HEADER HYDROLASE/DNA/RNA 09-JUN-18 6DOE 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 420 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 (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; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; 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, DOUBLE HELIX, RNA HYDROLYSIS, IN CRYSTALLO KEYWDS 2 CATALYSIS, METAL DEPENDENT CATALYSIS, MONOVALENT CATIONS, DIVALENT KEYWDS 3 CATIONS, HYDROLASE, HYDROLASE-DNA-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR N.L.SAMARA,W.YANG REVDAT 2 11-OCT-23 6DOE 1 LINK REVDAT 1 15-AUG-18 6DOE 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) : 31.01 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 3 NUMBER OF REFLECTIONS : 33083 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.172 REMARK 3 R VALUE (WORKING SET) : 0.170 REMARK 3 FREE R VALUE : 0.198 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.870 REMARK 3 FREE R VALUE TEST SET COUNT : 1610 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 31.0206 - 3.2258 0.96 2911 154 0.1375 0.1637 REMARK 3 2 3.2258 - 2.5608 0.99 2960 151 0.1612 0.1934 REMARK 3 3 2.5608 - 2.2372 0.99 2859 170 0.1734 0.2008 REMARK 3 4 2.2372 - 2.0327 0.99 2945 121 0.1701 0.2035 REMARK 3 5 2.0327 - 1.8870 0.99 2879 146 0.1939 0.1986 REMARK 3 6 1.8870 - 1.7758 1.00 2943 137 0.1834 0.2066 REMARK 3 7 1.7758 - 1.6868 0.99 2880 161 0.1849 0.2071 REMARK 3 8 1.6868 - 1.6134 0.99 2885 133 0.2026 0.2708 REMARK 3 9 1.6134 - 1.5513 0.98 2842 158 0.2153 0.2453 REMARK 3 10 1.5513 - 1.4978 0.95 2775 145 0.2539 0.3226 REMARK 3 11 1.4978 - 1.4509 0.90 2594 134 0.2662 0.2848 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) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.530 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.88 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.22 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 : 1.154 2062 REMARK 3 CHIRALITY : 0.082 225 REMARK 3 PLANARITY : 0.007 213 REMARK 3 DIHEDRAL : 23.766 593 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 THROUGH 87 ) REMARK 3 ORIGIN FOR THE GROUP (A): 25.5488 -5.5812 17.5305 REMARK 3 T TENSOR REMARK 3 T11: 0.1350 T22: 0.0633 REMARK 3 T33: 0.1221 T12: 0.0213 REMARK 3 T13: 0.0167 T23: 0.0045 REMARK 3 L TENSOR REMARK 3 L11: 6.1963 L22: 1.5580 REMARK 3 L33: 3.2835 L12: -1.3334 REMARK 3 L13: 1.6574 L23: -0.2158 REMARK 3 S TENSOR REMARK 3 S11: 0.3223 S12: 0.2487 S13: -0.2267 REMARK 3 S21: -0.1601 S22: -0.1825 S23: -0.0952 REMARK 3 S31: 0.3658 S32: 0.1406 S33: -0.0750 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 88 THROUGH 96 ) REMARK 3 ORIGIN FOR THE GROUP (A): 28.2585 -11.5403 24.1103 REMARK 3 T TENSOR REMARK 3 T11: 0.1868 T22: 0.1238 REMARK 3 T33: 0.2670 T12: 0.0565 REMARK 3 T13: -0.0029 T23: 0.0181 REMARK 3 L TENSOR REMARK 3 L11: 6.6022 L22: 5.7302 REMARK 3 L33: 6.7700 L12: -1.8909 REMARK 3 L13: -5.4198 L23: 0.4834 REMARK 3 S TENSOR REMARK 3 S11: -0.1850 S12: -0.2743 S13: -1.3679 REMARK 3 S21: 0.0498 S22: 0.1296 S23: -0.3367 REMARK 3 S31: 0.7332 S32: 0.2984 S33: 0.2078 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 97 THROUGH 133 ) REMARK 3 ORIGIN FOR THE GROUP (A): 21.6654 -1.2221 23.5477 REMARK 3 T TENSOR REMARK 3 T11: 0.0925 T22: 0.0641 REMARK 3 T33: 0.1006 T12: 0.0092 REMARK 3 T13: 0.0174 T23: 0.0031 REMARK 3 L TENSOR REMARK 3 L11: 3.6431 L22: 0.9495 REMARK 3 L33: 3.0579 L12: -0.1238 REMARK 3 L13: 1.4802 L23: 0.3832 REMARK 3 S TENSOR REMARK 3 S11: 0.0840 S12: -0.2257 S13: -0.0988 REMARK 3 S21: -0.0273 S22: -0.0864 S23: 0.0377 REMARK 3 S31: 0.0578 S32: -0.3047 S33: 0.0023 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 134 THROUGH 142 ) REMARK 3 ORIGIN FOR THE GROUP (A): 23.7408 9.4141 16.7375 REMARK 3 T TENSOR REMARK 3 T11: 0.2618 T22: 0.0786 REMARK 3 T33: 0.1785 T12: 0.0012 REMARK 3 T13: 0.0532 T23: 0.0333 REMARK 3 L TENSOR REMARK 3 L11: 3.2209 L22: 5.3022 REMARK 3 L33: 5.8227 L12: -2.8792 REMARK 3 L13: -0.2386 L23: -0.2987 REMARK 3 S TENSOR REMARK 3 S11: 0.2643 S12: 0.0620 S13: 0.5775 REMARK 3 S21: -0.0510 S22: -0.0396 S23: -0.1924 REMARK 3 S31: -1.1063 S32: 0.0128 S33: -0.0707 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 143 THROUGH 155 ) REMARK 3 ORIGIN FOR THE GROUP (A): 8.3368 7.2477 16.3566 REMARK 3 T TENSOR REMARK 3 T11: 0.2519 T22: 0.4019 REMARK 3 T33: 0.1907 T12: 0.2174 REMARK 3 T13: -0.0298 T23: -0.0951 REMARK 3 L TENSOR REMARK 3 L11: 7.6710 L22: 1.7404 REMARK 3 L33: 2.9284 L12: 0.2979 REMARK 3 L13: 2.4242 L23: -0.6101 REMARK 3 S TENSOR REMARK 3 S11: 0.3996 S12: 0.1613 S13: 0.6256 REMARK 3 S21: -0.2364 S22: -0.4526 S23: 0.5033 REMARK 3 S31: -0.5873 S32: -0.8034 S33: 0.0928 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 156 THROUGH 169 ) REMARK 3 ORIGIN FOR THE GROUP (A): 12.3061 5.6045 25.0397 REMARK 3 T TENSOR REMARK 3 T11: 0.1375 T22: 0.2149 REMARK 3 T33: 0.1421 T12: 0.0652 REMARK 3 T13: 0.0154 T23: -0.0405 REMARK 3 L TENSOR REMARK 3 L11: 3.5195 L22: 2.5463 REMARK 3 L33: 8.3630 L12: 1.2279 REMARK 3 L13: 5.3668 L23: 2.1763 REMARK 3 S TENSOR REMARK 3 S11: 0.1208 S12: -0.3317 S13: 0.1333 REMARK 3 S21: -0.0530 S22: -0.2984 S23: 0.2263 REMARK 3 S31: -0.1515 S32: -0.8644 S33: 0.1762 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 170 THROUGH 196 ) REMARK 3 ORIGIN FOR THE GROUP (A): 28.8942 -0.7694 17.9066 REMARK 3 T TENSOR REMARK 3 T11: 0.1134 T22: 0.1019 REMARK 3 T33: 0.0918 T12: 0.0323 REMARK 3 T13: 0.0077 T23: 0.0230 REMARK 3 L TENSOR REMARK 3 L11: 3.1228 L22: 2.8342 REMARK 3 L33: 4.8747 L12: -0.4895 REMARK 3 L13: -0.7934 L23: 1.2318 REMARK 3 S TENSOR REMARK 3 S11: 0.0413 S12: 0.3025 S13: -0.1153 REMARK 3 S21: -0.3009 S22: -0.0292 S23: -0.1287 REMARK 3 S31: 0.0605 S32: 0.1793 S33: -0.0667 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1 THROUGH 6 ) REMARK 3 ORIGIN FOR THE GROUP (A): 23.6592 0.8151 5.2474 REMARK 3 T TENSOR REMARK 3 T11: 0.3143 T22: 0.2287 REMARK 3 T33: 0.1375 T12: 0.0496 REMARK 3 T13: 0.0137 T23: 0.0165 REMARK 3 L TENSOR REMARK 3 L11: 3.1149 L22: 6.9301 REMARK 3 L33: 0.5906 L12: 0.8397 REMARK 3 L13: 1.1772 L23: -0.4770 REMARK 3 S TENSOR REMARK 3 S11: -0.1258 S12: 0.0835 S13: -0.1666 REMARK 3 S21: -0.7453 S22: -0.1602 S23: -0.2133 REMARK 3 S31: 0.1579 S32: 0.0613 S33: 0.2847 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 1 THROUGH 6 ) REMARK 3 ORIGIN FOR THE GROUP (A): 16.3348 3.5102 3.3516 REMARK 3 T TENSOR REMARK 3 T11: 0.4115 T22: 0.2154 REMARK 3 T33: 0.1486 T12: 0.0825 REMARK 3 T13: -0.0428 T23: 0.0053 REMARK 3 L TENSOR REMARK 3 L11: 2.7957 L22: 2.7908 REMARK 3 L33: 3.3216 L12: -1.1744 REMARK 3 L13: -2.6324 L23: 1.4644 REMARK 3 S TENSOR REMARK 3 S11: -0.1247 S12: 0.3026 S13: -0.1302 REMARK 3 S21: -0.8684 S22: -0.2748 S23: 0.1638 REMARK 3 S31: -0.2958 S32: -0.1970 S33: 0.4422 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 6DOE 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_1000234966. 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 : 40377 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.360 REMARK 200 RESOLUTION RANGE LOW (A) : 31.020 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 200 DATA REDUNDANCY : 1.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.36 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 82.9 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: NULL REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: PDBID 1ZBL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.39 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.48 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 14% PEG3350, 20% GLYCEROL, 200 MM KI, REMARK 280 AND 25 MM CACL2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 40.80600 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.01800 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 40.80600 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 19.01800 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: 6960 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7490 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -28.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, b, C REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 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 1.27 REMARK 500 O HOH A 357 O HOH A 441 1.95 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 302 O HOH A 302 2656 1.60 REMARK 500 O HOH A 387 O HOH A 387 2656 1.89 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 -0.124 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 U B 4 O5' - P - OP2 ANGL. DEV. = -5.5 DEGREES REMARK 500 DG C 2 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 DG C 5 O4' - C1' - N9 ANGL. DEV. = 2.5 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 458 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 104.4 REMARK 620 3 HOH A 301 O 172.8 78.7 REMARK 620 4 HOH A 306 O 87.9 88.5 85.7 REMARK 620 5 HOH A 310 O 88.4 89.5 98.2 175.2 REMARK 620 6 C b 5 OP3 160.1 95.4 17.5 91.2 93.4 REMARK 620 7 C b 5 OP1 93.7 161.8 83.1 91.2 92.0 66.4 REMARK 620 8 C b 5 OP1 97.2 157.4 80.5 98.6 84.8 63.2 8.1 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 96.6 REMARK 620 3 ASP A 132 OD1 124.4 101.9 REMARK 620 4 ASP A 132 OD2 99.7 151.4 49.5 REMARK 620 5 U B 4 O3' 152.3 89.9 80.0 86.5 REMARK 620 6 C b 5 OP1 88.3 108.6 131.8 95.3 64.1 REMARK 620 7 C b 5 OP1 91.3 117.1 123.4 86.0 62.0 9.4 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 348 O 51.8 REMARK 620 3 HOH B 211 O 156.1 114.2 REMARK 620 4 C b 5 OP2 83.3 126.7 117.1 REMARK 620 5 HOH b 102 O 138.8 166.9 58.8 58.3 REMARK 620 N 1 2 3 4 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 40.0 REMARK 620 3 HOH A 301 O 52.2 83.1 REMARK 620 4 HOH A 306 O 55.5 94.0 51.3 REMARK 620 5 HOH A 331 O 78.8 50.8 85.8 129.7 REMARK 620 6 G b 6 OP2 99.8 139.5 60.7 50.0 134.4 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 429 O REMARK 620 2 DT C 4 O4 96.1 REMARK 620 3 DG C 5 O6 162.8 75.1 REMARK 620 4 HOH C 212 O 84.9 85.8 79.8 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 6DOE A 61 196 UNP Q9KEI9 RNH1_BACHD 61 196 DBREF 6DOE B 1 4 PDB 6DOE 6DOE 1 4 DBREF 6DOE b 5 6 PDB 6DOE 6DOE 5 6 DBREF 6DOE C 1 6 PDB 6DOE 6DOE 1 6 SEQRES 1 A 136 GLU GLU ILE ILE TRP GLU SER LEU SER VAL ASP VAL GLY SEQRES 2 A 136 SER GLN GLY ASN PRO GLY ILE VAL GLU TYR LYS GLY VAL SEQRES 3 A 136 ASP THR LYS THR GLY GLU VAL LEU PHE GLU ARG GLU PRO SEQRES 4 A 136 ILE PRO ILE GLY THR ASN ASN MET GLY GLU PHE LEU ALA SEQRES 5 A 136 ILE VAL HIS GLY LEU ARG TYR LEU LYS GLU ARG ASN SER SEQRES 6 A 136 ARG LYS PRO ILE TYR SER ASP SER GLN THR ALA ILE LYS SEQRES 7 A 136 TRP VAL LYS ASP LYS LYS ALA LYS SER THR LEU VAL ARG SEQRES 8 A 136 ASN GLU GLU THR ALA LEU ILE TRP LYS LEU VAL ASP GLU SEQRES 9 A 136 ALA GLU GLU TRP LEU ASN THR HIS THR TYR GLU THR PRO SEQRES 10 A 136 ILE LEU LYS TRP GLN THR ASP LYS TRP GLY GLU ILE LYS SEQRES 11 A 136 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 2.01 LINK OD1 ASP A 71 MG MG A 202 1555 1555 2.01 LINK OE1 GLU A 109 MG MG A 202 1555 1555 2.02 LINK OD1 ASP A 132 MG MG A 202 1555 1555 2.13 LINK OD2 ASP A 132 MG MG A 202 1555 1555 2.84 LINK OD2 ASP A 132 K B K A 217 1555 1555 3.30 LINK OD1 ASP A 192 MG MG A 201 1555 1555 2.09 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 3.37 LINK MG MG A 201 O CHOH A 301 1555 1555 2.02 LINK MG MG A 201 O HOH A 306 1555 1555 2.10 LINK MG MG A 201 O HOH A 310 1555 1555 2.09 LINK MG MG A 201 OP3B C b 5 1555 1555 2.01 LINK MG MG A 201 OP1B C b 5 1555 1555 2.39 LINK MG MG A 201 OP1C C b 5 1555 1555 2.26 LINK MG MG A 202 O3'C U B 4 1555 1555 2.62 LINK MG MG A 202 OP1B C b 5 1555 1555 2.08 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 3.08 LINK K C K A 203 O HOH A 306 1555 1555 3.37 LINK K C K A 203 O HOH A 331 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 348 1555 1555 3.46 LINK K B K A 217 O HOH B 211 1555 1555 2.60 LINK K B K A 217 OP2B C b 5 1555 1555 2.57 LINK K B K A 217 O HOH b 102 1555 1555 3.41 LINK O HOH A 429 K A K C 101 4555 1555 3.23 LINK O4 DT C 4 K A K C 101 1555 1555 3.18 LINK O6 DG C 5 K A K C 101 1555 1555 2.69 LINK K A K C 101 O HOH C 212 1555 1555 3.39 CISPEP 1 ASN A 77 PRO A 78 0 -1.51 SITE 1 AC1 6 ASP A 71 ASP A 192 HOH A 301 HOH A 306 SITE 2 AC1 6 HOH A 310 C b 5 SITE 1 AC2 5 ASP A 71 GLU A 109 ASP A 132 U B 4 SITE 2 AC2 5 C b 5 SITE 1 AC3 8 ASP A 192 GLY A 194 ARG A 195 LYS A 196 SITE 2 AC3 8 HOH A 301 HOH A 331 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 423 HOH A 458 SITE 1 AC7 5 LYS A 143 THR A 173 TYR A 174 HOH A 308 SITE 2 AC7 5 HOH A 402 SITE 1 AC8 5 THR A 148 HOH A 324 HOH A 355 DT C 4 SITE 2 AC8 5 DG C 5 SITE 1 AC9 3 ILE A 80 PRO A 99 HOH A 349 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 6 HIS A 115 ARG A 118 ASN A 170 GOL A 213 SITE 2 AD2 6 HOH A 315 HOH A 376 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 379 SITE 3 AD3 9 HOH A 396 SITE 1 AD4 6 ILE A 102 VAL A 150 ASN A 152 GLU A 154 SITE 2 AD4 6 HOH A 325 HOH C 206 SITE 1 AD5 5 GLU A 66 SER A 125 LYS A 127 EDO A 211 SITE 2 AD5 5 HOH A 335 SITE 1 AD6 10 GLN A 134 LYS A 180 TRP A 181 GLN A 182 SITE 2 AD6 10 THR A 183 ASP A 184 IOD A 205 A B 3 SITE 3 AD6 10 U B 4 HOH B 203 SITE 1 AD7 5 ASP A 132 U B 4 HOH B 211 C b 5 SITE 2 AD7 5 HOH b 103 SITE 1 AD8 3 DT C 4 DG C 5 HOH C 207 SITE 1 AD9 6 ASN A 77 HOH A 313 HOH B 209 DG C 2 SITE 2 AD9 6 DA C 3 HOH C 213 CRYST1 81.612 38.036 62.403 90.00 96.29 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 0.012253 0.000000 0.001351 0.00000 SCALE2 0.000000 0.026291 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016122 0.00000