HEADER HYDROLASE/DNA/RNA 09-JUN-18 6DP4 TITLE CRYSTAL STRUCTURE OF BACILLUS HALODURANS RIBONUCLEASE H1 IN COMPLEX TITLE 2 WITH AN RNA/DNA HYBRID: REACTION IN 20 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 59-196; 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 CLEAVED 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 CLEAVED 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; 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 BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; 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, 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 6DP4 1 LINK REVDAT 2 22-AUG-18 6DP4 1 JRNL REVDAT 1 15-AUG-18 6DP4 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. 1.37 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) : 1.37 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.92 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.7 REMARK 3 NUMBER OF REFLECTIONS : 37956 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.158 REMARK 3 R VALUE (WORKING SET) : 0.157 REMARK 3 FREE R VALUE : 0.176 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 1904 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 19.9223 - 3.3076 0.97 2680 147 0.1313 0.1434 REMARK 3 2 3.3076 - 2.6272 0.99 2670 139 0.1466 0.1659 REMARK 3 3 2.6272 - 2.2957 0.99 2626 157 0.1539 0.1677 REMARK 3 4 2.2957 - 2.0860 0.98 2636 128 0.1504 0.1709 REMARK 3 5 2.0860 - 1.9366 0.96 2552 143 0.1569 0.1924 REMARK 3 6 1.9366 - 1.8226 0.95 2529 130 0.1777 0.1906 REMARK 3 7 1.8226 - 1.7313 0.95 2512 132 0.1683 0.2111 REMARK 3 8 1.7313 - 1.6560 0.95 2528 135 0.1692 0.1886 REMARK 3 9 1.6560 - 1.5923 0.96 2576 119 0.1840 0.1908 REMARK 3 10 1.5923 - 1.5374 0.97 2589 128 0.1955 0.2150 REMARK 3 11 1.5374 - 1.4893 0.97 2559 137 0.2158 0.2538 REMARK 3 12 1.4893 - 1.4467 0.98 2559 134 0.2434 0.2451 REMARK 3 13 1.4467 - 1.4087 0.99 2615 143 0.2657 0.3046 REMARK 3 14 1.4087 - 1.3743 0.91 2421 132 0.3027 0.3316 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) : 0.140 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.270 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.94 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.97 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 1491 REMARK 3 ANGLE : 1.066 2044 REMARK 3 CHIRALITY : 0.072 224 REMARK 3 PLANARITY : 0.007 210 REMARK 3 DIHEDRAL : 24.691 583 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): 25.4698 -5.6581 17.3318 REMARK 3 T TENSOR REMARK 3 T11: 0.1674 T22: 0.1262 REMARK 3 T33: 0.1409 T12: 0.0231 REMARK 3 T13: 0.0153 T23: 0.0024 REMARK 3 L TENSOR REMARK 3 L11: 6.7292 L22: 1.7993 REMARK 3 L33: 3.3622 L12: -1.6039 REMARK 3 L13: 1.1105 L23: -0.4167 REMARK 3 S TENSOR REMARK 3 S11: 0.2020 S12: 0.2310 S13: -0.2104 REMARK 3 S21: -0.1473 S22: -0.1297 S23: -0.1038 REMARK 3 S31: 0.2448 S32: 0.2698 S33: -0.0791 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 88 THROUGH 96 ) REMARK 3 ORIGIN FOR THE GROUP (A): 27.9125 -11.6443 24.0002 REMARK 3 T TENSOR REMARK 3 T11: 0.2188 T22: 0.1927 REMARK 3 T33: 0.3339 T12: 0.0655 REMARK 3 T13: -0.0188 T23: 0.0568 REMARK 3 L TENSOR REMARK 3 L11: 3.7308 L22: 5.9419 REMARK 3 L33: 6.8785 L12: -3.0751 REMARK 3 L13: -4.4473 L23: 1.3589 REMARK 3 S TENSOR REMARK 3 S11: -0.0387 S12: -0.6030 S13: -0.9526 REMARK 3 S21: 0.2501 S22: 0.0048 S23: -0.4811 REMARK 3 S31: 0.5842 S32: 0.5523 S33: 0.0408 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 97 THROUGH 133 ) REMARK 3 ORIGIN FOR THE GROUP (A): 21.9097 -0.9496 23.3232 REMARK 3 T TENSOR REMARK 3 T11: 0.1142 T22: 0.0930 REMARK 3 T33: 0.1200 T12: 0.0166 REMARK 3 T13: 0.0201 T23: 0.0082 REMARK 3 L TENSOR REMARK 3 L11: 4.9385 L22: 0.6931 REMARK 3 L33: 4.2774 L12: -0.0741 REMARK 3 L13: 2.9559 L23: 0.3859 REMARK 3 S TENSOR REMARK 3 S11: 0.0872 S12: -0.1771 S13: -0.0690 REMARK 3 S21: -0.0310 S22: -0.0899 S23: 0.0183 REMARK 3 S31: 0.0574 S32: -0.2151 S33: 0.0062 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 134 THROUGH 142 ) REMARK 3 ORIGIN FOR THE GROUP (A): 23.9410 9.3638 16.5668 REMARK 3 T TENSOR REMARK 3 T11: 0.2868 T22: 0.1491 REMARK 3 T33: 0.1912 T12: -0.0115 REMARK 3 T13: 0.0422 T23: 0.0481 REMARK 3 L TENSOR REMARK 3 L11: 6.7927 L22: 8.1755 REMARK 3 L33: 1.6225 L12: -6.5132 REMARK 3 L13: -1.3742 L23: 2.6706 REMARK 3 S TENSOR REMARK 3 S11: 0.3651 S12: 0.1580 S13: 0.3444 REMARK 3 S21: -0.3650 S22: -0.1285 S23: -0.4241 REMARK 3 S31: -0.7599 S32: 0.0574 S33: -0.2253 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 143 THROUGH 155 ) REMARK 3 ORIGIN FOR THE GROUP (A): 8.7270 7.9135 15.9367 REMARK 3 T TENSOR REMARK 3 T11: 0.2774 T22: 0.3042 REMARK 3 T33: 0.1995 T12: 0.1787 REMARK 3 T13: 0.0044 T23: -0.0561 REMARK 3 L TENSOR REMARK 3 L11: 8.2881 L22: 1.4278 REMARK 3 L33: 5.1719 L12: -0.6780 REMARK 3 L13: 2.3055 L23: -1.5540 REMARK 3 S TENSOR REMARK 3 S11: 0.1553 S12: 0.1573 S13: 0.5356 REMARK 3 S21: -0.1707 S22: -0.2490 S23: 0.4582 REMARK 3 S31: -0.3979 S32: -0.7430 S33: 0.0539 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 156 THROUGH 169 ) REMARK 3 ORIGIN FOR THE GROUP (A): 12.4567 5.8620 24.7924 REMARK 3 T TENSOR REMARK 3 T11: 0.1611 T22: 0.2052 REMARK 3 T33: 0.1555 T12: 0.0581 REMARK 3 T13: 0.0249 T23: -0.0148 REMARK 3 L TENSOR REMARK 3 L11: 4.5797 L22: 4.9728 REMARK 3 L33: 8.4807 L12: 3.4028 REMARK 3 L13: 6.1148 L23: 3.8235 REMARK 3 S TENSOR REMARK 3 S11: 0.1748 S12: -0.2214 S13: 0.1296 REMARK 3 S21: 0.0068 S22: -0.2594 S23: 0.1739 REMARK 3 S31: -0.1115 S32: -0.5200 S33: 0.0345 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 170 THROUGH 196 ) REMARK 3 ORIGIN FOR THE GROUP (A): 28.7827 -0.8551 17.9065 REMARK 3 T TENSOR REMARK 3 T11: 0.1419 T22: 0.1467 REMARK 3 T33: 0.1112 T12: 0.0603 REMARK 3 T13: -0.0060 T23: 0.0494 REMARK 3 L TENSOR REMARK 3 L11: 3.3170 L22: 3.4692 REMARK 3 L33: 5.9974 L12: -0.9771 REMARK 3 L13: -1.5078 L23: 2.4866 REMARK 3 S TENSOR REMARK 3 S11: 0.1482 S12: 0.2632 S13: -0.0809 REMARK 3 S21: -0.3076 S22: -0.0305 S23: -0.2042 REMARK 3 S31: -0.0142 S32: 0.3253 S33: -0.1531 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): 23.6960 0.6898 5.0338 REMARK 3 T TENSOR REMARK 3 T11: 0.3144 T22: 0.2954 REMARK 3 T33: 0.1726 T12: 0.0797 REMARK 3 T13: 0.0395 T23: 0.0285 REMARK 3 L TENSOR REMARK 3 L11: 3.0029 L22: 2.0664 REMARK 3 L33: 1.0351 L12: 0.2706 REMARK 3 L13: 1.4660 L23: -0.6186 REMARK 3 S TENSOR REMARK 3 S11: 0.0503 S12: 0.4026 S13: -0.0465 REMARK 3 S21: -0.4775 S22: -0.2156 S23: -0.1507 REMARK 3 S31: 0.2010 S32: 0.1670 S33: 0.1883 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 1 THROUGH 6 ) REMARK 3 ORIGIN FOR THE GROUP (A): 16.3992 3.5100 3.1937 REMARK 3 T TENSOR REMARK 3 T11: 0.4110 T22: 0.2595 REMARK 3 T33: 0.1574 T12: 0.0809 REMARK 3 T13: -0.0410 T23: 0.0183 REMARK 3 L TENSOR REMARK 3 L11: 2.9935 L22: 4.4999 REMARK 3 L33: 4.8204 L12: -0.7294 REMARK 3 L13: -2.7313 L23: 2.9283 REMARK 3 S TENSOR REMARK 3 S11: -0.0552 S12: 0.3550 S13: -0.1705 REMARK 3 S21: -0.9389 S22: -0.2842 S23: 0.1651 REMARK 3 S31: -0.3815 S32: -0.2193 S33: 0.3235 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 6DP4 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_1000235014. 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 : 23-ID-B 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 : 37958 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.370 REMARK 200 RESOLUTION RANGE LOW (A) : 19.920 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 200 DATA REDUNDANCY : 1.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.37 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.40 REMARK 200 COMPLETENESS FOR SHELL (%) : 88.3 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: 1ZBL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.55 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.44 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 40.76250 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.83700 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 40.76250 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 18.83700 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: 6030 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7690 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -46.0 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 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 A 406 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 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: 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 -0.132 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 DG C 2 O4' - C1' - N9 ANGL. DEV. = 2.2 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 455 DISTANCE = 5.93 ANGSTROMS REMARK 525 HOH A 456 DISTANCE = 6.04 ANGSTROMS REMARK 525 HOH A 457 DISTANCE = 6.32 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 106.0 REMARK 620 3 HOH A 301 O 171.8 77.8 REMARK 620 4 HOH A 310 O 86.8 89.7 86.0 REMARK 620 5 HOH A 311 O 89.4 87.5 98.0 174.5 REMARK 620 6 C b 5 OP3 156.4 97.5 20.4 91.6 93.4 REMARK 620 7 C b 5 OP1 95.1 157.1 82.5 100.5 83.8 62.1 REMARK 620 8 C b 5 OP1 93.4 159.8 83.7 97.0 87.2 63.4 3.8 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 99.4 REMARK 620 3 ASP A 132 OD1 140.1 93.0 REMARK 620 4 ASP A 132 OD2 102.8 149.9 57.0 REMARK 620 5 U B 4 O3' 146.1 80.2 73.4 92.2 REMARK 620 6 C b 5 OP1 91.3 107.4 120.9 92.2 57.5 REMARK 620 7 C b 5 OP1 85.2 108.0 126.6 93.9 63.3 6.1 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 204 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 188 OE1 REMARK 620 2 GLU A 188 OE2 41.5 REMARK 620 3 HOH A 311 O 89.4 49.1 REMARK 620 4 HOH A 369 O 87.2 62.2 62.4 REMARK 620 5 HOH B 108 O 90.0 129.2 175.7 113.3 REMARK 620 6 C b 5 OP2 123.6 115.7 81.3 132.7 102.6 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 40.6 REMARK 620 3 HOH A 301 O 51.4 84.4 REMARK 620 4 HOH A 310 O 55.7 93.8 51.5 REMARK 620 5 HOH A 336 O 80.4 52.1 89.8 133.2 REMARK 620 6 G b 6 OP2 99.3 139.8 60.7 49.6 138.1 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 DG C 5 O6 REMARK 620 2 HOH C 208 O 89.6 REMARK 620 N 1 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 K 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 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 GOL A 212 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 213 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 214 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K C 101 DBREF 6DP4 A 59 196 UNP Q9KEI9 RNH1_BACHD 59 196 DBREF 6DP4 B 1 4 PDB 6DP4 6DP4 1 4 DBREF 6DP4 b 5 6 PDB 6DP4 6DP4 5 6 DBREF 6DP4 C 1 6 PDB 6DP4 6DP4 1 6 SEQADV 6DP4 GLY A 55 UNP Q9KEI9 EXPRESSION TAG SEQADV 6DP4 SER A 56 UNP Q9KEI9 EXPRESSION TAG SEQADV 6DP4 HIS A 57 UNP Q9KEI9 EXPRESSION TAG SEQADV 6DP4 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 K 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 GOL A 212 6 HET GOL A 213 6 HET GOL A 214 6 HET K C 101 1 HETNAM MG MAGNESIUM ION HETNAM K POTASSIUM ION HETNAM IOD IODIDE ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 5 MG 2(MG 2+) FORMUL 7 K 3(K 1+) FORMUL 9 IOD 3(I 1-) FORMUL 12 GOL 7(C3 H8 O3) FORMUL 20 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 THR A 155 ASN A 170 1 16 HELIX 4 AA4 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'C U B 4 P C C b 5 1555 1555 1.58 LINK OD2 ASP A 71 MG MG A 201 1555 1555 2.01 LINK OD1 ASP A 71 MG MG A 202 1555 1555 1.97 LINK OE1 GLU A 109 MG MG A 202 1555 1555 2.06 LINK OD1 ASP A 132 MG MG A 202 1555 1555 2.15 LINK OD2 ASP A 132 MG MG A 202 1555 1555 2.35 LINK OE1 GLU A 188 K B K A 204 1555 1555 3.14 LINK OE2 GLU A 188 K B K A 204 1555 1555 3.01 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 2.82 LINK OD2 ASP A 192 K C K A 203 1555 1555 3.33 LINK MG MG A 201 O CHOH A 301 1555 1555 2.02 LINK MG MG A 201 O HOH A 310 1555 1555 2.09 LINK MG MG A 201 O HOH A 311 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 2.43 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 2.64 LINK MG MG A 202 OP1B C b 5 1555 1555 2.07 LINK MG MG A 202 OP1C C b 5 1555 1555 2.14 LINK K C K A 203 O CHOH A 301 1555 1555 3.07 LINK K C K A 203 O HOH A 310 1555 1555 3.36 LINK K C K A 203 O HOH A 336 1555 1555 2.61 LINK K C K A 203 OP2 G b 6 1555 1555 2.87 LINK K B K A 204 O HOH A 311 1555 1555 3.13 LINK K B K A 204 O HOH A 369 1555 1555 3.24 LINK K B K A 204 O HOH B 108 1555 1555 2.82 LINK K B K A 204 OP2B C b 5 1555 1555 2.55 LINK O6 DG C 5 K A K C 101 1555 1555 2.62 LINK K A K C 101 O HOH C 208 1555 1555 2.99 CISPEP 1 ASN A 77 PRO A 78 0 0.41 SITE 1 AC1 6 ASP A 71 ASP A 192 HOH A 301 HOH A 310 SITE 2 AC1 6 HOH A 311 C b 5 SITE 1 AC2 6 ASP A 71 GLU A 109 ASP A 132 HOH A 349 SITE 2 AC2 6 U B 4 C b 5 SITE 1 AC3 7 ASP A 192 GLY A 194 ARG A 195 LYS A 196 SITE 2 AC3 7 HOH A 301 HOH A 336 G b 6 SITE 1 AC4 4 GLU A 188 LYS A 196 HOH B 108 C b 5 SITE 1 AC5 1 TYR A 83 SITE 1 AC6 2 HOH A 419 HOH A 457 SITE 1 AC7 6 GLY A 76 ASN A 77 PRO A 78 HOH A 305 SITE 2 AC7 6 DG C 2 DA C 3 SITE 1 AC8 6 ILE A 102 VAL A 150 ASN A 152 GLU A 154 SITE 2 AC8 6 HOH A 387 HOH C 203 SITE 1 AC9 6 GLU A 66 LEU A 94 SER A 125 LYS A 127 SITE 2 AC9 6 HOH A 307 HOH A 332 SITE 1 AD1 8 HIS A 115 TYR A 119 GLU A 122 ARG A 123 SITE 2 AD1 8 GLU A 167 GOL A 212 HOH A 329 HOH A 347 SITE 1 AD2 5 HIS A 115 ARG A 118 ASN A 170 GOL A 211 SITE 2 AD2 5 HOH A 356 SITE 1 AD3 4 THR A 148 HOH A 314 DT C 4 DG C 5 SITE 1 AD4 4 LYS A 143 THR A 173 TYR A 174 HOH A 346 SITE 1 AD5 3 DG C 5 HOH C 204 HOH C 208 CRYST1 81.525 37.674 62.050 90.00 96.52 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 0.012266 0.000000 0.001401 0.00000 SCALE2 0.000000 0.026544 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016221 0.00000