HEADER HYDROLASE/DNA/RNA 09-JUN-18 6DP1 TITLE CRYSTAL STRUCTURE OF BACILLUS HALODURANS RIBONUCLEASE H1 IN COMPLEX TITLE 2 WITH AN RNA/DNA HYBRID: REACTION IN 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 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 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; 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 6DP1 1 LINK REVDAT 2 22-AUG-18 6DP1 1 JRNL REVDAT 1 15-AUG-18 6DP1 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. 1.42 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) : 1.42 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.16 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.7 REMARK 3 NUMBER OF REFLECTIONS : 34440 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.155 REMARK 3 R VALUE (WORKING SET) : 0.153 REMARK 3 FREE R VALUE : 0.190 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 1717 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 19.1664 - 3.2368 0.99 2913 140 0.1275 0.1709 REMARK 3 2 3.2368 - 2.5711 1.00 2842 154 0.1516 0.1739 REMARK 3 3 2.5711 - 2.2467 1.00 2839 125 0.1487 0.1786 REMARK 3 4 2.2467 - 2.0415 1.00 2830 141 0.1473 0.2044 REMARK 3 5 2.0415 - 1.8953 1.00 2816 161 0.1569 0.1798 REMARK 3 6 1.8953 - 1.7837 0.99 2771 149 0.1802 0.2307 REMARK 3 7 1.7837 - 1.6944 0.99 2773 155 0.1700 0.1826 REMARK 3 8 1.6944 - 1.6207 0.97 2709 150 0.1831 0.2041 REMARK 3 9 1.6207 - 1.5583 0.96 2697 153 0.1980 0.2812 REMARK 3 10 1.5583 - 1.5046 0.95 2661 123 0.2346 0.2642 REMARK 3 11 1.5046 - 1.4575 0.95 2645 149 0.2608 0.2745 REMARK 3 12 1.4575 - 1.4159 0.79 2227 117 0.3026 0.2921 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) : 20.580 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.66 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.35 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 : 0.007 1462 REMARK 3 ANGLE : 1.004 2022 REMARK 3 CHIRALITY : 0.071 220 REMARK 3 PLANARITY : 0.006 212 REMARK 3 DIHEDRAL : 23.387 575 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): 25.1866 -5.8515 16.9889 REMARK 3 T TENSOR REMARK 3 T11: 0.1818 T22: 0.1279 REMARK 3 T33: 0.1492 T12: 0.0372 REMARK 3 T13: 0.0215 T23: -0.0025 REMARK 3 L TENSOR REMARK 3 L11: 3.4362 L22: 2.1099 REMARK 3 L33: 3.7305 L12: -1.3736 REMARK 3 L13: 1.5645 L23: -0.5103 REMARK 3 S TENSOR REMARK 3 S11: 0.3915 S12: 0.2592 S13: -0.3755 REMARK 3 S21: -0.1696 S22: -0.1673 S23: -0.0224 REMARK 3 S31: 0.4056 S32: 0.1714 S33: -0.1318 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 88 THROUGH 96 ) REMARK 3 ORIGIN FOR THE GROUP (A): 28.1766 -11.5416 23.8057 REMARK 3 T TENSOR REMARK 3 T11: 0.2627 T22: 0.2133 REMARK 3 T33: 0.3728 T12: 0.0564 REMARK 3 T13: 0.0037 T23: 0.0232 REMARK 3 L TENSOR REMARK 3 L11: 5.7312 L22: 2.3733 REMARK 3 L33: 4.7038 L12: -1.6390 REMARK 3 L13: -5.0203 L23: 0.7649 REMARK 3 S TENSOR REMARK 3 S11: -0.0397 S12: -0.4040 S13: -1.1858 REMARK 3 S21: 0.0036 S22: 0.1586 S23: -0.3187 REMARK 3 S31: 0.7304 S32: 0.3931 S33: 0.0647 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 97 THROUGH 133 ) REMARK 3 ORIGIN FOR THE GROUP (A): 22.0683 -0.9624 23.1876 REMARK 3 T TENSOR REMARK 3 T11: 0.1222 T22: 0.0942 REMARK 3 T33: 0.1324 T12: 0.0165 REMARK 3 T13: 0.0284 T23: 0.0079 REMARK 3 L TENSOR REMARK 3 L11: 4.0838 L22: 0.6718 REMARK 3 L33: 4.5648 L12: -0.0889 REMARK 3 L13: 2.7529 L23: 0.3070 REMARK 3 S TENSOR REMARK 3 S11: 0.0616 S12: -0.2667 S13: -0.0693 REMARK 3 S21: -0.0486 S22: -0.0520 S23: 0.0278 REMARK 3 S31: 0.0416 S32: -0.2986 S33: -0.0240 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 134 THROUGH 142 ) REMARK 3 ORIGIN FOR THE GROUP (A): 24.0051 9.3864 16.5013 REMARK 3 T TENSOR REMARK 3 T11: 0.3025 T22: 0.1127 REMARK 3 T33: 0.2067 T12: -0.0072 REMARK 3 T13: 0.0409 T23: 0.0368 REMARK 3 L TENSOR REMARK 3 L11: 4.7909 L22: 8.2429 REMARK 3 L33: 6.9021 L12: -4.8861 REMARK 3 L13: -0.0919 L23: 0.6367 REMARK 3 S TENSOR REMARK 3 S11: 0.1771 S12: 0.1122 S13: 0.5457 REMARK 3 S21: -0.0235 S22: -0.1965 S23: -0.5214 REMARK 3 S31: -1.0121 S32: 0.1747 S33: -0.0564 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 143 THROUGH 155 ) REMARK 3 ORIGIN FOR THE GROUP (A): 8.7704 7.6060 16.0554 REMARK 3 T TENSOR REMARK 3 T11: 0.3033 T22: 0.5267 REMARK 3 T33: 0.2294 T12: 0.4191 REMARK 3 T13: -0.0084 T23: -0.1375 REMARK 3 L TENSOR REMARK 3 L11: 7.1335 L22: 3.5349 REMARK 3 L33: 3.3814 L12: 0.5425 REMARK 3 L13: 2.5710 L23: 0.2528 REMARK 3 S TENSOR REMARK 3 S11: 0.6484 S12: -0.2039 S13: 0.3957 REMARK 3 S21: -0.1834 S22: -0.7914 S23: 0.5068 REMARK 3 S31: -0.9995 S32: -1.2020 S33: 0.1452 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 156 THROUGH 169 ) REMARK 3 ORIGIN FOR THE GROUP (A): 12.4774 5.6692 24.7445 REMARK 3 T TENSOR REMARK 3 T11: 0.2089 T22: 0.2745 REMARK 3 T33: 0.1725 T12: 0.0950 REMARK 3 T13: 0.0371 T23: -0.0312 REMARK 3 L TENSOR REMARK 3 L11: 8.9949 L22: 2.0358 REMARK 3 L33: 8.0147 L12: 1.1078 REMARK 3 L13: 6.8684 L23: 2.1745 REMARK 3 S TENSOR REMARK 3 S11: 0.1987 S12: -0.3545 S13: 0.0081 REMARK 3 S21: 0.0052 S22: -0.2896 S23: 0.1187 REMARK 3 S31: -0.3516 S32: -0.8384 S33: 0.1377 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 170 THROUGH 196 ) REMARK 3 ORIGIN FOR THE GROUP (A): 29.1095 -0.3267 18.0787 REMARK 3 T TENSOR REMARK 3 T11: 0.1485 T22: 0.1363 REMARK 3 T33: 0.1321 T12: 0.0468 REMARK 3 T13: 0.0139 T23: 0.0425 REMARK 3 L TENSOR REMARK 3 L11: 3.9231 L22: 2.9667 REMARK 3 L33: 5.6136 L12: -0.8444 REMARK 3 L13: -0.9981 L23: 0.9217 REMARK 3 S TENSOR REMARK 3 S11: 0.1205 S12: 0.3831 S13: -0.0322 REMARK 3 S21: -0.2777 S22: -0.0744 S23: -0.1766 REMARK 3 S31: 0.0800 S32: 0.2744 S33: -0.0753 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): 23.8674 1.3035 4.4511 REMARK 3 T TENSOR REMARK 3 T11: 0.3328 T22: 0.2560 REMARK 3 T33: 0.1805 T12: 0.0857 REMARK 3 T13: 0.0377 T23: 0.0014 REMARK 3 L TENSOR REMARK 3 L11: 4.7009 L22: 5.9523 REMARK 3 L33: 5.5399 L12: -0.4738 REMARK 3 L13: 3.0175 L23: -0.6848 REMARK 3 S TENSOR REMARK 3 S11: 0.0720 S12: 0.6045 S13: -0.1213 REMARK 3 S21: -0.6322 S22: -0.1812 S23: -0.2205 REMARK 3 S31: 0.1403 S32: 0.3005 S33: 0.1573 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 1 THROUGH 6 ) REMARK 3 ORIGIN FOR THE GROUP (A): 16.4854 3.7523 3.1215 REMARK 3 T TENSOR REMARK 3 T11: 0.3772 T22: 0.2113 REMARK 3 T33: 0.1658 T12: 0.1071 REMARK 3 T13: -0.0077 T23: -0.0008 REMARK 3 L TENSOR REMARK 3 L11: 3.5936 L22: 4.0010 REMARK 3 L33: 6.8565 L12: -1.5946 REMARK 3 L13: -2.5792 L23: 0.7609 REMARK 3 S TENSOR REMARK 3 S11: 0.0815 S12: 0.3871 S13: -0.1524 REMARK 3 S21: -0.8461 S22: -0.3999 S23: 0.1753 REMARK 3 S31: -0.5074 S32: -0.4290 S33: 0.3519 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 6DP1 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_1000235008. 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 : 34456 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.420 REMARK 200 RESOLUTION RANGE LOW (A) : 19.160 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.8 REMARK 200 DATA REDUNDANCY : 1.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.42 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.44 REMARK 200 COMPLETENESS FOR SHELL (%) : 69.2 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 (%): 49.49 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 40.88200 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.71450 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 40.88200 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 18.71450 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: 5170 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8040 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -39.0 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 465 LYS A 196 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 GOL A 212 O HOH A 301 2.02 REMARK 500 O1 EDO A 213 O HOH A 302 2.07 REMARK 500 OH TYR A 174 O HOH A 303 2.11 REMARK 500 OG1 THR A 90 O HOH A 304 2.15 REMARK 500 OE2 GLU A 154 O HOH A 305 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 428 O HOH A 428 2656 1.81 REMARK 500 O HOH A 429 O HOH A 460 3545 2.11 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' -0.042 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 464 DISTANCE = 6.40 ANGSTROMS REMARK 525 HOH A 465 DISTANCE = 6.61 ANGSTROMS REMARK 525 HOH A 466 DISTANCE = 6.63 ANGSTROMS REMARK 525 HOH A 467 DISTANCE = 7.37 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 97.9 REMARK 620 3 HOH A 318 O 172.7 75.5 REMARK 620 4 HOH A 322 O 91.2 96.8 86.7 REMARK 620 5 HOH A 365 O 87.4 90.5 95.6 172.7 REMARK 620 6 C b 5 OP1 100.8 159.5 86.2 91.1 82.1 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 100.7 REMARK 620 3 ASP A 132 OD1 136.2 97.6 REMARK 620 4 ASP A 132 OD2 111.0 144.6 48.3 REMARK 620 5 U B 4 O3' 137.4 82.8 84.0 84.2 REMARK 620 6 C b 5 OP1 83.7 109.7 126.2 89.5 56.1 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 139.7 REMARK 620 3 HOH A 317 O 66.5 73.7 REMARK 620 4 HOH A 318 O 50.1 105.8 63.5 REMARK 620 5 HOH A 322 O 57.4 145.2 116.5 58.9 REMARK 620 6 G b 6 OP2 100.6 94.2 121.3 65.7 51.5 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 109 O REMARK 620 2 DT C 4 O4 158.1 REMARK 620 3 DG C 5 O6 91.2 73.5 REMARK 620 4 HOH C 209 O 108.8 84.6 81.1 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 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 GOL A 208 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 209 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL 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 EDO A 213 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K C 101 DBREF 6DP1 A 59 196 UNP Q9KEI9 RNH1_BACHD 59 196 DBREF 6DP1 B 1 4 PDB 6DP1 6DP1 1 4 DBREF 6DP1 b 5 6 PDB 6DP1 6DP1 5 6 DBREF 6DP1 C 1 6 PDB 6DP1 6DP1 1 6 SEQADV 6DP1 GLY A 55 UNP Q9KEI9 EXPRESSION TAG SEQADV 6DP1 SER A 56 UNP Q9KEI9 EXPRESSION TAG SEQADV 6DP1 HIS A 57 UNP Q9KEI9 EXPRESSION TAG SEQADV 6DP1 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 GOL A 208 6 HET GOL A 209 6 HET GOL A 210 6 HET EDO A 211 4 HET GOL A 212 6 HET EDO A 213 4 HET K C 101 1 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 15 EDO 2(C2 H6 O2) FORMUL 19 HOH *199(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' U B 4 P C b 5 1555 1555 1.59 LINK OD2 ASP A 71 MG MG A 201 1555 1555 2.03 LINK OD1 ASP A 71 MG MG A 202 1555 1555 2.12 LINK OE1 GLU A 109 MG MG A 202 1555 1555 2.27 LINK OD1 ASP A 132 MG MG A 202 1555 1555 2.33 LINK OD2 ASP A 132 MG MG A 202 1555 1555 2.87 LINK OD1 ASP A 192 MG MG A 201 1555 1555 1.97 LINK OD1 ASP A 192 K K A 203 1555 1555 3.17 LINK O ARG A 195 K K A 203 1555 1555 3.08 LINK MG MG A 201 O HOH A 318 1555 1555 2.20 LINK MG MG A 201 O HOH A 322 1555 1555 2.06 LINK MG MG A 201 O HOH A 365 1555 1555 2.09 LINK MG MG A 201 OP1 C b 5 1555 1555 2.14 LINK MG MG A 202 O3' U B 4 1555 1555 2.73 LINK MG MG A 202 OP1 C b 5 1555 1555 2.51 LINK K K A 203 O HOH A 317 1555 1555 2.84 LINK K K A 203 O HOH A 318 1555 1555 2.82 LINK K K A 203 O HOH A 322 1555 1555 3.11 LINK K K A 203 OP2 G b 6 1555 1555 3.10 LINK O HOH B 109 K A K C 101 1555 1555 3.06 LINK O4 DT C 4 K A K C 101 1555 1555 3.28 LINK O6 DG C 5 K A K C 101 1555 1555 2.66 LINK K A K C 101 O HOH C 209 1555 1555 3.30 CISPEP 1 ASN A 77 PRO A 78 0 1.10 SITE 1 AC1 6 ASP A 71 ASP A 192 HOH A 318 HOH A 322 SITE 2 AC1 6 HOH A 365 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 317 SITE 2 AC3 6 HOH A 318 G b 6 SITE 1 AC4 1 TYR A 83 SITE 1 AC5 1 HOH A 339 SITE 1 AC6 3 ILE A 64 HOH A 459 HOH A 464 SITE 1 AC7 2 HIS A 172 HOH A 447 SITE 1 AC8 6 GLY A 76 ASN A 77 PRO A 78 HOH A 312 SITE 2 AC8 6 DG C 2 DA C 3 SITE 1 AC9 7 HIS A 115 ARG A 118 TYR A 119 ARG A 123 SITE 2 AC9 7 GLU A 167 ASN A 170 HOH A 309 SITE 1 AD1 5 GLU A 66 SER A 125 LYS A 127 HOH A 308 SITE 2 AD1 5 HOH A 418 SITE 1 AD2 5 LYS A 143 THR A 173 TYR A 174 HOH A 366 SITE 2 AD2 5 HOH A 421 SITE 1 AD3 6 THR A 148 HOH A 301 HOH A 367 DT C 4 SITE 2 AD3 6 DG C 5 HOH C 208 SITE 1 AD4 5 LYS A 89 ALA A 156 HOH A 302 HOH A 307 SITE 2 AD4 5 HOH A 436 SITE 1 AD5 4 HOH B 109 DT C 4 DG C 5 HOH C 212 CRYST1 81.764 37.429 61.787 90.00 96.47 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 0.012230 0.000000 0.001387 0.00000 SCALE2 0.000000 0.026717 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016288 0.00000