HEADER HYDROLASE/DNA/RNA 09-JUN-18 6DOZ TITLE CRYSTAL STRUCTURE OF BACILLUS HALODURANS RIBONUCLEASE H1 IN COMPLEX TITLE 2 WITH AN RNA/DNA HYBRID: REACTION IN 1 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 6DOZ 1 LINK REVDAT 2 22-AUG-18 6DOZ 1 JRNL REVDAT 1 15-AUG-18 6DOZ 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. 1.57 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) : 1.57 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.36 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 3 NUMBER OF REFLECTIONS : 50222 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.154 REMARK 3 R VALUE (WORKING SET) : 0.152 REMARK 3 FREE R VALUE : 0.185 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.940 REMARK 3 FREE R VALUE TEST SET COUNT : 2482 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 19.3612 - 4.1100 0.99 2657 153 0.1238 0.1440 REMARK 3 2 4.1100 - 3.2673 1.00 2717 142 0.1278 0.1850 REMARK 3 3 3.2673 - 2.8558 1.00 2667 142 0.1577 0.1700 REMARK 3 4 2.8558 - 2.5954 1.00 2694 159 0.1560 0.1842 REMARK 3 5 2.5954 - 2.4097 1.00 2694 144 0.1622 0.1900 REMARK 3 6 2.4097 - 2.2679 1.00 2668 157 0.1585 0.1877 REMARK 3 7 2.2679 - 2.1545 1.00 2750 100 0.1527 0.2190 REMARK 3 8 2.1545 - 2.0608 1.00 2717 131 0.1581 0.2090 REMARK 3 9 2.0608 - 1.9815 1.00 2664 143 0.1626 0.2067 REMARK 3 10 1.9815 - 1.9132 1.00 2716 138 0.1701 0.2030 REMARK 3 11 1.9132 - 1.8534 1.00 2649 157 0.1835 0.1951 REMARK 3 12 1.8534 - 1.8005 1.00 2695 151 0.1985 0.2201 REMARK 3 13 1.8005 - 1.7531 1.00 2721 136 0.1976 0.2199 REMARK 3 14 1.7531 - 1.7104 1.00 2728 106 0.2127 0.2644 REMARK 3 15 1.7104 - 1.6715 1.00 2655 143 0.2313 0.2748 REMARK 3 16 1.6715 - 1.6360 0.98 2665 138 0.2558 0.2640 REMARK 3 17 1.6360 - 1.6033 0.95 2537 130 0.2756 0.2800 REMARK 3 18 1.6033 - 1.5730 0.79 2146 112 0.2953 0.3368 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) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.500 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 26.89 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.16 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 1448 REMARK 3 ANGLE : 1.056 2006 REMARK 3 CHIRALITY : 0.058 219 REMARK 3 PLANARITY : 0.007 210 REMARK 3 DIHEDRAL : 20.184 826 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): 25.4604 -5.7175 17.4435 REMARK 3 T TENSOR REMARK 3 T11: 0.2576 T22: 0.1747 REMARK 3 T33: 0.1909 T12: 0.0292 REMARK 3 T13: 0.0221 T23: -0.0036 REMARK 3 L TENSOR REMARK 3 L11: 5.4244 L22: 3.3267 REMARK 3 L33: 5.3455 L12: -2.4958 REMARK 3 L13: 2.7831 L23: -0.7761 REMARK 3 S TENSOR REMARK 3 S11: 0.4764 S12: 0.2766 S13: -0.4900 REMARK 3 S21: -0.1816 S22: -0.2199 S23: -0.0197 REMARK 3 S31: 0.4881 S32: 0.1521 S33: -0.3278 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 88 THROUGH 96 ) REMARK 3 ORIGIN FOR THE GROUP (A): 27.9907 -11.4893 24.0924 REMARK 3 T TENSOR REMARK 3 T11: 0.3050 T22: 0.2525 REMARK 3 T33: 0.4147 T12: 0.0271 REMARK 3 T13: -0.0038 T23: 0.0587 REMARK 3 L TENSOR REMARK 3 L11: 6.5703 L22: 7.1355 REMARK 3 L33: 5.5093 L12: -2.8801 REMARK 3 L13: -5.6528 L23: 1.0270 REMARK 3 S TENSOR REMARK 3 S11: -0.0661 S12: -0.4080 S13: -1.5953 REMARK 3 S21: -0.0885 S22: -0.1069 S23: -0.3741 REMARK 3 S31: 0.7904 S32: 0.2980 S33: 0.2368 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 97 THROUGH 133 ) REMARK 3 ORIGIN FOR THE GROUP (A): 21.8835 -0.9504 23.4437 REMARK 3 T TENSOR REMARK 3 T11: 0.1642 T22: 0.1625 REMARK 3 T33: 0.1683 T12: 0.0107 REMARK 3 T13: 0.0332 T23: 0.0016 REMARK 3 L TENSOR REMARK 3 L11: 5.5331 L22: 1.1355 REMARK 3 L33: 5.1066 L12: -0.2272 REMARK 3 L13: 3.8453 L23: 0.3456 REMARK 3 S TENSOR REMARK 3 S11: 0.0863 S12: -0.4516 S13: -0.1365 REMARK 3 S21: -0.0248 S22: -0.0735 S23: 0.0489 REMARK 3 S31: 0.0635 S32: -0.5151 S33: -0.0041 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 134 THROUGH 142 ) REMARK 3 ORIGIN FOR THE GROUP (A): 23.8282 9.3728 16.6824 REMARK 3 T TENSOR REMARK 3 T11: 0.4410 T22: 0.1815 REMARK 3 T33: 0.2926 T12: -0.0079 REMARK 3 T13: 0.0180 T23: 0.0482 REMARK 3 L TENSOR REMARK 3 L11: 8.4158 L22: 4.6605 REMARK 3 L33: 8.4586 L12: -5.9306 REMARK 3 L13: -1.8693 L23: 2.8809 REMARK 3 S TENSOR REMARK 3 S11: 0.1598 S12: 0.1092 S13: 0.6414 REMARK 3 S21: -0.2163 S22: -0.0888 S23: -0.6035 REMARK 3 S31: -1.3682 S32: -0.0506 S33: -0.0560 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 143 THROUGH 155 ) REMARK 3 ORIGIN FOR THE GROUP (A): 8.5555 7.4054 16.3041 REMARK 3 T TENSOR REMARK 3 T11: 0.4012 T22: 0.5845 REMARK 3 T33: 0.2759 T12: 0.4207 REMARK 3 T13: -0.0180 T23: -0.1671 REMARK 3 L TENSOR REMARK 3 L11: 3.5482 L22: 7.1942 REMARK 3 L33: 5.6993 L12: 1.9728 REMARK 3 L13: 2.8762 L23: 1.2020 REMARK 3 S TENSOR REMARK 3 S11: 0.4814 S12: -0.0807 S13: 0.7179 REMARK 3 S21: -0.1003 S22: -0.6523 S23: 0.6564 REMARK 3 S31: -1.0323 S32: -1.3336 S33: 0.1411 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 156 THROUGH 169 ) REMARK 3 ORIGIN FOR THE GROUP (A): 12.2993 5.6811 25.0086 REMARK 3 T TENSOR REMARK 3 T11: 0.2842 T22: 0.4072 REMARK 3 T33: 0.2388 T12: 0.1113 REMARK 3 T13: 0.0145 T23: -0.0641 REMARK 3 L TENSOR REMARK 3 L11: 8.8344 L22: 2.9733 REMARK 3 L33: 5.0526 L12: 3.2071 REMARK 3 L13: 6.5330 L23: 2.9793 REMARK 3 S TENSOR REMARK 3 S11: 0.0674 S12: -0.8967 S13: 0.1640 REMARK 3 S21: -0.0370 S22: -0.3494 S23: 0.0991 REMARK 3 S31: -0.3858 S32: -1.0399 S33: 0.3382 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 170 THROUGH 196 ) REMARK 3 ORIGIN FOR THE GROUP (A): 28.9820 -0.3234 18.3721 REMARK 3 T TENSOR REMARK 3 T11: 0.2269 T22: 0.2038 REMARK 3 T33: 0.1940 T12: 0.0391 REMARK 3 T13: 0.0201 T23: 0.0235 REMARK 3 L TENSOR REMARK 3 L11: 4.8011 L22: 2.2769 REMARK 3 L33: 5.4547 L12: -0.5812 REMARK 3 L13: 0.0371 L23: -0.0293 REMARK 3 S TENSOR REMARK 3 S11: 0.1306 S12: 0.4440 S13: -0.0722 REMARK 3 S21: -0.2935 S22: -0.1031 S23: -0.1665 REMARK 3 S31: 0.1996 S32: 0.1366 S33: -0.1390 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): 23.7471 1.2942 4.6211 REMARK 3 T TENSOR REMARK 3 T11: 0.3928 T22: 0.3513 REMARK 3 T33: 0.2288 T12: 0.0829 REMARK 3 T13: 0.0500 T23: 0.0069 REMARK 3 L TENSOR REMARK 3 L11: 5.5135 L22: 4.4498 REMARK 3 L33: 4.7349 L12: -0.4947 REMARK 3 L13: 3.5207 L23: -0.6720 REMARK 3 S TENSOR REMARK 3 S11: 0.0993 S12: 0.7304 S13: 0.0009 REMARK 3 S21: -0.5627 S22: -0.1912 S23: -0.0530 REMARK 3 S31: 0.1840 S32: 0.2134 S33: 0.1654 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 1 THROUGH 6 ) REMARK 3 ORIGIN FOR THE GROUP (A): 16.3679 3.6845 3.2803 REMARK 3 T TENSOR REMARK 3 T11: 0.5031 T22: 0.3206 REMARK 3 T33: 0.2009 T12: 0.0978 REMARK 3 T13: -0.0190 T23: -0.0001 REMARK 3 L TENSOR REMARK 3 L11: 4.1459 L22: 5.4971 REMARK 3 L33: 3.8643 L12: -1.5094 REMARK 3 L13: -1.9259 L23: 3.9219 REMARK 3 S TENSOR REMARK 3 S11: -0.0165 S12: 0.3307 S13: -0.1701 REMARK 3 S21: -1.2622 S22: -0.4768 S23: 0.2490 REMARK 3 S31: -0.8673 S32: -0.4035 S33: 0.4873 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 6DOZ 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_1000235004. 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 : 25891 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.570 REMARK 200 RESOLUTION RANGE LOW (A) : 19.360 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 200 DATA REDUNDANCY : 1.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.57 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.60 REMARK 200 COMPLETENESS FOR SHELL (%) : 77.1 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 (%): 49.99 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 40.78800 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.73750 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 40.78800 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 18.73750 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: 4730 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8170 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -37.0 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: 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 1.68 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 DG C 2 O3' DG C 2 C3' -0.052 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. = 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 438 DISTANCE = 6.27 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 96.3 REMARK 620 3 HOH A 321 O 91.2 105.5 REMARK 620 4 HOH A 362 O 174.7 78.9 92.1 REMARK 620 5 HOH A 368 O 90.4 86.5 167.7 87.2 REMARK 620 6 C b 5 OP1 99.3 159.1 88.1 84.9 79.6 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 104.4 REMARK 620 3 ASP A 132 OD1 137.3 92.6 REMARK 620 4 ASP A 132 OD2 113.0 139.3 48.6 REMARK 620 5 U B 4 O3' 138.6 80.2 82.3 82.3 REMARK 620 6 C b 5 OP1 85.6 108.5 126.0 90.4 55.0 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 149.2 REMARK 620 3 HOH A 310 O 69.4 79.9 REMARK 620 4 HOH A 321 O 63.8 141.9 128.6 REMARK 620 5 HOH A 362 O 60.4 108.7 72.9 66.2 REMARK 620 6 G b 6 OP2 113.5 87.9 139.0 54.1 74.3 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 B 108 O REMARK 620 2 DT C 4 O4 156.3 REMARK 620 3 DG C 5 O6 87.0 76.7 REMARK 620 4 HOH C 207 O 106.3 88.7 82.4 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 GOL 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 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 K C 101 DBREF 6DOZ A 59 196 UNP Q9KEI9 RNH1_BACHD 59 196 DBREF 6DOZ B 1 4 PDB 6DOZ 6DOZ 1 4 DBREF 6DOZ b 5 6 PDB 6DOZ 6DOZ 5 6 DBREF 6DOZ C 1 6 PDB 6DOZ 6DOZ 1 6 SEQADV 6DOZ GLY A 55 UNP Q9KEI9 EXPRESSION TAG SEQADV 6DOZ SER A 56 UNP Q9KEI9 EXPRESSION TAG SEQADV 6DOZ HIS A 57 UNP Q9KEI9 EXPRESSION TAG SEQADV 6DOZ 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 GOL A 207 6 HET GOL A 208 6 HET GOL A 209 6 HET EDO A 210 4 HET EDO A 211 4 HET K C 101 1 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 3(I 1-) FORMUL 11 GOL 3(C3 H8 O3) FORMUL 14 EDO 2(C2 H6 O2) FORMUL 17 HOH *169(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 2.02 LINK OD1 ASP A 71 MG MG A 202 1555 1555 2.11 LINK OE1 GLU A 109 MG MG A 202 1555 1555 2.41 LINK OD1 ASP A 132 MG MG A 202 1555 1555 2.38 LINK OD2 ASP A 132 MG MG A 202 1555 1555 2.86 LINK OD1 ASP A 192 MG MG A 201 1555 1555 2.12 LINK OD1 ASP A 192 K K A 203 1555 1555 3.04 LINK O ARG A 195 K K A 203 1555 1555 3.00 LINK MG MG A 201 O HOH A 321 1555 1555 1.92 LINK MG MG A 201 O HOH A 362 1555 1555 2.30 LINK MG MG A 201 O HOH A 368 1555 1555 2.22 LINK MG MG A 201 OP1 C b 5 1555 1555 2.29 LINK MG MG A 202 O3' U B 4 1555 1555 2.78 LINK MG MG A 202 OP1 C b 5 1555 1555 2.47 LINK K K A 203 O HOH A 310 1555 1555 2.53 LINK K K A 203 O HOH A 321 1555 1555 3.04 LINK K K A 203 O HOH A 362 1555 1555 2.47 LINK K K A 203 OP2 G b 6 1555 1555 3.06 LINK O HOH B 108 K A K C 101 1555 1555 3.25 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 2.63 LINK K A K C 101 O HOH C 207 1555 1555 3.07 CISPEP 1 ASN A 77 PRO A 78 0 -0.52 SITE 1 AC1 7 ASP A 71 ASP A 192 K A 203 HOH A 321 SITE 2 AC1 7 HOH A 362 HOH A 368 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 7 ASP A 192 ARG A 195 MG A 201 HOH A 310 SITE 2 AC3 7 HOH A 321 HOH A 362 G b 6 SITE 1 AC4 1 TYR A 83 SITE 1 AC5 1 HOH A 434 SITE 1 AC6 3 ILE A 64 HOH A 412 HOH A 438 SITE 1 AC7 6 GLY A 76 ASN A 77 PRO A 78 HOH A 301 SITE 2 AC7 6 DG C 2 DA C 3 SITE 1 AC8 8 HIS A 115 TYR A 119 GLU A 122 ARG A 123 SITE 2 AC8 8 GLU A 167 ASN A 170 HOH A 374 HOH A 394 SITE 1 AC9 6 GLU A 66 LEU A 94 SER A 125 LYS A 127 SITE 2 AC9 6 HOH A 305 HOH A 309 SITE 1 AD1 4 LYS A 143 THR A 173 TYR A 174 HOH A 399 SITE 1 AD2 4 LYS A 89 GLU A 153 ALA A 156 HOH A 333 SITE 1 AD3 4 DT C 4 DG C 5 HOH C 207 HOH C 212 CRYST1 81.576 37.475 62.495 90.00 96.67 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 0.001433 0.00000 SCALE2 0.000000 0.026684 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016110 0.00000