HEADER HYDROLASE/DNA/RNA 09-JUN-18 6DOA 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 480 S TITLE 3 AT 21 C CAVEAT 6DOA RESIDUES U B 4 AND C B 5 THAT ARE NEXT TO EACH OTHER IN THE CAVEAT 2 6DOA SAMPLE SEQUENCE ARE NOT PROPERLY LINKED: DISTANCE BETWEEN CAVEAT 3 6DOA O3' (B CONFORMER) AND P (B CONFORMER) IS 4.85.1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBONUCLEASE H; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CATALYTIC DOMAIN; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: RNA (5'-R(*AP*CP*AP*U)-3'); COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: RNA (5'-R(P*CP*G)-3'); COMPND 12 CHAIN: b; COMPND 13 ENGINEERED: YES; COMPND 14 MOL_ID: 4; COMPND 15 MOLECULE: DNA (5'-D(*CP*GP*AP*TP*GP*T)-3'); COMPND 16 CHAIN: C; COMPND 17 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS HALODURANS; SOURCE 3 ORGANISM_TAXID: 272558; SOURCE 4 GENE: RNHA, BH0863; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET15B; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 13 ORGANISM_TAXID: 32630; SOURCE 14 MOL_ID: 3; SOURCE 15 SYNTHETIC: YES; SOURCE 16 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 17 ORGANISM_TAXID: 32630; SOURCE 18 MOL_ID: 4; SOURCE 19 SYNTHETIC: YES; SOURCE 20 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 21 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 13-MAR-24 6DOA 1 LINK REVDAT 1 15-AUG-18 6DOA 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. 1.47 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) : 1.47 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.14 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 32223 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.161 REMARK 3 R VALUE (WORKING SET) : 0.160 REMARK 3 FREE R VALUE : 0.186 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.850 REMARK 3 FREE R VALUE TEST SET COUNT : 1563 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 31.1428 - 3.2770 0.98 2837 150 0.1325 0.1595 REMARK 3 2 3.2770 - 2.6015 1.00 2818 148 0.1532 0.1862 REMARK 3 3 2.6015 - 2.2728 1.00 2779 160 0.1565 0.1716 REMARK 3 4 2.2728 - 2.0650 1.00 2816 119 0.1592 0.2067 REMARK 3 5 2.0650 - 1.9170 1.00 2806 137 0.1637 0.1805 REMARK 3 6 1.9170 - 1.8040 1.00 2767 137 0.1740 0.1835 REMARK 3 7 1.8040 - 1.7137 1.00 2781 146 0.1649 0.2037 REMARK 3 8 1.7137 - 1.6391 1.00 2800 130 0.1812 0.2153 REMARK 3 9 1.6391 - 1.5760 1.00 2786 157 0.1987 0.2231 REMARK 3 10 1.5760 - 1.5216 1.00 2741 152 0.2316 0.2683 REMARK 3 11 1.5216 - 1.4740 0.97 2729 127 0.2842 0.2823 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) : 19.150 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.44 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.64 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 1508 REMARK 3 ANGLE : 1.156 2057 REMARK 3 CHIRALITY : 0.077 225 REMARK 3 PLANARITY : 0.007 213 REMARK 3 DIHEDRAL : 23.752 591 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): 25.382 -5.589 17.619 REMARK 3 T TENSOR REMARK 3 T11: 0.1391 T22: 0.0791 REMARK 3 T33: 0.1181 T12: 0.0187 REMARK 3 T13: 0.0172 T23: 0.0066 REMARK 3 L TENSOR REMARK 3 L11: 6.2869 L22: 1.6604 REMARK 3 L33: 3.4854 L12: -1.3239 REMARK 3 L13: 1.7502 L23: -0.1709 REMARK 3 S TENSOR REMARK 3 S11: 0.2489 S12: 0.2541 S13: -0.2451 REMARK 3 S21: -0.1472 S22: -0.1509 S23: -0.0973 REMARK 3 S31: 0.3171 S32: 0.1491 S33: -0.0768 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: ( CHAIN A AND RESID 88:96 ) REMARK 3 ORIGIN FOR THE GROUP (A): 28.034 -11.553 24.233 REMARK 3 T TENSOR REMARK 3 T11: 0.2054 T22: 0.1260 REMARK 3 T33: 0.2486 T12: 0.0588 REMARK 3 T13: -0.0130 T23: 0.0353 REMARK 3 L TENSOR REMARK 3 L11: 4.8298 L22: 6.2437 REMARK 3 L33: 6.9198 L12: -2.1460 REMARK 3 L13: -4.6277 L23: 0.5831 REMARK 3 S TENSOR REMARK 3 S11: -0.1382 S12: -0.2832 S13: -1.0990 REMARK 3 S21: 0.0055 S22: 0.0200 S23: -0.3732 REMARK 3 S31: 0.7471 S32: 0.3928 S33: 0.0282 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: ( CHAIN A AND RESID 97:133 ) REMARK 3 ORIGIN FOR THE GROUP (A): 21.516 -1.218 23.640 REMARK 3 T TENSOR REMARK 3 T11: 0.0891 T22: 0.0704 REMARK 3 T33: 0.0961 T12: 0.0116 REMARK 3 T13: 0.0175 T23: 0.0039 REMARK 3 L TENSOR REMARK 3 L11: 3.5322 L22: 1.0658 REMARK 3 L33: 2.9414 L12: -0.0747 REMARK 3 L13: 1.4314 L23: 0.4547 REMARK 3 S TENSOR REMARK 3 S11: 0.0661 S12: -0.1936 S13: -0.0949 REMARK 3 S21: -0.0291 S22: -0.0895 S23: 0.0552 REMARK 3 S31: 0.0373 S32: -0.2719 S33: 0.0074 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: ( CHAIN A AND RESID 134:142 ) REMARK 3 ORIGIN FOR THE GROUP (A): 23.655 9.388 16.825 REMARK 3 T TENSOR REMARK 3 T11: 0.2700 T22: 0.0789 REMARK 3 T33: 0.1578 T12: 0.0061 REMARK 3 T13: 0.0284 T23: 0.0348 REMARK 3 L TENSOR REMARK 3 L11: 3.6658 L22: 5.3770 REMARK 3 L33: 5.4355 L12: -3.6402 REMARK 3 L13: -0.4871 L23: -0.3140 REMARK 3 S TENSOR REMARK 3 S11: 0.1913 S12: 0.0860 S13: 0.4340 REMARK 3 S21: -0.1092 S22: -0.1023 S23: -0.2185 REMARK 3 S31: -0.8605 S32: 0.0456 S33: -0.0979 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: ( CHAIN A AND RESID 143:155 ) REMARK 3 ORIGIN FOR THE GROUP (A): 8.288 7.376 16.392 REMARK 3 T TENSOR REMARK 3 T11: 0.2993 T22: 0.4347 REMARK 3 T33: 0.1957 T12: 0.2350 REMARK 3 T13: -0.0274 T23: -0.1058 REMARK 3 L TENSOR REMARK 3 L11: 7.1252 L22: 2.3394 REMARK 3 L33: 2.3140 L12: 0.6636 REMARK 3 L13: 2.5076 L23: -0.4482 REMARK 3 S TENSOR REMARK 3 S11: 0.2399 S12: 0.1286 S13: 0.5516 REMARK 3 S21: -0.1610 S22: -0.3839 S23: 0.3995 REMARK 3 S31: -0.5338 S32: -0.7372 S33: 0.1711 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: ( CHAIN A AND RESID 156:169 ) REMARK 3 ORIGIN FOR THE GROUP (A): 12.209 5.675 25.118 REMARK 3 T TENSOR REMARK 3 T11: 0.1392 T22: 0.2264 REMARK 3 T33: 0.1445 T12: 0.0746 REMARK 3 T13: 0.0160 T23: -0.0387 REMARK 3 L TENSOR REMARK 3 L11: 3.6368 L22: 2.5376 REMARK 3 L33: 8.1580 L12: 1.0963 REMARK 3 L13: 5.4369 L23: 1.6924 REMARK 3 S TENSOR REMARK 3 S11: 0.1195 S12: -0.1911 S13: 0.1671 REMARK 3 S21: -0.0361 S22: -0.2622 S23: 0.2214 REMARK 3 S31: -0.1816 S32: -0.7379 S33: 0.1234 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: ( CHAIN A AND RESID 170:196 ) REMARK 3 ORIGIN FOR THE GROUP (A): 28.764 -0.813 18.008 REMARK 3 T TENSOR REMARK 3 T11: 0.1060 T22: 0.0963 REMARK 3 T33: 0.0835 T12: 0.0447 REMARK 3 T13: -0.0019 T23: 0.0395 REMARK 3 L TENSOR REMARK 3 L11: 3.2260 L22: 2.8217 REMARK 3 L33: 4.9430 L12: -0.3638 REMARK 3 L13: -0.7759 L23: 1.3959 REMARK 3 S TENSOR REMARK 3 S11: 0.0845 S12: 0.2836 S13: -0.1002 REMARK 3 S21: -0.2888 S22: -0.0254 S23: -0.1757 REMARK 3 S31: 0.0398 S32: 0.2286 S33: -0.0900 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): 23.606 0.774 5.333 REMARK 3 T TENSOR REMARK 3 T11: 0.2820 T22: 0.2236 REMARK 3 T33: 0.1217 T12: 0.0606 REMARK 3 T13: 0.0209 T23: 0.0162 REMARK 3 L TENSOR REMARK 3 L11: 2.9798 L22: 6.6704 REMARK 3 L33: 0.8823 L12: 0.4082 REMARK 3 L13: 1.5528 L23: -0.3223 REMARK 3 S TENSOR REMARK 3 S11: -0.1359 S12: 0.1934 S13: 0.0256 REMARK 3 S21: -0.6271 S22: -0.1322 S23: -0.2258 REMARK 3 S31: 0.0098 S32: 0.0264 S33: 0.2618 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: ( CHAIN C AND RESID 1:6 ) REMARK 3 ORIGIN FOR THE GROUP (A): 16.320 3.458 3.421 REMARK 3 T TENSOR REMARK 3 T11: 0.4041 T22: 0.2126 REMARK 3 T33: 0.1393 T12: 0.0848 REMARK 3 T13: -0.0515 T23: -0.0060 REMARK 3 L TENSOR REMARK 3 L11: 2.7865 L22: 2.7829 REMARK 3 L33: 3.2966 L12: -0.8743 REMARK 3 L13: -2.1375 L23: 1.4416 REMARK 3 S TENSOR REMARK 3 S11: -0.1147 S12: 0.2874 S13: -0.1293 REMARK 3 S21: -0.8039 S22: -0.2223 S23: 0.1480 REMARK 3 S31: -0.4643 S32: -0.2364 S33: 0.3817 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 6DOA 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_1000234956. 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 : 23-BM-B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.31 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32242 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.470 REMARK 200 RESOLUTION RANGE LOW (A) : 31.140 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 1.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.47 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.50 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.9 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.46 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 40.86550 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.94500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 40.86550 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 18.94500 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: 6670 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7530 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: 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 -0.126 REMARK 500 DG C 2 O3' DG C 2 C3' -0.050 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. = -5.4 DEGREES REMARK 500 DG C 5 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 455 DISTANCE = 6.34 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 105.7 REMARK 620 3 HOH A 301 O 172.9 78.6 REMARK 620 4 HOH A 307 O 87.3 89.1 87.2 REMARK 620 5 HOH A 320 O 88.6 88.5 97.3 174.4 REMARK 620 6 C b 5 OP3 158.2 96.0 18.0 92.0 93.3 REMARK 620 7 C b 5 OP1 94.0 159.7 82.3 96.7 87.3 64.5 REMARK 620 8 C b 5 OP1 96.4 155.9 80.4 101.5 82.7 62.4 5.3 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 98.0 REMARK 620 3 ASP A 132 OD1 128.6 98.2 REMARK 620 4 ASP A 132 OD2 100.5 152.5 54.4 REMARK 620 5 U B 4 O3' 150.6 86.3 78.9 87.4 REMARK 620 6 C b 5 OP1 90.3 110.2 127.9 89.9 61.1 REMARK 620 7 C b 5 OP1 91.1 116.4 123.3 83.4 61.5 6.5 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 216 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 132 OD2 REMARK 620 2 HOH A 368 O 54.2 REMARK 620 3 HOH B 208 O 157.2 116.4 REMARK 620 4 C b 5 OP2 82.2 128.6 113.8 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 41.2 REMARK 620 3 HOH A 301 O 51.4 83.6 REMARK 620 4 HOH A 307 O 54.5 93.8 51.6 REMARK 620 5 HOH A 337 O 80.6 52.4 86.2 130.8 REMARK 620 6 G b 6 OP2 98.8 139.8 60.8 50.2 134.2 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 432 O REMARK 620 2 DT C 4 O4 92.2 REMARK 620 3 DG C 5 O6 161.8 70.7 REMARK 620 4 HOH C 211 O 86.0 83.5 86.0 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 EDO A 208 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 209 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO 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 GOL A 213 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 214 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PGE A 215 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K A 216 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 6DOA A 61 196 UNP Q9KEI9 RNH1_BACHD 61 196 DBREF 6DOA B 1 4 PDB 6DOA 6DOA 1 4 DBREF 6DOA b 5 6 PDB 6DOA 6DOA 5 6 DBREF 6DOA C 1 6 PDB 6DOA 6DOA 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 PGE A 215 10 HET K A 216 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 4(C3 H8 O3) FORMUL 19 PGE C6 H14 O4 FORMUL 23 HOH *193(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 2.00 LINK OD1 ASP A 71 MG MG A 202 1555 1555 1.98 LINK OE1 GLU A 109 MG MG A 202 1555 1555 2.01 LINK OD1 ASP A 132 MG MG A 202 1555 1555 2.01 LINK OD2 ASP A 132 MG MG A 202 1555 1555 2.64 LINK OD2 ASP A 132 K B K A 216 1555 1555 3.32 LINK OD1 ASP A 192 MG MG A 201 1555 1555 2.03 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 3.31 LINK MG MG A 201 O CHOH A 301 1555 1555 2.02 LINK MG MG A 201 O HOH A 307 1555 1555 2.08 LINK MG MG A 201 O HOH A 320 1555 1555 2.10 LINK MG MG A 201 OP3B C b 5 1555 1555 2.01 LINK MG MG A 201 OP1B C b 5 1555 1555 2.41 LINK MG MG A 201 OP1C C b 5 1555 1555 2.28 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 2.07 LINK MG MG A 202 OP1C C b 5 1555 1555 2.15 LINK K C K A 203 O CHOH A 301 1555 1555 3.08 LINK K C K A 203 O HOH A 307 1555 1555 3.38 LINK K C K A 203 O HOH A 337 1555 1555 2.61 LINK K C K A 203 OP2 G b 6 1555 1555 2.86 LINK K B K A 216 O HOH A 368 1555 1555 3.35 LINK K B K A 216 O HOH B 208 1555 1555 2.61 LINK K B K A 216 OP2B C b 5 1555 1555 2.56 LINK O HOH A 432 K A K C 101 4555 1555 3.26 LINK O4 DT C 4 K A K C 101 1555 1555 3.46 LINK O6 DG C 5 K A K C 101 1555 1555 2.61 LINK K A K C 101 O HOH C 211 1555 1555 3.20 CISPEP 1 ASN A 77 PRO A 78 0 -0.52 SITE 1 AC1 6 ASP A 71 ASP A 192 HOH A 301 HOH A 307 SITE 2 AC1 6 HOH A 320 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 337 C b 5 G b 6 SITE 1 AC4 1 TYR A 83 SITE 1 AC5 1 PGE A 215 SITE 1 AC6 3 ILE A 64 HOH A 425 HOH A 455 SITE 1 AC7 1 HOH A 418 SITE 1 AC8 5 LYS A 143 THR A 173 TYR A 174 HOH A 345 SITE 2 AC8 5 HOH A 391 SITE 1 AC9 5 THR A 148 HOH A 305 HOH A 341 DT C 4 SITE 2 AC9 5 DG C 5 SITE 1 AD1 3 ILE A 80 PRO A 99 HOH A 365 SITE 1 AD2 5 TRP A 65 GLU A 66 SER A 67 ASP A 87 SITE 2 AD2 5 LYS A 127 SITE 1 AD3 5 HIS A 115 ARG A 118 ASN A 170 GOL A 213 SITE 2 AD3 5 HOH A 304 SITE 1 AD4 9 HIS A 115 TYR A 119 GLU A 122 ARG A 123 SITE 2 AD4 9 GLU A 167 ASN A 170 GOL A 212 HOH A 372 SITE 3 AD4 9 HOH A 399 SITE 1 AD5 4 VAL A 150 ASN A 152 GLU A 154 HOH A 321 SITE 1 AD6 11 GLN A 134 LYS A 180 TRP A 181 GLN A 182 SITE 2 AD6 11 THR A 183 ASP A 184 IOD A 205 HOH A 414 SITE 3 AD6 11 A B 3 U B 4 HOH B 202 SITE 1 AD7 6 ASP A 132 GLU A 188 HOH A 308 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 210 SITE 1 AD9 7 GLY A 76 ASN A 77 HOH A 323 HOH B 209 SITE 2 AD9 7 DG C 2 DA C 3 HOH C 213 CRYST1 81.731 37.890 62.695 90.00 96.66 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 0.012235 0.000000 0.001429 0.00000 SCALE2 0.000000 0.026392 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016059 0.00000