HEADER HYDROLASE/RNA/DNA 09-JUN-18 6DOG 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 600 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, HYDROLASE-RNA-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR N.L.SAMARA,W.YANG REVDAT 2 11-OCT-23 6DOG 1 LINK REVDAT 1 15-AUG-18 6DOG 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. 1.29 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) : 1.29 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.27 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 3 NUMBER OF REFLECTIONS : 47261 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.162 REMARK 3 R VALUE (WORKING SET) : 0.161 REMARK 3 FREE R VALUE : 0.183 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.850 REMARK 3 FREE R VALUE TEST SET COUNT : 2290 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 20.2762 - 3.2334 0.92 2751 145 0.1446 0.1751 REMARK 3 2 3.2334 - 2.5681 0.99 2890 147 0.1543 0.1688 REMARK 3 3 2.5681 - 2.2439 0.99 2856 165 0.1551 0.1847 REMARK 3 4 2.2439 - 2.0390 1.00 2903 119 0.1500 0.1833 REMARK 3 5 2.0390 - 1.8929 1.00 2877 144 0.1569 0.1677 REMARK 3 6 1.8929 - 1.7814 1.00 2850 139 0.1571 0.1667 REMARK 3 7 1.7814 - 1.6922 0.99 2870 152 0.1512 0.1746 REMARK 3 8 1.6922 - 1.6186 1.00 2866 136 0.1559 0.1630 REMARK 3 9 1.6186 - 1.5563 1.00 2839 160 0.1608 0.1621 REMARK 3 10 1.5563 - 1.5026 1.00 2872 156 0.1747 0.1989 REMARK 3 11 1.5026 - 1.4557 1.00 2808 149 0.1901 0.2155 REMARK 3 12 1.4557 - 1.4141 1.00 2883 156 0.2144 0.2220 REMARK 3 13 1.4141 - 1.3768 1.00 2852 162 0.2321 0.2809 REMARK 3 14 1.3768 - 1.3433 1.00 2863 133 0.2395 0.2920 REMARK 3 15 1.3433 - 1.3127 0.99 2838 120 0.2630 0.2729 REMARK 3 16 1.3127 - 1.2848 0.76 2153 107 0.2942 0.2802 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) : 0.120 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.260 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.26 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.43 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 1514 REMARK 3 ANGLE : 1.104 2062 REMARK 3 CHIRALITY : 0.078 225 REMARK 3 PLANARITY : 0.007 213 REMARK 3 DIHEDRAL : 24.069 593 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): 25.549 -5.591 17.451 REMARK 3 T TENSOR REMARK 3 T11: 0.1503 T22: 0.0860 REMARK 3 T33: 0.1227 T12: 0.0210 REMARK 3 T13: 0.0196 T23: 0.0122 REMARK 3 L TENSOR REMARK 3 L11: 5.8451 L22: 1.6410 REMARK 3 L33: 3.5243 L12: -1.6086 REMARK 3 L13: 1.5370 L23: -0.3729 REMARK 3 S TENSOR REMARK 3 S11: 0.2319 S12: 0.1702 S13: -0.2038 REMARK 3 S21: -0.1618 S22: -0.1513 S23: -0.0769 REMARK 3 S31: 0.3482 S32: 0.1712 S33: -0.0735 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: ( CHAIN A AND RESID 88:96 ) REMARK 3 ORIGIN FOR THE GROUP (A): 28.186 -11.579 24.053 REMARK 3 T TENSOR REMARK 3 T11: 0.2175 T22: 0.1581 REMARK 3 T33: 0.2840 T12: 0.0638 REMARK 3 T13: 0.0110 T23: 0.0585 REMARK 3 L TENSOR REMARK 3 L11: 3.8351 L22: 4.0694 REMARK 3 L33: 5.7064 L12: -1.0303 REMARK 3 L13: -3.0648 L23: 1.3857 REMARK 3 S TENSOR REMARK 3 S11: -0.0362 S12: -0.3282 S13: -1.0557 REMARK 3 S21: 0.1169 S22: -0.0040 S23: -0.4732 REMARK 3 S31: 0.7826 S32: 0.3773 S33: 0.0488 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: ( CHAIN A AND RESID 97:133 ) REMARK 3 ORIGIN FOR THE GROUP (A): 21.716 -1.218 23.441 REMARK 3 T TENSOR REMARK 3 T11: 0.0870 T22: 0.0780 REMARK 3 T33: 0.0875 T12: 0.0129 REMARK 3 T13: 0.0203 T23: 0.0055 REMARK 3 L TENSOR REMARK 3 L11: 3.2929 L22: 0.9637 REMARK 3 L33: 3.0323 L12: -0.0118 REMARK 3 L13: 1.4592 L23: 0.2560 REMARK 3 S TENSOR REMARK 3 S11: 0.0771 S12: -0.2100 S13: -0.0808 REMARK 3 S21: -0.0362 S22: -0.0956 S23: 0.0275 REMARK 3 S31: 0.0575 S32: -0.2358 S33: 0.0111 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: ( CHAIN A AND RESID 134:142 ) REMARK 3 ORIGIN FOR THE GROUP (A): 23.877 9.389 16.644 REMARK 3 T TENSOR REMARK 3 T11: 0.2414 T22: 0.0938 REMARK 3 T33: 0.1629 T12: 0.0092 REMARK 3 T13: 0.0371 T23: 0.0303 REMARK 3 L TENSOR REMARK 3 L11: 3.8599 L22: 6.0415 REMARK 3 L33: 6.7919 L12: -3.1762 REMARK 3 L13: 0.0558 L23: -0.4703 REMARK 3 S TENSOR REMARK 3 S11: 0.2196 S12: 0.1721 S13: 0.4261 REMARK 3 S21: -0.2675 S22: -0.2013 S23: -0.2849 REMARK 3 S31: -0.8356 S32: 0.0974 S33: -0.0287 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: ( CHAIN A AND RESID 143:155 ) REMARK 3 ORIGIN FOR THE GROUP (A): 8.521 7.452 16.160 REMARK 3 T TENSOR REMARK 3 T11: 0.2927 T22: 0.4132 REMARK 3 T33: 0.2136 T12: 0.3270 REMARK 3 T13: -0.0280 T23: -0.1277 REMARK 3 L TENSOR REMARK 3 L11: 4.6311 L22: 2.5284 REMARK 3 L33: 2.3722 L12: 0.4226 REMARK 3 L13: 2.0731 L23: 0.1801 REMARK 3 S TENSOR REMARK 3 S11: 0.2206 S12: -0.0392 S13: 0.3719 REMARK 3 S21: -0.0930 S22: -0.3367 S23: 0.3907 REMARK 3 S31: -0.4576 S32: -0.8718 S33: 0.2299 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: ( CHAIN A AND RESID 156:169 ) REMARK 3 ORIGIN FOR THE GROUP (A): 12.445 5.745 24.903 REMARK 3 T TENSOR REMARK 3 T11: 0.1345 T22: 0.2208 REMARK 3 T33: 0.1304 T12: 0.0689 REMARK 3 T13: 0.0271 T23: -0.0367 REMARK 3 L TENSOR REMARK 3 L11: 7.3427 L22: 1.8557 REMARK 3 L33: 5.7527 L12: 0.8670 REMARK 3 L13: 5.8639 L23: 1.6539 REMARK 3 S TENSOR REMARK 3 S11: 0.1756 S12: -0.2428 S13: 0.0715 REMARK 3 S21: 0.0198 S22: -0.2866 S23: 0.1766 REMARK 3 S31: -0.1151 S32: -0.6524 S33: 0.0971 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: ( CHAIN A AND RESID 170:196 ) REMARK 3 ORIGIN FOR THE GROUP (A): 28.952 -0.835 17.830 REMARK 3 T TENSOR REMARK 3 T11: 0.1259 T22: 0.1160 REMARK 3 T33: 0.0839 T12: 0.0530 REMARK 3 T13: 0.0056 T23: 0.0362 REMARK 3 L TENSOR REMARK 3 L11: 3.0567 L22: 2.7897 REMARK 3 L33: 5.0413 L12: -0.3438 REMARK 3 L13: -0.9859 L23: 1.1919 REMARK 3 S TENSOR REMARK 3 S11: 0.0889 S12: 0.2478 S13: -0.1197 REMARK 3 S21: -0.3956 S22: -0.0437 S23: -0.1870 REMARK 3 S31: 0.0412 S32: 0.2337 S33: -0.0952 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): 23.776 0.746 5.147 REMARK 3 T TENSOR REMARK 3 T11: 0.3143 T22: 0.2274 REMARK 3 T33: 0.1306 T12: 0.0752 REMARK 3 T13: 0.0391 T23: 0.0143 REMARK 3 L TENSOR REMARK 3 L11: 2.8145 L22: 6.5024 REMARK 3 L33: 1.1453 L12: 0.2234 REMARK 3 L13: 1.4625 L23: -1.2101 REMARK 3 S TENSOR REMARK 3 S11: -0.1414 S12: 0.1383 S13: -0.1621 REMARK 3 S21: -0.6881 S22: -0.1851 S23: -0.2272 REMARK 3 S31: 0.1528 S32: 0.1231 S33: 0.3440 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: ( CHAIN C AND RESID 1:6 ) REMARK 3 ORIGIN FOR THE GROUP (A): 16.453 3.435 3.284 REMARK 3 T TENSOR REMARK 3 T11: 0.3998 T22: 0.2010 REMARK 3 T33: 0.1498 T12: 0.0840 REMARK 3 T13: -0.0359 T23: -0.0084 REMARK 3 L TENSOR REMARK 3 L11: 3.0505 L22: 2.8056 REMARK 3 L33: 3.9317 L12: -1.1167 REMARK 3 L13: -2.8641 L23: 0.6852 REMARK 3 S TENSOR REMARK 3 S11: -0.1401 S12: 0.4189 S13: -0.2119 REMARK 3 S21: -0.9042 S22: -0.2831 S23: 0.2753 REMARK 3 S31: -0.3482 S32: -0.3209 S33: 0.3670 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 6DOG 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_1000234970. 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 : 47264 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.280 REMARK 200 RESOLUTION RANGE LOW (A) : 20.270 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 : 7.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.28 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.31 REMARK 200 COMPLETENESS FOR SHELL (%) : 69.8 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 (%): 50.05 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.46 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 40.78700 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.94450 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 40.78700 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 18.94450 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: 6980 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7470 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 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 2.07 REMARK 500 O2 DC C 1 O HOH C 201 2.17 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 1.74 REMARK 500 O HOH A 395 O HOH A 395 2656 1.84 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 -0.135 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 5 O4' - C1' - N9 ANGL. DEV. = 1.9 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 = 6.16 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 106.6 REMARK 620 3 HOH A 302 O 174.1 76.6 REMARK 620 4 HOH A 310 O 90.1 90.5 84.9 REMARK 620 5 HOH A 323 O 88.1 87.7 97.0 177.0 REMARK 620 6 C b 5 OP3 159.5 93.9 18.2 90.4 92.1 REMARK 620 7 C b 5 OP1 95.9 156.7 81.5 95.8 86.8 63.7 REMARK 620 8 C b 5 OP1 98.4 152.9 79.4 99.9 82.7 61.3 4.9 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 96.9 REMARK 620 3 ASP A 132 OD1 128.9 96.5 REMARK 620 4 ASP A 132 OD2 102.3 149.0 52.5 REMARK 620 5 U B 4 O3' 153.1 90.3 75.4 83.5 REMARK 620 6 C b 5 OP1 90.9 109.7 129.4 94.3 62.3 REMARK 620 7 C b 5 OP1 91.6 115.6 125.3 88.2 62.1 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 217 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 132 OD2 REMARK 620 2 HOH A 323 O 46.2 REMARK 620 3 HOH A 368 O 53.7 60.0 REMARK 620 4 HOH B 208 O 154.2 156.0 116.8 REMARK 620 5 C b 5 OP2 85.5 71.8 130.5 111.7 REMARK 620 6 HOH b 101 O 136.4 120.2 167.9 57.5 54.3 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 40.9 REMARK 620 3 HOH A 302 O 50.4 83.9 REMARK 620 4 HOH A 310 O 56.6 95.1 51.4 REMARK 620 5 HOH A 328 O 78.5 52.4 85.6 130.7 REMARK 620 6 G b 6 OP2 100.3 141.0 60.8 50.8 132.2 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 428 O REMARK 620 2 DT C 4 O4 96.7 REMARK 620 3 DG C 5 O6 165.6 75.7 REMARK 620 4 HOH C 210 O 81.5 85.5 85.7 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 6DOG A 59 196 UNP Q9KEI9 RNH1_BACHD 59 196 DBREF 6DOG B 1 4 PDB 6DOG 6DOG 1 4 DBREF 6DOG b 5 6 PDB 6DOG 6DOG 5 6 DBREF 6DOG C 1 6 PDB 6DOG 6DOG 1 6 SEQADV 6DOG GLY A 55 UNP Q9KEI9 EXPRESSION TAG SEQADV 6DOG SER A 56 UNP Q9KEI9 EXPRESSION TAG SEQADV 6DOG HIS A 57 UNP Q9KEI9 EXPRESSION TAG SEQADV 6DOG 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 1.59 LINK OD2 ASP A 71 MG MG A 201 1555 1555 1.96 LINK OD1 ASP A 71 MG MG A 202 1555 1555 1.99 LINK OE1 GLU A 109 MG MG A 202 1555 1555 2.03 LINK OD1 ASP A 132 MG MG A 202 1555 1555 2.15 LINK OD2 ASP A 132 MG MG A 202 1555 1555 2.65 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 2.04 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 3.30 LINK MG MG A 201 O CHOH A 302 1555 1555 2.02 LINK MG MG A 201 O HOH A 310 1555 1555 2.07 LINK MG MG A 201 O HOH A 323 1555 1555 2.09 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 2.26 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 2.05 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 310 1555 1555 3.28 LINK K C K A 203 O HOH A 328 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 323 1555 1555 3.49 LINK K B K A 217 O HOH A 368 1555 1555 3.37 LINK K B K A 217 O HOH B 208 1555 1555 2.60 LINK K B K A 217 OP2B C b 5 1555 1555 2.55 LINK K B K A 217 O HOH b 101 1555 1555 3.49 LINK O HOH A 428 K A K C 101 4555 1555 3.34 LINK O4 DT C 4 K A K C 101 1555 1555 3.20 LINK O6 DG C 5 K A K C 101 1555 1555 2.59 LINK K A K C 101 O HOH C 210 1555 1555 3.15 CISPEP 1 ASN A 77 PRO A 78 0 -1.20 SITE 1 AC1 6 ASP A 71 ASP A 192 HOH A 302 HOH A 310 SITE 2 AC1 6 HOH A 323 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 328 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 425 HOH A 458 SITE 1 AC7 4 LYS A 143 THR A 173 TYR A 174 HOH A 309 SITE 1 AC8 5 THR A 148 HOH A 314 DT C 4 DG C 5 SITE 2 AC8 5 HOH C 205 SITE 1 AC9 4 ILE A 80 PRO A 99 HOH A 324 HOH A 359 SITE 1 AD1 7 TRP A 65 GLU A 66 SER A 67 ASP A 87 SITE 2 AD1 7 LYS A 127 GOL A 215 HOH A 383 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 380 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 390 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 336 HOH A 383 SITE 1 AD6 10 GLN A 134 LYS A 180 GLN A 182 THR A 183 SITE 2 AD6 10 ASP A 184 IOD A 205 HOH A 413 A B 3 SITE 3 AD6 10 U B 4 HOH B 203 SITE 1 AD7 6 ASP A 132 GLU A 188 HOH A 316 U B 4 SITE 2 AD7 6 HOH B 208 C b 5 SITE 1 AD8 3 DT C 4 DG C 5 HOH C 213 SITE 1 AD9 8 GLY A 76 ASN A 77 PRO A 78 HOH A 306 SITE 2 AD9 8 HOH B 210 DG C 2 DA C 3 HOH C 217 CRYST1 81.574 37.889 62.247 90.00 96.22 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 0.012259 0.000000 0.001335 0.00000 SCALE2 0.000000 0.026393 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016160 0.00000