HEADER HYDROLASE/DNA/RNA 09-JUN-18 6DOB 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 200 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-DNA-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR N.L.SAMARA,W.YANG REVDAT 2 13-MAR-24 6DOB 1 LINK REVDAT 1 15-AUG-18 6DOB 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. 1.34 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) : 1.34 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.29 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.4 REMARK 3 NUMBER OF REFLECTIONS : 40941 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.170 REMARK 3 R VALUE (WORKING SET) : 0.169 REMARK 3 FREE R VALUE : 0.196 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.830 REMARK 3 FREE R VALUE TEST SET COUNT : 1979 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 32.2988 - 3.2364 0.92 2742 144 0.1325 0.1652 REMARK 3 2 3.2364 - 2.5692 0.96 2803 141 0.1493 0.1770 REMARK 3 3 2.5692 - 2.2445 0.97 2761 160 0.1587 0.1709 REMARK 3 4 2.2445 - 2.0393 0.97 2850 116 0.1576 0.1946 REMARK 3 5 2.0393 - 1.8932 0.98 2814 139 0.1786 0.1756 REMARK 3 6 1.8932 - 1.7816 0.98 2825 140 0.1670 0.1873 REMARK 3 7 1.7816 - 1.6924 0.99 2849 159 0.1622 0.2052 REMARK 3 8 1.6924 - 1.6187 0.99 2862 133 0.1794 0.2260 REMARK 3 9 1.6187 - 1.5564 0.99 2810 157 0.2074 0.2420 REMARK 3 10 1.5564 - 1.5027 0.99 2855 157 0.2534 0.3278 REMARK 3 11 1.5027 - 1.4557 0.99 2836 133 0.2631 0.2726 REMARK 3 12 1.4557 - 1.4141 0.98 2836 132 0.2954 0.3174 REMARK 3 13 1.4141 - 1.3768 0.96 2737 147 0.3240 0.3224 REMARK 3 14 1.3768 - 1.3433 0.83 2382 121 0.3628 0.4301 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.130 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.17 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.87 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 : 0.009 1514 REMARK 3 ANGLE : 1.116 2062 REMARK 3 CHIRALITY : 0.078 225 REMARK 3 PLANARITY : 0.007 213 REMARK 3 DIHEDRAL : 23.822 593 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): 25.484 -5.607 17.406 REMARK 3 T TENSOR REMARK 3 T11: 0.1508 T22: 0.0931 REMARK 3 T33: 0.0974 T12: 0.0220 REMARK 3 T13: 0.0217 T23: 0.0097 REMARK 3 L TENSOR REMARK 3 L11: 5.9176 L22: 1.8537 REMARK 3 L33: 3.3939 L12: -1.6096 REMARK 3 L13: 1.6472 L23: -0.3168 REMARK 3 S TENSOR REMARK 3 S11: 0.3160 S12: 0.2569 S13: -0.2409 REMARK 3 S21: -0.1861 S22: -0.1862 S23: -0.0669 REMARK 3 S31: 0.3498 S32: 0.1882 S33: -0.0601 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: ( CHAIN A AND RESID 88:96 ) REMARK 3 ORIGIN FOR THE GROUP (A): 28.125 -11.589 24.024 REMARK 3 T TENSOR REMARK 3 T11: 0.2423 T22: 0.1580 REMARK 3 T33: 0.2646 T12: 0.0627 REMARK 3 T13: 0.0071 T23: 0.0568 REMARK 3 L TENSOR REMARK 3 L11: 8.7237 L22: 4.5884 REMARK 3 L33: 5.8585 L12: -0.2002 REMARK 3 L13: -4.0130 L23: 0.4440 REMARK 3 S TENSOR REMARK 3 S11: -0.0721 S12: -0.3578 S13: -1.3614 REMARK 3 S21: 0.0770 S22: -0.0087 S23: -0.4659 REMARK 3 S31: 0.8159 S32: 0.3646 S33: 0.0475 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: ( CHAIN A AND RESID 97:133 ) REMARK 3 ORIGIN FOR THE GROUP (A): 21.663 -1.219 23.407 REMARK 3 T TENSOR REMARK 3 T11: 0.1082 T22: 0.0871 REMARK 3 T33: 0.0900 T12: 0.0120 REMARK 3 T13: 0.0217 T23: 0.0040 REMARK 3 L TENSOR REMARK 3 L11: 3.5334 L22: 0.9906 REMARK 3 L33: 2.9279 L12: -0.0300 REMARK 3 L13: 1.6349 L23: 0.3128 REMARK 3 S TENSOR REMARK 3 S11: 0.0745 S12: -0.2216 S13: -0.1013 REMARK 3 S21: -0.0227 S22: -0.0864 S23: 0.0199 REMARK 3 S31: 0.0440 S32: -0.2359 S33: 0.0184 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: ( CHAIN A AND RESID 134:142 ) REMARK 3 ORIGIN FOR THE GROUP (A): 23.808 9.389 16.605 REMARK 3 T TENSOR REMARK 3 T11: 0.2622 T22: 0.0992 REMARK 3 T33: 0.1460 T12: 0.0052 REMARK 3 T13: 0.0377 T23: 0.0355 REMARK 3 L TENSOR REMARK 3 L11: 3.6786 L22: 4.1684 REMARK 3 L33: 6.4540 L12: -2.6915 REMARK 3 L13: -0.7256 L23: -0.6012 REMARK 3 S TENSOR REMARK 3 S11: 0.2576 S12: 0.1088 S13: 0.4148 REMARK 3 S21: -0.2154 S22: -0.2140 S23: -0.3085 REMARK 3 S31: -0.9364 S32: 0.0619 S33: -0.0689 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: ( CHAIN A AND RESID 143:155 ) REMARK 3 ORIGIN FOR THE GROUP (A): 8.462 7.449 16.136 REMARK 3 T TENSOR REMARK 3 T11: 0.3085 T22: 0.4795 REMARK 3 T33: 0.1961 T12: 0.3024 REMARK 3 T13: -0.0188 T23: -0.1099 REMARK 3 L TENSOR REMARK 3 L11: 6.1235 L22: 2.6357 REMARK 3 L33: 2.1654 L12: 1.0734 REMARK 3 L13: 1.9250 L23: -0.1939 REMARK 3 S TENSOR REMARK 3 S11: 0.4226 S12: 0.0610 S13: 0.5508 REMARK 3 S21: -0.0815 S22: -0.5038 S23: 0.4499 REMARK 3 S31: -0.8906 S32: -1.0231 S33: 0.0820 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: ( CHAIN A AND RESID 156:169 ) REMARK 3 ORIGIN FOR THE GROUP (A): 12.409 5.770 24.873 REMARK 3 T TENSOR REMARK 3 T11: 0.1489 T22: 0.2128 REMARK 3 T33: 0.1281 T12: 0.0598 REMARK 3 T13: 0.0188 T23: -0.0442 REMARK 3 L TENSOR REMARK 3 L11: 7.7210 L22: 2.2979 REMARK 3 L33: 6.0059 L12: 0.9428 REMARK 3 L13: 5.5112 L23: 1.7384 REMARK 3 S TENSOR REMARK 3 S11: 0.1522 S12: -0.2748 S13: 0.1297 REMARK 3 S21: 0.0059 S22: -0.3356 S23: 0.1639 REMARK 3 S31: -0.1062 S32: -0.7130 S33: 0.2272 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: ( CHAIN A AND RESID 170:196 ) REMARK 3 ORIGIN FOR THE GROUP (A): 28.887 -0.831 17.778 REMARK 3 T TENSOR REMARK 3 T11: 0.1465 T22: 0.1213 REMARK 3 T33: 0.0837 T12: 0.0491 REMARK 3 T13: 0.0020 T23: 0.0331 REMARK 3 L TENSOR REMARK 3 L11: 3.0773 L22: 2.7490 REMARK 3 L33: 5.1762 L12: -0.4129 REMARK 3 L13: -0.7800 L23: 1.4728 REMARK 3 S TENSOR REMARK 3 S11: 0.1153 S12: 0.3074 S13: -0.1140 REMARK 3 S21: -0.4068 S22: -0.0580 S23: -0.1848 REMARK 3 S31: -0.0360 S32: 0.1989 S33: -0.0830 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): 23.685 0.746 5.103 REMARK 3 T TENSOR REMARK 3 T11: 0.3142 T22: 0.2384 REMARK 3 T33: 0.1322 T12: 0.0791 REMARK 3 T13: 0.0199 T23: 0.0128 REMARK 3 L TENSOR REMARK 3 L11: 2.8534 L22: 6.5592 REMARK 3 L33: 0.9269 L12: 0.2516 REMARK 3 L13: 1.4583 L23: -0.8262 REMARK 3 S TENSOR REMARK 3 S11: -0.0180 S12: 0.1777 S13: -0.1494 REMARK 3 S21: -0.6828 S22: -0.2244 S23: -0.2242 REMARK 3 S31: 0.2075 S32: 0.1144 S33: 0.2594 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: ( CHAIN C AND RESID 1:6 ) REMARK 3 ORIGIN FOR THE GROUP (A): 16.356 3.404 3.249 REMARK 3 T TENSOR REMARK 3 T11: 0.4050 T22: 0.2255 REMARK 3 T33: 0.1412 T12: 0.0815 REMARK 3 T13: -0.0361 T23: -0.0030 REMARK 3 L TENSOR REMARK 3 L11: 2.4601 L22: 2.3938 REMARK 3 L33: 3.6768 L12: -1.2462 REMARK 3 L13: -2.6714 L23: 0.6156 REMARK 3 S TENSOR REMARK 3 S11: -0.1176 S12: 0.2988 S13: -0.1403 REMARK 3 S21: -0.8323 S22: -0.3316 S23: 0.1939 REMARK 3 S31: -0.4161 S32: -0.2936 S33: 0.4205 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 6DOB 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_1000234961. 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 : 40966 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.340 REMARK 200 RESOLUTION RANGE LOW (A) : 32.290 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.7 REMARK 200 DATA REDUNDANCY : 1.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.34 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.37 REMARK 200 COMPLETENESS FOR SHELL (%) : 78.3 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 (%): 50.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.47 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 40.68800 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.04700 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 40.68800 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 19.04700 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: -25.0 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 OE2 GLU A 175 O HOH A 301 2.01 REMARK 500 O HOH A 375 O HOH A 430 2.09 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 301 O HOH A 301 2656 1.61 REMARK 500 O HOH A 412 O HOH A 412 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 -0.134 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. = 2.0 DEGREES REMARK 500 DG C 5 O4' - C1' - N9 ANGL. DEV. = 2.0 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 456 DISTANCE = 6.33 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 104.2 REMARK 620 3 HOH A 302 O 173.1 79.1 REMARK 620 4 HOH A 306 O 86.5 89.8 87.5 REMARK 620 5 HOH A 318 O 89.3 86.9 97.0 173.8 REMARK 620 6 C b 5 OP3 158.8 96.8 18.1 90.6 94.9 REMARK 620 7 C b 5 OP1 95.1 159.9 82.5 97.1 87.8 64.4 REMARK 620 8 C b 5 OP1 95.7 158.8 82.0 98.8 86.2 63.9 1.7 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 99.0 REMARK 620 3 ASP A 132 OD1 130.0 98.0 REMARK 620 4 ASP A 132 OD2 101.6 150.5 52.5 REMARK 620 5 U B 4 O3' 151.2 87.4 76.0 84.6 REMARK 620 6 C b 5 OP1 91.1 109.3 126.2 91.2 60.5 REMARK 620 7 C b 5 OP1 89.6 113.0 125.3 88.1 62.3 3.8 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 364 O 54.5 REMARK 620 3 HOH B 212 O 156.0 115.3 REMARK 620 4 C b 5 OP2 85.1 131.3 112.0 REMARK 620 N 1 2 3 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 41.0 REMARK 620 3 HOH A 302 O 51.5 83.3 REMARK 620 4 HOH A 306 O 55.1 94.3 52.0 REMARK 620 5 HOH A 323 O 80.5 52.6 85.6 131.0 REMARK 620 6 G b 6 OP2 100.3 140.7 60.7 52.1 131.4 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 A 423 O REMARK 620 2 DT C 4 O4 99.0 REMARK 620 3 DG C 5 O6 158.9 74.1 REMARK 620 4 HOH C 215 O 77.4 85.8 82.2 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 EDO A 208 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 209 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 210 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO 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 GOL A 215 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PGE A 216 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K A 217 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K C 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL C 102 DBREF 6DOB A 59 196 UNP Q9KEI9 RNH1_BACHD 59 196 DBREF 6DOB B 1 4 PDB 6DOB 6DOB 1 4 DBREF 6DOB b 5 6 PDB 6DOB 6DOB 5 6 DBREF 6DOB C 1 6 PDB 6DOB 6DOB 1 6 SEQADV 6DOB GLY A 55 UNP Q9KEI9 EXPRESSION TAG SEQADV 6DOB SER A 56 UNP Q9KEI9 EXPRESSION TAG SEQADV 6DOB HIS A 57 UNP Q9KEI9 EXPRESSION TAG SEQADV 6DOB 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 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'C U B 4 P C C b 5 1555 1555 1.58 LINK OD2 ASP A 71 MG MG A 201 1555 1555 2.02 LINK OD1 ASP A 71 MG MG A 202 1555 1555 1.97 LINK OE1 GLU A 109 MG MG A 202 1555 1555 2.03 LINK OD1 ASP A 132 MG MG A 202 1555 1555 2.13 LINK OD2 ASP A 132 MG MG A 202 1555 1555 2.66 LINK OD2 ASP A 132 K B K A 217 1555 1555 3.31 LINK OD1 ASP A 192 MG MG A 201 1555 1555 2.02 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 3.28 LINK MG MG A 201 O CHOH A 302 1555 1555 2.02 LINK MG MG A 201 O HOH A 306 1555 1555 2.04 LINK MG MG A 201 O HOH A 318 1555 1555 2.04 LINK MG MG A 201 OP3B C b 5 1555 1555 2.02 LINK MG MG A 201 OP1B C b 5 1555 1555 2.40 LINK MG MG A 201 OP1C C b 5 1555 1555 2.27 LINK MG MG A 202 O3'C U B 4 1555 1555 2.63 LINK MG MG A 202 OP1B C b 5 1555 1555 2.08 LINK MG MG A 202 OP1C C b 5 1555 1555 2.14 LINK K C K A 203 O CHOH A 302 1555 1555 3.08 LINK K C K A 203 O HOH A 306 1555 1555 3.31 LINK K C K A 203 O HOH A 323 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 364 1555 1555 3.32 LINK K B K A 217 O HOH B 212 1555 1555 2.60 LINK K B K A 217 OP2B C b 5 1555 1555 2.55 LINK O HOH A 423 K A K C 101 4555 1555 3.31 LINK O4 DT C 4 K A K C 101 1555 1555 3.25 LINK O6 DG C 5 K A K C 101 1555 1555 2.62 LINK K A K C 101 O HOH C 215 1555 1555 3.21 CISPEP 1 ASN A 77 PRO A 78 0 -0.25 SITE 1 AC1 6 ASP A 71 ASP A 192 HOH A 302 HOH A 306 SITE 2 AC1 6 HOH A 318 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 302 HOH A 323 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 456 SITE 1 AC7 4 LYS A 143 THR A 173 TYR A 174 HOH A 319 SITE 1 AC8 5 THR A 148 HOH A 313 DT C 4 DG C 5 SITE 2 AC8 5 HOH C 212 SITE 1 AC9 3 ILE A 80 PRO A 99 HOH A 357 SITE 1 AD1 6 TRP A 65 GLU A 66 SER A 67 ASP A 87 SITE 2 AD1 6 LYS A 127 GOL A 215 SITE 1 AD2 5 HIS A 115 ARG A 118 ASN A 170 GOL A 213 SITE 2 AD2 5 HOH A 307 SITE 1 AD3 9 HIS A 115 TYR A 119 GLU A 122 ARG A 123 SITE 2 AD3 9 GLU A 167 ASN A 170 GOL A 212 HOH A 360 SITE 3 AD3 9 HOH A 386 SITE 1 AD4 6 ILE A 102 VAL A 150 ASN A 152 GLU A 154 SITE 2 AD4 6 HOH A 379 HOH C 208 SITE 1 AD5 6 GLU A 66 SER A 125 LYS A 127 EDO A 211 SITE 2 AD5 6 HOH A 358 HOH A 408 SITE 1 AD6 9 GLN A 134 LYS A 180 GLN A 182 THR A 183 SITE 2 AD6 9 ASP A 184 IOD A 205 A B 3 U B 4 SITE 3 AD6 9 HOH B 202 SITE 1 AD7 6 ASP A 132 GLU A 188 HOH A 310 U B 4 SITE 2 AD7 6 HOH B 212 C b 5 SITE 1 AD8 3 DT C 4 DG C 5 HOH C 214 SITE 1 AD9 8 GLY A 76 ASN A 77 PRO A 78 HOH B 209 SITE 2 AD9 8 DG C 2 DA C 3 HOH C 204 HOH C 216 CRYST1 81.376 38.094 62.117 90.00 96.16 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 0.012289 0.000000 0.001326 0.00000 SCALE2 0.000000 0.026251 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016192 0.00000