HEADER HYDROLASE/DNA/RNA 09-JUN-18 6DP0 TITLE CRYSTAL STRUCTURE OF BACILLUS HALODURANS RIBONUCLEASE H1 IN COMPLEX TITLE 2 WITH AN RNA/DNA HYBRID: REACTION IN 2.5 MM MG2+ AND 75 MM K+ FOR 40 S TITLE 3 AT 21 C COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBONUCLEASE H; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CATALYTIC DOMAIN RESIDUES 61-195; COMPND 5 SYNONYM: RNASE H; COMPND 6 EC: 3.1.26.4; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: 5'-R(*AP*CP*AP*U)-3' PORTION OF UNCLEAVED RNA 5'- COMPND 10 R(*AP*CP*AP*UP*CP*G)-3'; COMPND 11 CHAIN: B; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: 5'-R(P*CP*G)-3' PORTION OF UNCLEAVED RNA 5'- COMPND 15 R(*AP*CP*AP*UP*CP*G)-3'; COMPND 16 CHAIN: b; COMPND 17 ENGINEERED: YES; COMPND 18 MOL_ID: 4; COMPND 19 MOLECULE: DNA (5'-D(*CP*GP*AP*TP*GP*T)-3'); COMPND 20 CHAIN: C; COMPND 21 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS HALODURANS (STRAIN ATCC BAA-125 / DSM SOURCE 3 18197 / FERM 7344 / JCM 9153 / C-125); SOURCE 4 ORGANISM_TAXID: 272558; SOURCE 5 STRAIN: ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125; SOURCE 6 GENE: RNHA, BH0863; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET15B; SOURCE 12 MOL_ID: 2; SOURCE 13 SYNTHETIC: YES; SOURCE 14 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 15 ORGANISM_TAXID: 32630; SOURCE 16 MOL_ID: 3; SOURCE 17 SYNTHETIC: YES; SOURCE 18 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 19 ORGANISM_TAXID: 32630; SOURCE 20 MOL_ID: 4; SOURCE 21 SYNTHETIC: YES; SOURCE 22 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 23 ORGANISM_TAXID: 32630 KEYWDS PROTEIN-RNA-DNA COMPLEX, RNA HYDROLYSIS, IN CRYSTALLO CATALYSIS, KEYWDS 2 METAL DEPENDENT CATALYSIS, HYDROLASE-DNA-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR N.L.SAMARA,W.YANG REVDAT 3 11-OCT-23 6DP0 1 LINK REVDAT 2 22-AUG-18 6DP0 1 SOURCE JRNL REVDAT 1 15-AUG-18 6DP0 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. 1.45 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) : 1.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.88 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 88.0 REMARK 3 NUMBER OF REFLECTIONS : 29304 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.192 REMARK 3 R VALUE (WORKING SET) : 0.190 REMARK 3 FREE R VALUE : 0.236 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.030 REMARK 3 FREE R VALUE TEST SET COUNT : 1474 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 19.8783 - 3.2221 0.93 2773 146 0.1256 0.1772 REMARK 3 2 3.2221 - 2.5592 0.88 2562 132 0.1577 0.2156 REMARK 3 3 2.5592 - 2.2362 0.83 2415 118 0.2138 0.2521 REMARK 3 4 2.2362 - 2.0320 0.82 2359 128 0.2411 0.2569 REMARK 3 5 2.0320 - 1.8865 0.82 2326 136 0.2708 0.3061 REMARK 3 6 1.8865 - 1.7753 0.87 2507 119 0.2182 0.3057 REMARK 3 7 1.7753 - 1.6865 0.89 2564 154 0.2065 0.2328 REMARK 3 8 1.6865 - 1.6131 0.91 2574 143 0.1977 0.2375 REMARK 3 9 1.6131 - 1.5510 0.92 2602 142 0.2505 0.2728 REMARK 3 10 1.5510 - 1.4975 0.91 2611 134 0.4104 0.4729 REMARK 3 11 1.4975 - 1.4507 0.90 2537 122 0.4063 0.3910 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) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.180 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.53 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.02 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 1462 REMARK 3 ANGLE : 0.974 2022 REMARK 3 CHIRALITY : 0.070 220 REMARK 3 PLANARITY : 0.006 212 REMARK 3 DIHEDRAL : 22.713 575 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 THROUGH 87 ) REMARK 3 ORIGIN FOR THE GROUP (A): 25.2640 -5.8477 16.9830 REMARK 3 T TENSOR REMARK 3 T11: 0.1805 T22: 0.1185 REMARK 3 T33: 0.1381 T12: 0.0240 REMARK 3 T13: 0.0120 T23: 0.0036 REMARK 3 L TENSOR REMARK 3 L11: 4.4775 L22: 1.6523 REMARK 3 L33: 3.7384 L12: -1.5191 REMARK 3 L13: 2.0731 L23: -0.2111 REMARK 3 S TENSOR REMARK 3 S11: 0.2248 S12: 0.3359 S13: -0.2610 REMARK 3 S21: -0.0388 S22: -0.0908 S23: -0.0062 REMARK 3 S31: 0.2563 S32: 0.2225 S33: -0.1224 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 88 THROUGH 96 ) REMARK 3 ORIGIN FOR THE GROUP (A): 28.2871 -11.5226 23.8169 REMARK 3 T TENSOR REMARK 3 T11: 0.2305 T22: 0.1857 REMARK 3 T33: 0.2977 T12: 0.0442 REMARK 3 T13: -0.0238 T23: 0.0497 REMARK 3 L TENSOR REMARK 3 L11: 5.0943 L22: 6.9220 REMARK 3 L33: 9.2274 L12: -3.0384 REMARK 3 L13: -6.4990 L23: 1.6890 REMARK 3 S TENSOR REMARK 3 S11: -0.2102 S12: -0.5953 S13: -1.0283 REMARK 3 S21: 0.0465 S22: 0.0405 S23: -0.2441 REMARK 3 S31: 0.6815 S32: 0.5891 S33: 0.2001 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 97 THROUGH 133 ) REMARK 3 ORIGIN FOR THE GROUP (A): 22.1034 -0.9719 23.1972 REMARK 3 T TENSOR REMARK 3 T11: 0.1235 T22: 0.0888 REMARK 3 T33: 0.1304 T12: 0.0145 REMARK 3 T13: 0.0333 T23: 0.0084 REMARK 3 L TENSOR REMARK 3 L11: 4.2341 L22: 0.6748 REMARK 3 L33: 4.4905 L12: -0.1047 REMARK 3 L13: 3.0678 L23: 0.6125 REMARK 3 S TENSOR REMARK 3 S11: 0.0194 S12: -0.2688 S13: -0.0807 REMARK 3 S21: -0.0369 S22: -0.0625 S23: 0.0228 REMARK 3 S31: -0.0299 S32: -0.3080 S33: 0.0403 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 134 THROUGH 142 ) REMARK 3 ORIGIN FOR THE GROUP (A): 23.9322 9.4152 16.4771 REMARK 3 T TENSOR REMARK 3 T11: 0.2814 T22: 0.1369 REMARK 3 T33: 0.1882 T12: -0.0198 REMARK 3 T13: 0.0412 T23: 0.0435 REMARK 3 L TENSOR REMARK 3 L11: 5.6624 L22: 7.3151 REMARK 3 L33: 2.2441 L12: -5.7371 REMARK 3 L13: -0.8785 L23: 1.5763 REMARK 3 S TENSOR REMARK 3 S11: 0.1251 S12: 0.0053 S13: 0.4354 REMARK 3 S21: -0.2615 S22: -0.0729 S23: -0.3495 REMARK 3 S31: -0.8943 S32: 0.2063 S33: -0.0809 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 143 THROUGH 155 ) REMARK 3 ORIGIN FOR THE GROUP (A): 8.6139 7.3575 16.0773 REMARK 3 T TENSOR REMARK 3 T11: 0.3452 T22: 0.4819 REMARK 3 T33: 0.2211 T12: 0.2196 REMARK 3 T13: 0.0094 T23: -0.1240 REMARK 3 L TENSOR REMARK 3 L11: 5.8438 L22: 4.4978 REMARK 3 L33: 2.2338 L12: 2.4290 REMARK 3 L13: 1.0819 L23: 1.5043 REMARK 3 S TENSOR REMARK 3 S11: 0.4551 S12: 0.1887 S13: 0.3274 REMARK 3 S21: -0.0381 S22: -0.5712 S23: 0.4581 REMARK 3 S31: -0.3654 S32: -0.9053 S33: -0.1293 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 156 THROUGH 169 ) REMARK 3 ORIGIN FOR THE GROUP (A): 12.4853 5.6486 24.7905 REMARK 3 T TENSOR REMARK 3 T11: 0.1530 T22: 0.2299 REMARK 3 T33: 0.1585 T12: 0.0676 REMARK 3 T13: 0.0292 T23: -0.0475 REMARK 3 L TENSOR REMARK 3 L11: 8.5060 L22: 1.6682 REMARK 3 L33: 6.9331 L12: 1.1723 REMARK 3 L13: 6.0620 L23: 1.8166 REMARK 3 S TENSOR REMARK 3 S11: 0.0734 S12: -0.3308 S13: 0.0154 REMARK 3 S21: -0.0377 S22: -0.2311 S23: 0.1743 REMARK 3 S31: -0.2635 S32: -0.7489 S33: 0.1597 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 170 THROUGH 196 ) REMARK 3 ORIGIN FOR THE GROUP (A): 29.1940 -0.2760 18.0759 REMARK 3 T TENSOR REMARK 3 T11: 0.2164 T22: 0.1413 REMARK 3 T33: 0.1258 T12: 0.0383 REMARK 3 T13: 0.0118 T23: 0.0459 REMARK 3 L TENSOR REMARK 3 L11: 4.2014 L22: 2.7554 REMARK 3 L33: 5.1865 L12: -0.9239 REMARK 3 L13: -1.2983 L23: 1.1456 REMARK 3 S TENSOR REMARK 3 S11: 0.1251 S12: 0.4051 S13: -0.0542 REMARK 3 S21: -0.3839 S22: -0.0581 S23: -0.1974 REMARK 3 S31: 0.2432 S32: 0.1795 S33: -0.1049 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: (CHAIN 'B' AND (RESID 1 THROUGH 4 )) OR (CHAIN 'B' REMARK 3 AND (RESID 5 THROUGH 6 )) REMARK 3 ORIGIN FOR THE GROUP (A): 23.8592 1.3227 4.4381 REMARK 3 T TENSOR REMARK 3 T11: 0.3202 T22: 0.2790 REMARK 3 T33: 0.1729 T12: 0.0664 REMARK 3 T13: 0.0543 T23: 0.0368 REMARK 3 L TENSOR REMARK 3 L11: 3.7888 L22: 5.8675 REMARK 3 L33: 6.3442 L12: -1.7083 REMARK 3 L13: 2.8425 L23: 0.4837 REMARK 3 S TENSOR REMARK 3 S11: -0.0366 S12: 0.6725 S13: 0.1118 REMARK 3 S21: -0.6813 S22: -0.1881 S23: -0.3577 REMARK 3 S31: 0.1297 S32: 0.4194 S33: 0.2588 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 1 THROUGH 6 ) REMARK 3 ORIGIN FOR THE GROUP (A): 16.4125 3.6341 3.1128 REMARK 3 T TENSOR REMARK 3 T11: 0.4818 T22: 0.2414 REMARK 3 T33: 0.1817 T12: 0.1276 REMARK 3 T13: -0.0230 T23: -0.0122 REMARK 3 L TENSOR REMARK 3 L11: 3.0078 L22: 1.1891 REMARK 3 L33: 7.2183 L12: -1.3273 REMARK 3 L13: -2.0091 L23: 1.6347 REMARK 3 S TENSOR REMARK 3 S11: 0.0391 S12: 0.3502 S13: -0.1339 REMARK 3 S21: -0.8329 S22: -0.4347 S23: 0.1383 REMARK 3 S31: -0.2390 S32: -0.2991 S33: 0.3690 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 6DP0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-JUN-18. REMARK 100 THE DEPOSITION ID IS D_1000235006. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-JUN-17 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 : 29454 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.450 REMARK 200 RESOLUTION RANGE LOW (A) : 19.880 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 88.5 REMARK 200 DATA REDUNDANCY : 1.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.48 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.9 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 1ZBL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.83 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.45 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 40.73900 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.88700 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 40.73900 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 18.88700 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: 5210 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8060 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -37.0 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 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 OD2 ASP A 163 O HOH A 301 2.18 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 409 O HOH A 409 2656 1.89 REMARK 500 O HOH A 405 O HOH A 405 2656 2.00 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 DG C 2 O3' DG C 2 C3' -0.065 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 146 58.05 -91.81 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 445 DISTANCE = 5.91 ANGSTROMS REMARK 525 HOH A 446 DISTANCE = 6.05 ANGSTROMS REMARK 525 HOH A 447 DISTANCE = 6.39 ANGSTROMS REMARK 525 HOH A 448 DISTANCE = 7.65 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 97.4 REMARK 620 3 HOH A 322 O 168.9 74.3 REMARK 620 4 HOH A 335 O 89.2 98.3 84.8 REMARK 620 5 HOH A 342 O 90.2 85.7 96.4 176.0 REMARK 620 6 C b 5 OP1 101.8 158.0 87.9 92.9 83.4 REMARK 620 N 1 2 3 4 5 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 101.9 REMARK 620 3 ASP A 132 OD1 136.4 95.2 REMARK 620 4 ASP A 132 OD2 111.2 141.7 47.2 REMARK 620 5 U B 4 O3' 137.9 83.1 83.4 85.1 REMARK 620 6 C b 5 OP1 84.2 114.8 123.9 88.0 56.9 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 ARG A 195 O 124.2 REMARK 620 3 HOH A 310 O 57.2 67.0 REMARK 620 4 HOH A 322 O 46.7 100.8 56.3 REMARK 620 5 HOH A 335 O 54.6 155.3 106.8 59.3 REMARK 620 6 G b 6 OP2 100.1 108.1 122.2 69.7 53.4 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 B 113 O REMARK 620 2 DT C 4 O4 155.4 REMARK 620 3 DG C 5 O6 90.3 72.4 REMARK 620 4 HOH C 210 O 111.7 82.9 79.5 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 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 206 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 207 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 208 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 209 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 210 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 211 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 212 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K C 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO C 102 DBREF 6DP0 A 61 195 UNP Q9KEI9 RNH1_BACHD 61 195 DBREF 6DP0 B 1 4 PDB 6DP0 6DP0 1 4 DBREF 6DP0 b 5 6 PDB 6DP0 6DP0 5 6 DBREF 6DP0 C 1 6 PDB 6DP0 6DP0 1 6 SEQRES 1 A 135 GLU GLU ILE ILE TRP GLU SER LEU SER VAL ASP VAL GLY SEQRES 2 A 135 SER GLN GLY ASN PRO GLY ILE VAL GLU TYR LYS GLY VAL SEQRES 3 A 135 ASP THR LYS THR GLY GLU VAL LEU PHE GLU ARG GLU PRO SEQRES 4 A 135 ILE PRO ILE GLY THR ASN ASN MET GLY GLU PHE LEU ALA SEQRES 5 A 135 ILE VAL HIS GLY LEU ARG TYR LEU LYS GLU ARG ASN SER SEQRES 6 A 135 ARG LYS PRO ILE TYR SER ASP SER GLN THR ALA ILE LYS SEQRES 7 A 135 TRP VAL LYS ASP LYS LYS ALA LYS SER THR LEU VAL ARG SEQRES 8 A 135 ASN GLU GLU THR ALA LEU ILE TRP LYS LEU VAL ASP GLU SEQRES 9 A 135 ALA GLU GLU TRP LEU ASN THR HIS THR TYR GLU THR PRO SEQRES 10 A 135 ILE LEU LYS TRP GLN THR ASP LYS TRP GLY GLU ILE LYS SEQRES 11 A 135 ALA ASP TYR GLY ARG 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 GOL A 208 6 HET GOL A 209 6 HET GOL A 210 6 HET GOL A 211 6 HET EDO A 212 4 HET K C 101 1 HET EDO C 102 4 HETNAM MG MAGNESIUM ION HETNAM K POTASSIUM ION HETNAM IOD IODIDE ION HETNAM GOL GLYCEROL HETNAM EDO 1,2-ETHANEDIOL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 5 MG 2(MG 2+) FORMUL 7 K 2(K 1+) FORMUL 8 IOD 4(I 1-) FORMUL 12 GOL 4(C3 H8 O3) FORMUL 16 EDO 2(C2 H6 O2) FORMUL 19 HOH *182(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 ASN A 170 1 16 HELIX 5 AA5 GLN A 182 GLY A 187 1 6 SHEET 1 AA1 5 VAL A 93 GLY A 103 0 SHEET 2 AA1 5 GLY A 79 ASP A 87 -1 N VAL A 81 O ILE A 100 SHEET 3 AA1 5 LEU A 68 GLN A 75 -1 N SER A 69 O VAL A 86 SHEET 4 AA1 5 ILE A 129 SER A 131 1 O TYR A 130 N LEU A 68 SHEET 5 AA1 5 ILE A 178 LYS A 180 1 O LEU A 179 N ILE A 129 LINK O3' U B 4 P C b 5 1555 1555 1.60 LINK OD2 ASP A 71 MG MG A 201 1555 1555 2.04 LINK OD1 ASP A 71 MG MG A 202 1555 1555 2.11 LINK OE1 GLU A 109 MG MG A 202 1555 1555 2.35 LINK OD1 ASP A 132 MG MG A 202 1555 1555 2.40 LINK OD2 ASP A 132 MG MG A 202 1555 1555 2.93 LINK OD1 ASP A 192 MG MG A 201 1555 1555 1.94 LINK OD1 ASP A 192 K K A 203 1555 1555 3.49 LINK O ARG A 195 K K A 203 1555 1555 3.33 LINK MG MG A 201 O HOH A 322 1555 1555 2.31 LINK MG MG A 201 O HOH A 335 1555 1555 2.07 LINK MG MG A 201 O HOH A 342 1555 1555 2.21 LINK MG MG A 201 OP1 C b 5 1555 1555 2.12 LINK MG MG A 202 O3' U B 4 1555 1555 2.69 LINK MG MG A 202 OP1 C b 5 1555 1555 2.40 LINK K K A 203 O HOH A 310 1555 1555 3.16 LINK K K A 203 O HOH A 322 1555 1555 2.89 LINK K K A 203 O HOH A 335 1555 1555 3.09 LINK K K A 203 OP2 G b 6 1555 1555 2.85 LINK O HOH B 113 K A K C 101 1555 1555 2.77 LINK O4 DT C 4 K A K C 101 1555 1555 3.22 LINK O6 DG C 5 K A K C 101 1555 1555 2.73 LINK K A K C 101 O HOH C 210 1555 1555 3.30 CISPEP 1 ASN A 77 PRO A 78 0 2.33 SITE 1 AC1 6 ASP A 71 ASP A 192 HOH A 322 HOH A 335 SITE 2 AC1 6 HOH A 342 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 6 ASP A 192 GLY A 194 ARG A 195 HOH A 322 SITE 2 AC3 6 HOH A 335 G b 6 SITE 1 AC4 1 TYR A 83 SITE 1 AC5 3 ILE A 64 HOH A 443 HOH A 447 SITE 1 AC6 1 HIS A 172 SITE 1 AC7 6 GLY A 76 ASN A 77 PRO A 78 HOH B 103 SITE 2 AC7 6 DG C 2 DA C 3 SITE 1 AC8 7 TYR A 119 ARG A 123 GLU A 167 ASN A 170 SITE 2 AC8 7 GOL A 211 HOH A 302 HOH A 378 SITE 1 AC9 6 GLU A 66 SER A 125 LYS A 127 HOH A 313 SITE 2 AC9 6 HOH A 326 HOH A 358 SITE 1 AD1 8 HIS A 115 ARG A 118 ASN A 170 GOL A 209 SITE 2 AD1 8 HOH A 349 HOH A 381 HOH A 385 HOH A 404 SITE 1 AD2 3 LYS A 143 THR A 173 TYR A 174 SITE 1 AD3 4 HOH B 113 DT C 4 DG C 5 HOH C 212 SITE 1 AD4 3 DA C 3 DT C 4 HOH C 202 CRYST1 81.478 37.774 61.811 90.00 96.13 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 0.012273 0.000000 0.001317 0.00000 SCALE2 0.000000 0.026473 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016271 0.00000