -0.2721 S12: -0.2909 S13: -1.2607 REMARK 3 S21: 0.0153 S22: 0.0403 S23: -0.5133 REMARK 3 S31: 0.8163 S32: 0.4534 S33: 0.1438 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: ( CHAIN A AND RESID 97:133 ) REMARK 3 ORIGIN FOR THE GROUP (A): 21.459 -1.222 23.604 REMARK 3 T TENSOR REMARK 3 T11: 0.1019 T22: 0.0812 REMARK 3 T33: 0.1167 T12: 0.0033 REMARK 3 T13: 0.0131 T23: 0.0092 REMARK 3 L TENSOR REMARK 3 L11: 3.7536 L22: 1.1190 REMARK 3 L33: 3.0475 L12: -0.1212 REMARK 3 L13: 1.3384 L23: 0.4312 REMARK 3 S TENSOR REMARK 3 S11: 0.0750 S12: -0.2476 S13: -0.1704 REMARK 3 S21: -0.0014 S22: -0.0850 S23: 0.0583 REMARK 3 S31: 0.0596 S32: -0.2990 S33: 0.0102 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: ( CHAIN A AND RESID 134:142 ) REMARK 3 ORIGIN FOR THE GROUP (A): 23.643 9.377 16.816 REMARK 3 T TENSOR REMARK 3 T11: 0.2768 T22: 0.1068 REMARK 3 T33: 0.1859 T12: 0.0034 REMARK 3 T13: 0.0245 T23: 0.0401 REMARK 3 L TENSOR REMARK 3 L11: 4.0225 L22: 5.8042 REMARK 3 L33: 6.3850 L12: -4.3152 REMARK 3 L13: -0.6142 L23: -0.4007 REMARK 3 S TENSOR REMARK 3 S11: 0.2323 S12: 0.1480 S13: 0.4522 REMARK 3 S21: -0.1326 S22: -0.1364 S23: -0.3252 REMARK 3 S31: -0.9401 S32: -0.0308 S33: -0.0915 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: ( CHAIN A AND RESID 143:155 ) REMARK 3 ORIGIN FOR THE GROUP (A): 8.300 7.492 16.363 REMARK 3 T TENSOR REMARK 3 T11: 0.3628 T22: 0.4750 REMARK 3 T33: 0.2267 T12: 0.2552 REMARK 3 T13: -0.0179 T23: -0.0927 REMARK 3 L TENSOR REMARK 3 L11: 8.0166 L22: 2.0171 REMARK 3 L33: 2.6255 L12: 0.7177 REMARK 3 L13: 3.0075 L23: -0.9071 REMARK 3 S TENSOR REMARK 3 S11: 0.2342 S12: -0.0100 S13: 0.6350 REMARK 3 S21: -0.1496 S22: -0.3872 S23: 0.5510 REMARK 3 S31: -0.5905 S32: -0.8512 S33: 0.1473 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: ( CHAIN A AND RESID 156:169 ) REMARK 3 ORIGIN FOR THE GROUP (A): 12.209 5.717 25.082 REMARK 3 T TENSOR REMARK 3 T11: 0.1741 T22: 0.2488 REMARK 3 T33: 0.1565 T12: 0.0750 REMARK 3 T13: 0.0238 T23: -0.0417 REMARK 3 L TENSOR REMARK 3 L11: 8.8916 L22: 2.9877 REMARK 3 L33: 7.7605 L12: 1.4306 REMARK 3 L13: 7.2905 L23: 2.3431 REMARK 3 S TENSOR REMARK 3 S11: 0.0948 S12: -0.2775 S13: 0.1718 REMARK 3 S21: -0.0602 S22: -0.3021 S23: 0.2782 REMARK 3 S31: -0.1930 S32: -0.7771 S33: 0.1982 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: ( CHAIN A AND RESID 170:196 ) REMARK 3 ORIGIN FOR THE GROUP (A): 28.689 -0.861 17.988 REMARK 3 T TENSOR REMARK 3 T11: 0.1370 T22: 0.1221 REMARK 3 T33: 0.1044 T12: 0.0383 REMARK 3 T13: -0.0080 T23: 0.0422 REMARK 3 L TENSOR REMARK 3 L11: 3.5079 L22: 3.0271 REMARK 3 L33: 4.0259 L12: -0.5499 REMARK 3 L13: -0.9134 L23: 1.2944 REMARK 3 S TENSOR REMARK 3 S11: 0.1016 S12: 0.2895 S13: -0.1188 REMARK 3 S21: -0.2790 S22: -0.0401 S23: -0.1892 REMARK 3 S31: 0.0566 S32: 0.2034 S33: -0.1402 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: ( CHAIN B AND RESID 1:4 ) OR ( CHAIN B AND RESID 5:6 REMARK 3 ) REMARK 3 ORIGIN FOR THE GROUP (A): 23.555 0.753 5.339 REMARK 3 T TENSOR REMARK 3 T11: 0.3211 T22: 0.2449 REMARK 3 T33: 0.1597 T12: 0.0642 REMARK 3 T13: 0.0221 T23: 0.0255 REMARK 3 L TENSOR REMARK 3 L11: 2.7681 L22: 6.2754 REMARK 3 L33: 0.7910 L12: 0.3449 REMARK 3 L13: 1.4404 L23: -0.1758 REMARK 3 S TENSOR REMARK 3 S11: -0.1603 S12: 0.2541 S13: 0.0388 REMARK 3 S21: -0.7042 S22: -0.0948 S23: -0.2902 REMARK 3 S31: -0.0017 S32: 0.1000 S33: 0.2630 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: ( CHAIN C AND RESID 1:6 ) REMARK 3 ORIGIN FOR THE GROUP (A): 16.331 3.482 3.415 REMARK 3 T TENSOR REMARK 3 T11: 0.4455 T22: 0.2224 REMARK 3 T33: 0.1577 T12: 0.0937 REMARK 3 T13: -0.0462 T23: 0.0066 REMARK 3 L TENSOR REMARK 3 L11: 2.3785 L22: 3.3762 REMARK 3 L33: 3.6316 L12: -1.1225 REMARK 3 L13: -2.3105 L23: 1.7387 REMARK 3 S TENSOR REMARK 3 S11: -0.0533 S12: 0.2898 S13: -0.1255 REMARK 3 S21: -0.9224 S22: -0.2853 S23: 0.1235 REMARK 3 S31: -0.5111 S32: -0.2903 S33: 0.3431 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: STRUCTURES REFINED IN PHENIX AND REMARK 3 NUCLEIC ACID AND PROTEIN RESIDUES BUILT IN COOT REMARK 4 REMARK 4 6DOD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-JUN-18. REMARK 100 THE DEPOSITION ID IS D_1000234962. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-JUL-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.31 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28132 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.535 REMARK 200 RESOLUTION RANGE LOW (A) : 31.091 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 1.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.54 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.56 REMARK 200 COMPLETENESS FOR SHELL (%) : 74.3 REMARK 200 DATA REDUNDANCY IN SHELL : 1.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.32 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.48 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 14% PEG3350, 20% GLYCEROL, 200 MM KI, REMARK 280 AND 25 MM CACL2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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+1/2,Y+1/2,Z 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 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 40.86300 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.91750 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 40.86300 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 18.91750 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6970 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7460 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -28.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, 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 GLY A 55 REMARK 465 SER A 56 REMARK 465 HIS A 57 REMARK 465 MET A 58 REMARK 465 ALA A 59 REMARK 465 LYS A 60 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 A B 1 O2' REMARK 470 G b 6 O2' 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 O2 EDO A 211 O1 GOL A 215 1.26 REMARK 500 O HOH A 376 O HOH A 438 2.05 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 304 O HOH A 304 2656 1.69 REMARK 500 O HOH A 387 O HOH A 387 2656 1.73 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 C b 5 P C b 5 OP3 -0.123 REMARK 500 DG C 2 O3' DG C 2 C3' -0.036 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 U B 4 C5 - C6 - N1 ANGL. DEV. = -3.4 DEGREES REMARK 500 DG C 2 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DG C 5 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 459 DISTANCE = 6.27 ANGSTROMS 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 MG A 201 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 71 OD2 REMARK 620 2 ASP A 192 OD1 105.8 REMARK 620 3 HOH A 301 O 174.0 78.5 REMARK 620 4 HOH A 319 O 89.3 86.2 86.8 REMARK 620 5 HOH A 326 O 85.9 88.5 98.4 171.6 REMARK 620 6 C b 5 OP3 158.2 96.0 17.8 91.5 95.5 REMARK 620 7 C b 5 OP1 93.8 159.7 82.3 99.4 87.8 64.5 REMARK 620 8 C b 5 OP1 94.1 159.0 82.1 100.8 86.4 64.3 1.4 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 202 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 71 OD1 REMARK 620 2 GLU A 109 OE1 97.2 REMARK 620 3 ASP A 132 OD1 129.9 101.2 REMARK 620 4 ASP A 132 OD2 102.5 154.1 53.1 REMARK 620 5 U B 4 O3' 147.5 84.2 80.9 88.1 REMARK 620 6 C b 5 OP1 90.5 109.7 124.9 86.9 59.0 REMARK 620 7 C b 5 OP1 88.2 113.5 124.4 84.0 62.1 4.2 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 217 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 132 OD2 REMARK 620 2 HOH A 354 O 52.8 REMARK 620 3 U B 4 OP1 80.4 70.9 REMARK 620 4 HOH B 210 O 156.1 114.7 75.9 REMARK 620 5 C b 5 OP2 83.9 128.5 134.1 115.2 REMARK 620 6 HOH b 102 O 136.4 167.0 116.7 60.3 54.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 203 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 192 OD1 REMARK 620 2 ASP A 192 OD2 40.5 REMARK 620 3 HOH A 301 O 51.8 83.4 REMARK 620 4 HOH A 319 O 53.3 91.9 51.4 REMARK 620 5 HOH A 345 O 81.3 52.8 87.8 131.0 REMARK 620 6 G b 6 OP2 98.0 138.4 60.7 50.0 136.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K C 101 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 440 O REMARK 620 2 DG C 5 O6 156.1 REMARK 620 3 HOH C 210 O 90.9 84.8 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 206 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 207 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 208 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 209 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 210 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 211 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 212 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 213 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 214 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 215 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PGE A 216 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K A 217 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K C 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL C 102 DBREF 6DOD A 59 196 UNP Q9KEI9 RNH1_BACHD 59 196 DBREF 6DOD B 1 4 PDB 6DOD 6DOD 1 4 DBREF 6DOD b 5 6 PDB 6DOD 6DOD 5 6 DBREF 6DOD C 1 6 PDB 6DOD 6DOD 1 6 SEQADV 6DOD GLY A 55 UNP Q9KEI9 EXPRESSION TAG SEQADV 6DOD SER A 56 UNP Q9KEI9 EXPRESSION TAG SEQADV 6DOD HIS A 57 UNP Q9KEI9 EXPRESSION TAG SEQADV 6DOD MET A 58 UNP Q9KEI9 EXPRESSION TAG SEQRES 1 A 142 GLY SER HIS MET ALA LYS GLU GLU ILE ILE TRP GLU SER SEQRES 2 A 142 LEU SER VAL ASP VAL GLY SER GLN GLY ASN PRO GLY ILE SEQRES 3 A 142 VAL GLU TYR LYS GLY VAL ASP THR LYS THR GLY GLU VAL SEQRES 4 A 142 LEU PHE GLU ARG GLU PRO ILE PRO ILE GLY THR ASN ASN SEQRES 5 A 142 MET GLY GLU PHE LEU ALA ILE VAL HIS GLY LEU ARG TYR SEQRES 6 A 142 LEU LYS GLU ARG ASN SER ARG LYS PRO ILE TYR SER ASP SEQRES 7 A 142 SER GLN THR ALA ILE LYS TRP VAL LYS ASP LYS LYS ALA SEQRES 8 A 142 LYS SER THR LEU VAL ARG ASN GLU GLU THR ALA LEU ILE SEQRES 9 A 142 TRP LYS LEU VAL ASP GLU ALA GLU GLU TRP LEU ASN THR SEQRES 10 A 142 HIS THR TYR GLU THR PRO ILE LEU LYS TRP GLN THR ASP SEQRES 11 A 142 LYS TRP GLY GLU ILE LYS ALA ASP TYR GLY ARG LYS SEQRES 1 B 4 A C A U SEQRES 1 b 2 C G SEQRES 1 C 6 DC DG DA DT DG DT HET MG A 201 1 HET MG A 202 1 HET K A 203 1 HET IOD A 204 1 HET IOD A 205 1 HET IOD A 206 1 HET IOD A 207 1 HET EDO A 208 4 HET EDO A 209 4 HET EDO A 210 4 HET EDO A 211 4 HET GOL A 212 6 HET GOL A 213 6 HET GOL A 214 6 HET GOL A 215 6 HET PGE A 216 10 HET K A 217 1 HET K C 101 1 HET GOL C 102 6 HETNAM MG MAGNESIUM ION HETNAM K POTASSIUM ION HETNAM IOD IODIDE ION HETNAM EDO 1,2-ETHANEDIOL HETNAM GOL GLYCEROL HETNAM PGE TRIETHYLENE GLYCOL HETSYN EDO ETHYLENE GLYCOL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 5 MG 2(MG 2+) FORMUL 7 K 3(K 1+) FORMUL 8 IOD 4(I 1-) FORMUL 12 EDO 4(C2 H6 O2) FORMUL 16 GOL 5(C3 H8 O3) FORMUL 20 PGE C6 H14 O4 FORMUL 24 HOH *196(H2 O) HELIX 1 AA1 THR A 104 ARG A 123 1 20 HELIX 2 AA2 SER A 133 LYS A 143 1 11 HELIX 3 AA3 ASN A 152 GLU A 154 5 3 HELIX 4 AA4 THR A 155 HIS A 172 1 18 HELIX 5 AA5 GLN A 182 GLY A 187 1 6 SHEET 1 AA1 3 VAL A 93 GLU A 96 0 SHEET 2 AA1 3 GLY A 79 ASP A 87 -1 N GLY A 85 O LEU A 94 SHEET 3 AA1 3 ILE A 100 GLY A 103 -1 O ILE A 100 N VAL A 81 SHEET 1 AA2 5 VAL A 93 GLU A 96 0 SHEET 2 AA2 5 GLY A 79 ASP A 87 -1 N GLY A 85 O LEU A 94 SHEET 3 AA2 5 LEU A 68 GLN A 75 -1 N SER A 69 O VAL A 86 SHEET 4 AA2 5 ILE A 129 SER A 131 1 O TYR A 130 N LEU A 68 SHEET 5 AA2 5 ILE A 178 LYS A 180 1 O LEU A 179 N ILE A 129 LINK O3'C U B 4 P C C b 5 1555 1555 1.57 LINK OD2 ASP A 71 MG MG A 201 1555 1555 1.99 LINK OD1 ASP A 71 MG MG A 202 1555 1555 1.96 LINK OE1 GLU A 109 MG MG A 202 1555 1555 2.03 LINK OD1 ASP A 132 MG MG A 202 1555 1555 1.96 LINK OD2 ASP A 132 MG MG A 202 1555 1555 2.67 LINK OD2 ASP A 132 K B K A 217 1555 1555 3.32 LINK OD1 ASP A 192 MG MG A 201 1555 1555 2.06 LINK OD1 ASP A 192 K C K A 203 1555 1555 2.81 LINK OD2 ASP A 192 K C K A 203 1555 1555 3.36 LINK MG MG A 201 O CHOH A 301 1555 1555 2.02 LINK MG MG A 201 O HOH A 319 1555 1555 2.08 LINK MG MG A 201 O HOH A 326 1555 1555 2.08 LINK MG MG A 201 OP3B C b 5 1555 1555 2.02 LINK MG MG A 201 OP1B C b 5 1555 1555 2.42 LINK MG MG A 201 OP1C C b 5 1555 1555 2.26 LINK MG MG A 202 O3'C U B 4 1555 1555 2.62 LINK MG MG A 202 OP1B C b 5 1555 1555 2.09 LINK MG MG A 202 OP1C C b 5 1555 1555 2.15 LINK K C K A 203 O CHOH A 301 1555 1555 3.08 LINK K C K A 203 O HOH A 319 1555 1555 3.39 LINK K C K A 203 O HOH A 345 1555 1555 2.61 LINK K C K A 203 OP2 G b 6 1555 1555 2.86 LINK K B K A 217 O HOH A 354 1555 1555 3.39 LINK K B K A 217 OP1 U B 4 1555 1555 3.47 LINK K B K A 217 O HOH B 210 1555 1555 2.59 LINK K B K A 217 OP2B C b 5 1555 1555 2.56 LINK K B K A 217 O HOH b 102 1555 1555 3.44 LINK O HOH A 440 K A K C 101 4555 1555 3.19 LINK O6 DG C 5 K A K C 101 1555 1555 2.57 LINK K A K C 101 O HOH C 210 1555 1555 3.18 CISPEP 1 ASN A 77 PRO A 78 0 -0.82 SITE 1 AC1 6 ASP A 71 ASP A 192 HOH A 301 HOH A 319 SITE 2 AC1 6 HOH A 326 C b 5 SITE 1 AC2 5 ASP A 71 GLU A 109 ASP A 132 U B 4 SITE 2 AC2 5 C b 5 SITE 1 AC3 8 ASP A 192 GLY A 194 ARG A 195 LYS A 196 SITE 2 AC3 8 HOH A 301 HOH A 345 C b 5 G b 6 SITE 1 AC4 1 TYR A 83 SITE 1 AC5 1 PGE A 216 SITE 1 AC6 3 ILE A 64 HOH A 424 HOH A 459 SITE 1 AC7 1 HOH A 420 SITE 1 AC8 4 LYS A 143 THR A 173 TYR A 174 HOH A 316 SITE 1 AC9 5 THR A 148 HOH A 318 HOH A 360 DT C 4 SITE 2 AC9 5 DG C 5 SITE 1 AD1 3 ILE A 80 PRO A 99 HOH A 372 SITE 1 AD2 7 TRP A 65 GLU A 66 SER A 67 ASP A 87 SITE 2 AD2 7 LYS A 127 GOL A 215 HOH A 351 SITE 1 AD3 5 HIS A 115 ARG A 118 ASN A 170 GOL A 213 SITE 2 AD3 5 HOH A 314 SITE 1 AD4 8 HIS A 115 TYR A 119 ARG A 123 GLU A 167 SITE 2 AD4 8 ASN A 170 GOL A 212 HOH A 355 HOH A 378 SITE 1 AD5 4 VAL A 150 ASN A 152 GLU A 154 HOH A 328 SITE 1 AD6 5 GLU A 66 SER A 125 LYS A 127 EDO A 211 SITE 2 AD6 5 HOH A 353 SITE 1 AD7 9 GLN A 134 LYS A 180 GLN A 182 THR A 183 SITE 2 AD7 9 ASP A 184 IOD A 205 A B 3 U B 4 SITE 3 AD7 9 HOH B 204 SITE 1 AD8 6 ASP A 132 GLU A 188 HOH A 308 U B 4 SITE 2 AD8 6 HOH B 210 C b 5 SITE 1 AD9 3 DT C 4 DG C 5 HOH C 212 SITE 1 AE1 7 GLY A 76 ASN A 77 HOH A 338 HOH B 211 SITE 2 AE1 7 DG C 2 DA C 3 HOH C 217 CRYST1 81.726 37.835 62.619 90.00 96.77 90.00 C 1 2 1 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 0.012236 0.000000 0.001453 0.00000 SCALE2 0.000000 0.026431 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016082 0.00000