HEADER HYDROLASE/DNA/RNA 09-JUN-18 6DPD TITLE CRYSTAL STRUCTURE OF BACILLUS HALODURANS RIBONUCLEASE H1 IN COMPLEX TITLE 2 WITH AN RNA/DNA HYBRID: REACTION IN 16 MM MN2+ AND 200 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 SYNONYM: RNASE H; COMPND 5 EC: 3.1.26.4; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: RNA (5'-R(*AP*CP*AP*U)-3'); COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: RNA (5'-R(P*CP*G)-3'); COMPND 13 CHAIN: b; COMPND 14 ENGINEERED: YES; COMPND 15 MOL_ID: 4; COMPND 16 MOLECULE: DNA (5'-D(*CP*GP*AP*TP*GP*T)-3'); COMPND 17 CHAIN: C; COMPND 18 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS HALODURANS (STRAIN ATCC BAA-125 / DSM SOURCE 3 18197 / FERM 7344 / JCM 9153 / C-125); SOURCE 4 ORGANISM_TAXID: 272558; SOURCE 5 STRAIN: ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125; SOURCE 6 GENE: RNHA, BH0863; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET15B; SOURCE 12 MOL_ID: 2; SOURCE 13 SYNTHETIC: YES; SOURCE 14 ORGANISM_SCIENTIFIC: SYNTHETIC; SOURCE 15 ORGANISM_TAXID: 32630; SOURCE 16 MOL_ID: 3; SOURCE 17 SYNTHETIC: YES; SOURCE 18 ORGANISM_SCIENTIFIC: SYNTHETIC; SOURCE 19 ORGANISM_TAXID: 32630; SOURCE 20 MOL_ID: 4; SOURCE 21 SYNTHETIC: YES; SOURCE 22 ORGANISM_SCIENTIFIC: SYNTHETIC; SOURCE 23 ORGANISM_TAXID: 32630 KEYWDS PROTEIN-RNA-DNA COMPLEX, DOUBLE HELIX, RNA HYDROLYSIS, IN CRYSTALLO KEYWDS 2 CATALYSIS, METAL DEPENDENT CATALYSIS, MONOVALENT CATIONS, DIVALENT KEYWDS 3 CATIONS, HYDROLASE-DNA-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR N.L.SAMARA,W.YANG REVDAT 2 11-OCT-23 6DPD 1 LINK REVDAT 1 15-AUG-18 6DPD 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. 1.46 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) : 1.46 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.84 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 32488 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.152 REMARK 3 R VALUE (WORKING SET) : 0.151 REMARK 3 FREE R VALUE : 0.173 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.050 REMARK 3 FREE R VALUE TEST SET COUNT : 1642 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 19.8465 - 3.3277 1.00 2703 128 0.1184 0.1168 REMARK 3 2 3.3277 - 2.6433 1.00 2600 143 0.1435 0.1716 REMARK 3 3 2.6433 - 2.3097 0.99 2604 144 0.1515 0.2016 REMARK 3 4 2.3097 - 2.0988 0.99 2595 136 0.1505 0.1796 REMARK 3 5 2.0988 - 1.9485 0.99 2551 140 0.1534 0.1699 REMARK 3 6 1.9485 - 1.8337 1.00 2593 154 0.1717 0.2086 REMARK 3 7 1.8337 - 1.7419 0.99 2583 134 0.1772 0.2264 REMARK 3 8 1.7419 - 1.6661 0.99 2535 130 0.1846 0.1832 REMARK 3 9 1.6661 - 1.6020 0.99 2562 147 0.2021 0.2415 REMARK 3 10 1.6020 - 1.5468 0.99 2582 127 0.2270 0.2674 REMARK 3 11 1.5468 - 1.4984 0.99 2557 136 0.2529 0.2826 REMARK 3 12 1.4984 - 1.4556 0.92 2381 123 0.2935 0.3058 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.930 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.53 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.41 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 : 0.007 1467 REMARK 3 ANGLE : 0.960 2020 REMARK 3 CHIRALITY : 0.068 219 REMARK 3 PLANARITY : 0.006 211 REMARK 3 DIHEDRAL : 22.917 573 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 11 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ( CHAIN A AND RESID 61:87 ) REMARK 3 ORIGIN FOR THE GROUP (A): 25.070 -5.741 16.692 REMARK 3 T TENSOR REMARK 3 T11: 0.1598 T22: 0.1444 REMARK 3 T33: 0.1104 T12: 0.0312 REMARK 3 T13: 0.0345 T23: -0.0045 REMARK 3 L TENSOR REMARK 3 L11: 3.1907 L22: 1.9977 REMARK 3 L33: 4.3594 L12: -0.5095 REMARK 3 L13: 1.6516 L23: -0.4845 REMARK 3 S TENSOR REMARK 3 S11: 0.1701 S12: 0.2361 S13: -0.1909 REMARK 3 S21: -0.0846 S22: -0.1298 S23: -0.1406 REMARK 3 S31: 0.2348 S32: 0.3703 S33: -0.0500 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: ( CHAIN A AND RESID 88:96 ) REMARK 3 ORIGIN FOR THE GROUP (A): 28.028 -11.663 23.511 REMARK 3 T TENSOR REMARK 3 T11: 0.2791 T22: 0.2260 REMARK 3 T33: 0.2688 T12: 0.0684 REMARK 3 T13: -0.0124 T23: 0.0508 REMARK 3 L TENSOR REMARK 3 L11: 7.3380 L22: 9.7478 REMARK 3 L33: 8.7435 L12: -2.6658 REMARK 3 L13: -7.0785 L23: 1.4642 REMARK 3 S TENSOR REMARK 3 S11: -0.0715 S12: -0.2803 S13: -1.2940 REMARK 3 S21: 0.2149 S22: -0.1527 S23: -0.3072 REMARK 3 S31: 0.6981 S32: 0.5337 S33: 0.1828 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: ( CHAIN A AND RESID 97:104 ) REMARK 3 ORIGIN FOR THE GROUP (A): 10.365 -4.985 18.253 REMARK 3 T TENSOR REMARK 3 T11: 0.2316 T22: 0.2870 REMARK 3 T33: 0.1924 T12: -0.0100 REMARK 3 T13: -0.0006 T23: -0.0410 REMARK 3 L TENSOR REMARK 3 L11: 8.3239 L22: 4.7374 REMARK 3 L33: 6.9048 L12: -2.2387 REMARK 3 L13: 2.5915 L23: -5.7006 REMARK 3 S TENSOR REMARK 3 S11: 0.0947 S12: -0.3251 S13: -0.4017 REMARK 3 S21: -0.0567 S22: 0.3143 S23: 0.5219 REMARK 3 S31: 0.1834 S32: -0.8446 S33: -0.3602 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: ( CHAIN A AND RESID 105:141 ) REMARK 3 ORIGIN FOR THE GROUP (A): 24.631 1.895 22.419 REMARK 3 T TENSOR REMARK 3 T11: 0.1561 T22: 0.1154 REMARK 3 T33: 0.1221 T12: -0.0065 REMARK 3 T13: 0.0372 T23: 0.0080 REMARK 3 L TENSOR REMARK 3 L11: 4.6718 L22: 1.8142 REMARK 3 L33: 5.0863 L12: -1.3375 REMARK 3 L13: 2.5076 L23: 0.2838 REMARK 3 S TENSOR REMARK 3 S11: 0.0840 S12: -0.0315 S13: 0.0417 REMARK 3 S21: -0.0355 S22: -0.0601 S23: -0.0671 REMARK 3 S31: -0.1214 S32: -0.0101 S33: -0.0471 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: ( CHAIN A AND RESID 142:155 ) REMARK 3 ORIGIN FOR THE GROUP (A): 9.618 8.165 16.101 REMARK 3 T TENSOR REMARK 3 T11: 0.3304 T22: 0.3607 REMARK 3 T33: 0.2118 T12: 0.1728 REMARK 3 T13: 0.0182 T23: -0.0766 REMARK 3 L TENSOR REMARK 3 L11: 2.8585 L22: 2.6902 REMARK 3 L33: 6.4838 L12: -0.5565 REMARK 3 L13: 3.3522 L23: 0.3138 REMARK 3 S TENSOR REMARK 3 S11: 0.0387 S12: 0.0023 S13: 0.4573 REMARK 3 S21: -0.1957 S22: -0.2646 S23: 0.5440 REMARK 3 S31: -0.6291 S32: -0.8481 S33: 0.2883 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: ( CHAIN A AND RESID 156:169 ) REMARK 3 ORIGIN FOR THE GROUP (A): 12.432 5.798 24.510 REMARK 3 T TENSOR REMARK 3 T11: 0.2182 T22: 0.2435 REMARK 3 T33: 0.1340 T12: 0.0529 REMARK 3 T13: 0.0483 T23: -0.0286 REMARK 3 L TENSOR REMARK 3 L11: 8.4274 L22: 3.7328 REMARK 3 L33: 6.3838 L12: 1.0253 REMARK 3 L13: 5.5096 L23: 1.4523 REMARK 3 S TENSOR REMARK 3 S11: 0.1232 S12: -0.1719 S13: 0.1094 REMARK 3 S21: -0.0135 S22: -0.2624 S23: 0.1855 REMARK 3 S31: -0.1212 S32: -0.5982 S33: 0.1595 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: ( CHAIN A AND RESID 170:177 ) REMARK 3 ORIGIN FOR THE GROUP (A): 26.475 8.362 29.946 REMARK 3 T TENSOR REMARK 3 T11: 0.2536 T22: 0.2096 REMARK 3 T33: 0.1983 T12: -0.0128 REMARK 3 T13: 0.0297 T23: -0.0039 REMARK 3 L TENSOR REMARK 3 L11: 5.5667 L22: 6.1108 REMARK 3 L33: 4.3865 L12: -4.8527 REMARK 3 L13: -1.2275 L23: 3.8516 REMARK 3 S TENSOR REMARK 3 S11: 0.0907 S12: -0.4642 S13: 0.5802 REMARK 3 S21: -0.0442 S22: 0.2444 S23: -0.4713 REMARK 3 S31: -0.3295 S32: 0.4098 S33: -0.3351 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: ( CHAIN A AND RESID 178:186 ) REMARK 3 ORIGIN FOR THE GROUP (A): 34.378 -0.840 11.905 REMARK 3 T TENSOR REMARK 3 T11: 0.2401 T22: 0.3487 REMARK 3 T33: 0.1730 T12: 0.0409 REMARK 3 T13: 0.0777 T23: 0.0228 REMARK 3 L TENSOR REMARK 3 L11: 0.5657 L22: 8.5438 REMARK 3 L33: 8.3326 L12: 0.1087 REMARK 3 L13: 1.5831 L23: 6.1149 REMARK 3 S TENSOR REMARK 3 S11: 0.1607 S12: 0.4831 S13: 0.0875 REMARK 3 S21: -0.5505 S22: 0.0245 S23: -0.5372 REMARK 3 S31: -0.1115 S32: 0.5746 S33: -0.1966 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: ( CHAIN A AND RESID 187:196 ) REMARK 3 ORIGIN FOR THE GROUP (A): 25.126 -9.685 11.106 REMARK 3 T TENSOR REMARK 3 T11: 0.3253 T22: 0.1987 REMARK 3 T33: 0.1637 T12: 0.0881 REMARK 3 T13: -0.0029 T23: -0.0421 REMARK 3 L TENSOR REMARK 3 L11: 7.7137 L22: 6.5196 REMARK 3 L33: 5.2448 L12: 3.4614 REMARK 3 L13: -1.5255 L23: 2.1363 REMARK 3 S TENSOR REMARK 3 S11: 0.0348 S12: 0.5675 S13: -0.4055 REMARK 3 S21: -0.2831 S22: 0.0579 S23: 0.0872 REMARK 3 S31: 0.3960 S32: 0.1874 S33: -0.0547 REMARK 3 TLS GROUP : 10 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): 23.796 1.217 4.296 REMARK 3 T TENSOR REMARK 3 T11: 0.3313 T22: 0.2991 REMARK 3 T33: 0.1515 T12: 0.0824 REMARK 3 T13: 0.0711 T23: 0.0262 REMARK 3 L TENSOR REMARK 3 L11: 2.1688 L22: 6.5897 REMARK 3 L33: 3.0576 L12: -1.6354 REMARK 3 L13: 2.4246 L23: -0.5138 REMARK 3 S TENSOR REMARK 3 S11: 0.1171 S12: 0.3082 S13: 0.1486 REMARK 3 S21: -0.6255 S22: -0.3811 S23: -0.4479 REMARK 3 S31: 0.0302 S32: 0.3068 S33: 0.2851 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: ( CHAIN C AND RESID 1:6 ) REMARK 3 ORIGIN FOR THE GROUP (A): 16.401 3.606 2.923 REMARK 3 T TENSOR REMARK 3 T11: 0.4334 T22: 0.2487 REMARK 3 T33: 0.1466 T12: 0.0818 REMARK 3 T13: -0.0154 T23: 0.0095 REMARK 3 L TENSOR REMARK 3 L11: 1.7882 L22: 3.2224 REMARK 3 L33: 4.3203 L12: -1.5401 REMARK 3 L13: -2.7136 L23: 1.7154 REMARK 3 S TENSOR REMARK 3 S11: 0.0444 S12: 0.1934 S13: -0.0782 REMARK 3 S21: -0.8099 S22: -0.3737 S23: 0.1512 REMARK 3 S31: -0.6791 S32: -0.2573 S33: 0.3142 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 6DPD 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_1000235018. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-DEC-16 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 : 32500 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.460 REMARK 200 RESOLUTION RANGE LOW (A) : 19.840 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 1.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.46 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.48 REMARK 200 COMPLETENESS FOR SHELL (%) : 88.3 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 (%): 49.27 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.42 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 40.66200 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.99400 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 40.66200 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 18.99400 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: 5960 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8360 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -41.0 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 400 REMARK 400 COMPOUND REMARK 400 NOTE THAT CHAIN B WAS SPLIT INTO 2 CHAINS (B AND B) AT THE POSITION REMARK 400 4-5, WHERE THE CLEAVAGE OCCURS 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 -0.114 REMARK 500 DG C 2 O3' DG C 2 C3' -0.041 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 2 O4' - C1' - N9 ANGL. DEV. = 2.1 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 452 DISTANCE = 5.89 ANGSTROMS REMARK 525 HOH A 453 DISTANCE = 5.96 ANGSTROMS REMARK 525 HOH A 454 DISTANCE = 6.56 ANGSTROMS REMARK 525 HOH A 455 DISTANCE = 6.77 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 MN A 201 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 71 OD2 REMARK 620 2 ASP A 192 OD1 111.3 REMARK 620 3 HOH A 321 O 84.9 85.0 REMARK 620 4 HOH A 359 O 90.5 86.3 167.9 REMARK 620 5 C b 5 OP3 152.4 96.2 94.7 94.5 REMARK 620 6 C b 5 OP1 93.3 154.1 105.8 85.6 60.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 202 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 71 OD1 REMARK 620 2 GLU A 109 OE1 98.5 REMARK 620 3 ASP A 132 OD1 132.5 93.7 REMARK 620 4 ASP A 132 OD2 102.3 149.5 55.8 REMARK 620 5 C b 5 OP1 99.5 110.9 118.5 87.6 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 204 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 163 OD1 REMARK 620 2 GLU A 166 OE1 99.0 REMARK 620 3 HOH A 343 O 103.4 156.8 REMARK 620 4 HOH A 346 O 93.3 87.7 96.9 REMARK 620 5 HOH A 361 O 172.1 87.7 69.6 91.2 REMARK 620 6 HOH A 415 O 87.8 99.8 75.3 172.2 86.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 206 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 188 OE2 REMARK 620 2 HOH A 371 O 67.0 REMARK 620 3 HOH B 211 O 122.8 128.1 REMARK 620 4 C b 5 OP2 105.6 127.3 100.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 205 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS A 196 O REMARK 620 2 HOH C 105 O 83.8 REMARK 620 3 HOH C 106 O 174.1 90.6 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 203 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 207 O REMARK 620 2 C b 5 OP3 105.9 REMARK 620 3 G b 6 OP2 65.5 93.0 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B 101 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 314 O REMARK 620 2 HOH B 212 O 101.4 REMARK 620 3 G b 6 O6 94.2 99.4 REMARK 620 4 HOH C 103 O 77.6 167.4 93.3 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 MN A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K 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 IOD A 209 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 211 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 212 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 213 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 214 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 215 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 216 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 217 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PGE A 218 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN B 101 DBREF 6DPD A 61 196 UNP Q9KEI9 RNH1_BACHD 61 196 DBREF 6DPD B 1 4 PDB 6DPD 6DPD 1 4 DBREF 6DPD b 5 6 PDB 6DPD 6DPD 5 6 DBREF 6DPD C 1 6 PDB 6DPD 6DPD 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 MN A 201 1 HET MN A 202 1 HET MN A 203 1 HET MN A 204 1 HET MN A 205 1 HET K A 206 1 HET IOD A 207 1 HET IOD A 208 1 HET IOD A 209 1 HET IOD A 210 1 HET GOL A 211 6 HET GOL A 212 6 HET GOL A 213 6 HET EDO A 214 4 HET EDO A 215 4 HET EDO A 216 4 HET EDO A 217 4 HET PGE A 218 10 HET MN B 101 1 HET IOD B 102 1 HETNAM MN MANGANESE (II) ION HETNAM K POTASSIUM ION HETNAM IOD IODIDE ION HETNAM GOL GLYCEROL HETNAM EDO 1,2-ETHANEDIOL HETNAM PGE TRIETHYLENE GLYCOL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 5 MN 6(MN 2+) FORMUL 10 K K 1+ FORMUL 11 IOD 5(I 1-) FORMUL 15 GOL 3(C3 H8 O3) FORMUL 18 EDO 4(C2 H6 O2) FORMUL 22 PGE C6 H14 O4 FORMUL 25 HOH *186(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 THR A 155 HIS A 172 1 18 HELIX 4 AA4 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 OD2 ASP A 71 MN MN A 201 1555 1555 2.05 LINK OD1 ASP A 71 MN MN A 202 1555 1555 2.03 LINK OE1 GLU A 109 MN MN A 202 1555 1555 2.11 LINK OD1 ASP A 132 MN MN A 202 1555 1555 2.09 LINK OD2 ASP A 132 MN MN A 202 1555 1555 2.52 LINK OD1 ASP A 163 MN MN A 204 1555 1555 2.48 LINK OE1 GLU A 166 MN MN A 204 1555 1555 2.09 LINK OE2 GLU A 188 K K A 206 1555 1555 2.99 LINK OD1 ASP A 192 MN MN A 201 1555 1555 2.09 LINK O LYS A 196 MN MN A 205 1555 1555 2.25 LINK MN MN A 201 O HOH A 321 1555 1555 2.18 LINK MN MN A 201 O HOH A 359 1555 1555 2.05 LINK MN MN A 201 OP3 C b 5 1555 1555 2.14 LINK MN MN A 201 OP1 C b 5 1555 1555 2.59 LINK MN MN A 202 OP1 C b 5 1555 1555 1.98 LINK MN B MN A 203 O HOH B 207 1555 1555 2.71 LINK MN B MN A 203 OP3 C b 5 1555 1555 2.11 LINK MN B MN A 203 OP2 G b 6 1555 1555 2.45 LINK MN MN A 204 O HOH A 343 1555 4556 2.24 LINK MN MN A 204 O HOH A 346 1555 1555 2.42 LINK MN MN A 204 O HOH A 361 1555 4556 2.04 LINK MN MN A 204 O HOH A 415 1555 1555 2.19 LINK MN MN A 205 O HOH C 105 1555 4545 2.20 LINK MN MN A 205 O HOH C 106 1555 4545 2.05 LINK K K A 206 O HOH A 371 1555 1555 3.32 LINK K K A 206 O HOH B 211 1555 1555 2.62 LINK K K A 206 OP2 C b 5 1555 1555 2.72 LINK O HOH A 314 MN MN B 101 1555 1555 2.56 LINK MN MN B 101 O HOH B 212 1555 1555 2.47 LINK MN MN B 101 O6 G b 6 1555 1555 2.71 LINK MN MN B 101 O HOH C 103 1555 4545 2.27 CISPEP 1 ASN A 77 PRO A 78 0 1.98 SITE 1 AC1 5 ASP A 71 ASP A 192 HOH A 321 HOH A 359 SITE 2 AC1 5 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 5 ASP A 192 LYS A 196 HOH B 207 C b 5 SITE 2 AC3 5 G b 6 SITE 1 AC4 6 ASP A 163 GLU A 166 HOH A 343 HOH A 346 SITE 2 AC4 6 HOH A 361 HOH A 415 SITE 1 AC5 4 LYS A 196 HOH A 392 HOH C 105 HOH C 106 SITE 1 AC6 4 GLU A 188 U B 4 HOH B 211 C b 5 SITE 1 AC7 1 TYR A 83 SITE 1 AC8 3 ILE A 64 HOH A 449 HOH A 454 SITE 1 AC9 6 GLY A 76 ASN A 77 PRO A 78 HOH A 309 SITE 2 AC9 6 DG C 2 DA C 3 SITE 1 AD1 6 HIS A 115 TYR A 119 ARG A 123 GLU A 167 SITE 2 AD1 6 ASN A 170 GOL A 213 SITE 1 AD2 5 HIS A 115 ARG A 118 ASN A 170 GOL A 212 SITE 2 AD2 5 HOH A 302 SITE 1 AD3 4 LYS A 143 THR A 173 TYR A 174 HOH A 304 SITE 1 AD4 3 THR A 148 DT C 4 DG C 5 SITE 1 AD5 3 GLU A 66 LYS A 127 HOH A 370 SITE 1 AD6 5 GLU A 62 ILE A 63 TRP A 65 ARG A 151 SITE 2 AD6 5 HOH A 385 SITE 1 AD7 7 THR A 148 LEU A 149 VAL A 150 ASN A 152 SITE 2 AD7 7 GLU A 154 HOH A 310 HOH C 107 SITE 1 AD8 5 HOH A 314 HOH B 210 HOH B 212 HOH C 103 SITE 2 AD8 5 G b 6 CRYST1 81.324 37.988 61.323 90.00 96.32 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 0.012296 0.000000 0.001363 0.00000 SCALE2 0.000000 0.026324 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016407 0.00000