HEADER HYDROLASE/DNA/RNA 09-JUN-18 6DP2 TITLE CRYSTAL STRUCTURE OF BACILLUS HALODURANS RIBONUCLEASE H1 IN COMPLEX TITLE 2 WITH AN RNA/DNA HYBRID: REACTION IN 7.5 MM MG2+ AND 75 MM K+ FOR 40 S TITLE 3 AT 21 C COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBONUCLEASE H; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CATALYTIC DOMAIN RESIDUES 59-196; COMPND 5 SYNONYM: RNASE H; COMPND 6 EC: 3.1.26.4; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: 5'-R(*AP*CP*AP*U)-3' PORTION OF UNCLEAVED RNA 5'- COMPND 10 R(*AP*CP*AP*UP*CP*G)-3'; COMPND 11 CHAIN: B; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: 5'-R(P*CP*G)-3' PORTION OF UNCLEAVED RNA 5'- COMPND 15 R(*AP*CP*AP*UP*CP*G)-3'; COMPND 16 CHAIN: b; COMPND 17 ENGINEERED: YES; COMPND 18 MOL_ID: 4; COMPND 19 MOLECULE: DNA (5'-D(*CP*GP*AP*TP*GP*T)-3'); COMPND 20 CHAIN: C; COMPND 21 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS HALODURANS; SOURCE 3 ORGANISM_TAXID: 272558; SOURCE 4 STRAIN: ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125; SOURCE 5 GENE: RNHA, BH0863; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET15B; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 14 ORGANISM_TAXID: 32630; SOURCE 15 MOL_ID: 3; SOURCE 16 SYNTHETIC: YES; SOURCE 17 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 18 ORGANISM_TAXID: 32630; SOURCE 19 MOL_ID: 4; SOURCE 20 SYNTHETIC: YES; SOURCE 21 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 22 ORGANISM_TAXID: 32630 KEYWDS PROTEIN-RNA-DNA COMPLEX, RNA HYDROLYSIS, IN CRYSTALLO CATALYSIS, KEYWDS 2 METAL DEPENDENT CATALYSIS, HYDROLASE-DNA-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR N.L.SAMARA,W.YANG REVDAT 3 11-OCT-23 6DP2 1 LINK REVDAT 2 22-AUG-18 6DP2 1 JRNL REVDAT 1 15-AUG-18 6DP2 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. 1.66 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) : 1.66 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.02 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.1 REMARK 3 NUMBER OF REFLECTIONS : 41233 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.159 REMARK 3 R VALUE (WORKING SET) : 0.157 REMARK 3 FREE R VALUE : 0.196 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 2065 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 20.0248 - 4.0870 0.99 2709 116 0.1286 0.1630 REMARK 3 2 4.0870 - 3.2484 0.98 2692 157 0.1292 0.1724 REMARK 3 3 3.2484 - 2.8391 0.99 2665 129 0.1557 0.1742 REMARK 3 4 2.8391 - 2.5801 0.98 2738 96 0.1589 0.2103 REMARK 3 5 2.5801 - 2.3955 0.98 2646 162 0.1591 0.2122 REMARK 3 6 2.3955 - 2.2545 0.97 2635 140 0.1629 0.2046 REMARK 3 7 2.2545 - 2.1417 0.97 2619 149 0.1713 0.1899 REMARK 3 8 2.1417 - 2.0486 0.97 2669 127 0.1841 0.2591 REMARK 3 9 2.0486 - 1.9698 0.97 2554 163 0.1749 0.2293 REMARK 3 10 1.9698 - 1.9019 0.96 2672 150 0.2225 0.2156 REMARK 3 11 1.9019 - 1.8424 0.96 2631 131 0.2258 0.2717 REMARK 3 12 1.8424 - 1.7898 0.96 2532 152 0.2254 0.2722 REMARK 3 13 1.7898 - 1.7427 0.96 2689 118 0.2346 0.2604 REMARK 3 14 1.7427 - 1.7002 0.95 2556 141 0.2659 0.3117 REMARK 3 15 1.7002 - 1.6616 0.80 2161 134 0.3040 0.3332 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) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.460 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 27.92 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.46 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 1452 REMARK 3 ANGLE : 1.038 2010 REMARK 3 CHIRALITY : 0.057 219 REMARK 3 PLANARITY : 0.007 211 REMARK 3 DIHEDRAL : 18.929 826 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): 25.0130 -5.7305 17.1698 REMARK 3 T TENSOR REMARK 3 T11: 0.2385 T22: 0.1839 REMARK 3 T33: 0.2050 T12: 0.0304 REMARK 3 T13: 0.0301 T23: 0.0004 REMARK 3 L TENSOR REMARK 3 L11: 4.7162 L22: 2.0996 REMARK 3 L33: 4.1242 L12: -1.1969 REMARK 3 L13: 2.1705 L23: -0.8115 REMARK 3 S TENSOR REMARK 3 S11: 0.2868 S12: 0.2965 S13: -0.3884 REMARK 3 S21: -0.1598 S22: -0.1635 S23: -0.0796 REMARK 3 S31: 0.4147 S32: 0.2534 S33: -0.1113 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 88 THROUGH 96 ) REMARK 3 ORIGIN FOR THE GROUP (A): 27.8684 -11.5488 24.0764 REMARK 3 T TENSOR REMARK 3 T11: 0.2856 T22: 0.2370 REMARK 3 T33: 0.4250 T12: 0.0491 REMARK 3 T13: 0.0286 T23: 0.0299 REMARK 3 L TENSOR REMARK 3 L11: 3.8753 L22: 3.3987 REMARK 3 L33: 6.0224 L12: -3.0552 REMARK 3 L13: -3.3484 L23: 1.0927 REMARK 3 S TENSOR REMARK 3 S11: -0.1215 S12: -0.2321 S13: -1.2779 REMARK 3 S21: 0.0622 S22: 0.0063 S23: -0.3968 REMARK 3 S31: 0.6024 S32: 0.4437 S33: 0.0437 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 97 THROUGH 133 ) REMARK 3 ORIGIN FOR THE GROUP (A): 21.8323 -0.9267 23.4052 REMARK 3 T TENSOR REMARK 3 T11: 0.1779 T22: 0.1806 REMARK 3 T33: 0.1949 T12: 0.0263 REMARK 3 T13: 0.0358 T23: 0.0073 REMARK 3 L TENSOR REMARK 3 L11: 5.0236 L22: 0.8782 REMARK 3 L33: 5.1966 L12: -0.0811 REMARK 3 L13: 3.5981 L23: 0.5395 REMARK 3 S TENSOR REMARK 3 S11: 0.0918 S12: -0.3140 S13: -0.1306 REMARK 3 S21: -0.0419 S22: -0.0552 S23: 0.0564 REMARK 3 S31: 0.0345 S32: -0.3666 S33: -0.0237 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 134 THROUGH 142 ) REMARK 3 ORIGIN FOR THE GROUP (A): 23.8064 9.3555 16.6514 REMARK 3 T TENSOR REMARK 3 T11: 0.3908 T22: 0.1878 REMARK 3 T33: 0.2798 T12: -0.0284 REMARK 3 T13: 0.0487 T23: 0.0519 REMARK 3 L TENSOR REMARK 3 L11: 7.1038 L22: 6.9250 REMARK 3 L33: 7.7509 L12: -6.1136 REMARK 3 L13: -1.4436 L23: 3.6950 REMARK 3 S TENSOR REMARK 3 S11: 0.2065 S12: 0.0899 S13: 0.4413 REMARK 3 S21: -0.3678 S22: -0.0990 S23: -0.5229 REMARK 3 S31: -1.1545 S32: 0.1242 S33: -0.0960 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 143 THROUGH 155 ) REMARK 3 ORIGIN FOR THE GROUP (A): 8.5895 7.6126 16.2021 REMARK 3 T TENSOR REMARK 3 T11: 0.4254 T22: 0.4716 REMARK 3 T33: 0.2972 T12: 0.2728 REMARK 3 T13: -0.0006 T23: -0.1139 REMARK 3 L TENSOR REMARK 3 L11: 8.2504 L22: 3.1432 REMARK 3 L33: 6.2889 L12: -1.1364 REMARK 3 L13: 1.6657 L23: 0.2508 REMARK 3 S TENSOR REMARK 3 S11: 0.0614 S12: 0.1572 S13: 0.4474 REMARK 3 S21: -0.1499 S22: -0.4256 S23: 0.6065 REMARK 3 S31: -0.6960 S32: -1.0711 S33: 0.2587 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 156 THROUGH 169 ) REMARK 3 ORIGIN FOR THE GROUP (A): 12.3108 5.7481 24.9392 REMARK 3 T TENSOR REMARK 3 T11: 0.2718 T22: 0.3485 REMARK 3 T33: 0.2609 T12: 0.0804 REMARK 3 T13: 0.0349 T23: -0.0294 REMARK 3 L TENSOR REMARK 3 L11: 7.8138 L22: 3.7196 REMARK 3 L33: 7.9523 L12: 2.2978 REMARK 3 L13: 7.0903 L23: 2.8755 REMARK 3 S TENSOR REMARK 3 S11: 0.1890 S12: -0.6082 S13: 0.1112 REMARK 3 S21: 0.0081 S22: -0.2640 S23: 0.2350 REMARK 3 S31: -0.2438 S32: -0.7451 S33: 0.1378 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 170 THROUGH 196 ) REMARK 3 ORIGIN FOR THE GROUP (A): 28.8759 -0.3751 18.3114 REMARK 3 T TENSOR REMARK 3 T11: 0.2154 T22: 0.2074 REMARK 3 T33: 0.2096 T12: 0.0412 REMARK 3 T13: 0.0330 T23: 0.0445 REMARK 3 L TENSOR REMARK 3 L11: 4.5472 L22: 3.4314 REMARK 3 L33: 6.8333 L12: -1.6994 REMARK 3 L13: -1.0414 L23: 1.8384 REMARK 3 S TENSOR REMARK 3 S11: 0.2171 S12: 0.3186 S13: 0.0353 REMARK 3 S21: -0.2871 S22: -0.0868 S23: -0.2220 REMARK 3 S31: 0.0212 S32: 0.3312 S33: -0.1583 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: (CHAIN 'B' AND (RESID 1 THROUGH 4 )) OR (CHAIN 'B' REMARK 3 AND (RESID 5 THROUGH 6 )) REMARK 3 ORIGIN FOR THE GROUP (A): 23.6769 1.1690 4.6333 REMARK 3 T TENSOR REMARK 3 T11: 0.3998 T22: 0.3794 REMARK 3 T33: 0.2471 T12: 0.0731 REMARK 3 T13: 0.0598 T23: 0.0133 REMARK 3 L TENSOR REMARK 3 L11: 5.6250 L22: 2.0691 REMARK 3 L33: 2.9483 L12: 1.1091 REMARK 3 L13: 3.6251 L23: -0.3453 REMARK 3 S TENSOR REMARK 3 S11: -0.0686 S12: 0.6178 S13: 0.0024 REMARK 3 S21: -0.6214 S22: -0.1104 S23: -0.0803 REMARK 3 S31: 0.0469 S32: 0.2963 S33: 0.2202 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 1 THROUGH 6 ) REMARK 3 ORIGIN FOR THE GROUP (A): 16.3380 3.6091 3.3001 REMARK 3 T TENSOR REMARK 3 T11: 0.4863 T22: 0.3041 REMARK 3 T33: 0.2237 T12: 0.1135 REMARK 3 T13: -0.0192 T23: -0.0025 REMARK 3 L TENSOR REMARK 3 L11: 3.9147 L22: 5.0188 REMARK 3 L33: 8.8045 L12: -0.8813 REMARK 3 L13: -1.6531 L23: 3.2533 REMARK 3 S TENSOR REMARK 3 S11: -0.0217 S12: 0.3484 S13: -0.1878 REMARK 3 S21: -1.0012 S22: -0.2428 S23: 0.2846 REMARK 3 S31: -0.4133 S32: -0.3293 S33: 0.2892 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 6DP2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-JUN-18. REMARK 100 THE DEPOSITION ID IS D_1000235009. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-MAR-18 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-ID 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 : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.31 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21230 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.660 REMARK 200 RESOLUTION RANGE LOW (A) : 20.020 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 200 DATA REDUNDANCY : 1.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.66 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 76.5 REMARK 200 DATA REDUNDANCY IN SHELL : 1.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 1ZBL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.54 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.44 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 14% PEG3350, 20% GLYCEROL, 200 MM KI, REMARK 280 AND 25 MM CACL2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 40.69800 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.65450 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 40.69800 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 18.65450 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: 5010 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8080 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -38.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, b, C REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A 55 REMARK 465 SER A 56 REMARK 465 HIS A 57 REMARK 465 MET A 58 REMARK 465 ALA A 59 REMARK 465 LYS A 60 REMARK 465 LYS A 196 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 A B 1 O2' REMARK 470 G b 6 O2' REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 DG C 2 O3' DG C 2 C3' -0.052 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 432 DISTANCE = 6.20 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 98.3 REMARK 620 3 HOH A 321 O 173.8 76.0 REMARK 620 4 HOH A 323 O 89.3 93.2 88.6 REMARK 620 5 HOH A 361 O 88.7 88.8 93.5 177.4 REMARK 620 6 C b 5 OP1 101.1 159.8 84.9 93.0 85.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 202 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 71 OD1 REMARK 620 2 GLU A 109 OE1 103.1 REMARK 620 3 ASP A 132 OD1 135.4 93.6 REMARK 620 4 ASP A 132 OD2 112.7 140.0 48.1 REMARK 620 5 U B 4 O3' 140.0 82.7 82.4 81.3 REMARK 620 6 C b 5 OP1 86.3 111.4 125.4 88.7 55.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 203 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 192 OD1 REMARK 620 2 ARG A 195 O 122.5 REMARK 620 3 HOH A 309 O 65.1 57.3 REMARK 620 4 HOH A 321 O 48.0 105.1 66.7 REMARK 620 5 HOH A 323 O 52.2 159.9 113.2 56.0 REMARK 620 6 G b 6 OP2 98.2 116.5 127.8 66.5 52.6 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 DT C 4 O4 REMARK 620 2 DG C 5 O6 70.7 REMARK 620 3 HOH C 211 O 86.0 82.6 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 206 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 207 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 208 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 209 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 210 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 211 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K C 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL C 102 DBREF 6DP2 A 59 196 UNP Q9KEI9 RNH1_BACHD 59 196 DBREF 6DP2 B 1 4 PDB 6DP2 6DP2 1 4 DBREF 6DP2 b 5 6 PDB 6DP2 6DP2 5 6 DBREF 6DP2 C 1 6 PDB 6DP2 6DP2 1 6 SEQADV 6DP2 GLY A 55 UNP Q9KEI9 EXPRESSION TAG SEQADV 6DP2 SER A 56 UNP Q9KEI9 EXPRESSION TAG SEQADV 6DP2 HIS A 57 UNP Q9KEI9 EXPRESSION TAG SEQADV 6DP2 MET A 58 UNP Q9KEI9 EXPRESSION TAG SEQRES 1 A 142 GLY SER HIS MET ALA LYS GLU GLU ILE ILE TRP GLU SER SEQRES 2 A 142 LEU SER VAL ASP VAL GLY SER GLN GLY ASN PRO GLY ILE SEQRES 3 A 142 VAL GLU TYR LYS GLY VAL ASP THR LYS THR GLY GLU VAL SEQRES 4 A 142 LEU PHE GLU ARG GLU PRO ILE PRO ILE GLY THR ASN ASN SEQRES 5 A 142 MET GLY GLU PHE LEU ALA ILE VAL HIS GLY LEU ARG TYR SEQRES 6 A 142 LEU LYS GLU ARG ASN SER ARG LYS PRO ILE TYR SER ASP SEQRES 7 A 142 SER GLN THR ALA ILE LYS TRP VAL LYS ASP LYS LYS ALA SEQRES 8 A 142 LYS SER THR LEU VAL ARG ASN GLU GLU THR ALA LEU ILE SEQRES 9 A 142 TRP LYS LEU VAL ASP GLU ALA GLU GLU TRP LEU ASN THR SEQRES 10 A 142 HIS THR TYR GLU THR PRO ILE LEU LYS TRP GLN THR ASP SEQRES 11 A 142 LYS TRP GLY GLU ILE LYS ALA ASP TYR GLY ARG LYS SEQRES 1 B 4 A C A U SEQRES 1 b 2 C G SEQRES 1 C 6 DC DG DA DT DG DT HET MG A 201 1 HET MG A 202 1 HET K A 203 1 HET IOD A 204 1 HET IOD A 205 1 HET IOD A 206 1 HET IOD A 207 1 HET GOL A 208 6 HET GOL A 209 6 HET GOL A 210 6 HET EDO A 211 4 HET K C 101 1 HET GOL C 102 6 HETNAM MG MAGNESIUM ION HETNAM K POTASSIUM ION HETNAM IOD IODIDE ION HETNAM GOL GLYCEROL HETNAM EDO 1,2-ETHANEDIOL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 5 MG 2(MG 2+) FORMUL 7 K 2(K 1+) FORMUL 8 IOD 4(I 1-) FORMUL 12 GOL 4(C3 H8 O3) FORMUL 15 EDO C2 H6 O2 FORMUL 18 HOH *159(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' U B 4 P C b 5 1555 1555 1.61 LINK OD2 ASP A 71 MG MG A 201 1555 1555 1.99 LINK OD1 ASP A 71 MG MG A 202 1555 1555 2.09 LINK OE1 GLU A 109 MG MG A 202 1555 1555 2.29 LINK OD1 ASP A 132 MG MG A 202 1555 1555 2.37 LINK OD2 ASP A 132 MG MG A 202 1555 1555 2.86 LINK OD1 ASP A 192 MG MG A 201 1555 1555 2.02 LINK OD1 ASP A 192 K K A 203 1555 1555 3.37 LINK O ARG A 195 K K A 203 1555 1555 3.37 LINK MG MG A 201 O HOH A 321 1555 1555 2.22 LINK MG MG A 201 O HOH A 323 1555 1555 2.01 LINK MG MG A 201 O HOH A 361 1555 1555 2.11 LINK MG MG A 201 OP1 C b 5 1555 1555 2.10 LINK MG MG A 202 O3' U B 4 1555 1555 2.72 LINK MG MG A 202 OP1 C b 5 1555 1555 2.44 LINK K K A 203 O HOH A 309 1555 1555 2.96 LINK K K A 203 O HOH A 321 1555 1555 2.99 LINK K K A 203 O HOH A 323 1555 1555 3.28 LINK K K A 203 OP2 G b 6 1555 1555 2.83 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 2.64 LINK K A K C 101 O HOH C 211 1555 1555 3.15 CISPEP 1 ASN A 77 PRO A 78 0 0.78 SITE 1 AC1 6 ASP A 71 ASP A 192 HOH A 321 HOH A 323 SITE 2 AC1 6 HOH A 361 C b 5 SITE 1 AC2 5 ASP A 71 GLU A 109 ASP A 132 U B 4 SITE 2 AC2 5 C b 5 SITE 1 AC3 6 ASP A 192 GLY A 194 ARG A 195 HOH A 309 SITE 2 AC3 6 HOH A 321 G b 6 SITE 1 AC4 1 TYR A 83 SITE 1 AC5 2 HOH A 352 HOH A 429 SITE 1 AC6 3 ILE A 64 HOH A 410 HOH A 432 SITE 1 AC7 2 HIS A 172 HOH A 422 SITE 1 AC8 6 HIS A 115 ARG A 123 GLU A 167 GOL A 210 SITE 2 AC8 6 HOH A 302 HOH A 374 SITE 1 AC9 4 GLU A 66 SER A 125 LYS A 127 HOH A 313 SITE 1 AD1 6 HIS A 115 ARG A 118 ASN A 170 GOL A 208 SITE 2 AD1 6 HOH A 322 HOH A 390 SITE 1 AD2 4 LYS A 143 THR A 173 TYR A 174 HOH A 373 SITE 1 AD3 3 DT C 4 DG C 5 HOH C 209 SITE 1 AD4 6 GLY A 76 ASN A 77 PRO A 78 DG C 2 SITE 2 AD4 6 DA C 3 HOH C 201 CRYST1 81.396 37.309 62.340 90.00 96.62 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 0.012286 0.000000 0.001427 0.00000 SCALE2 0.000000 0.026803 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016149 0.00000