HEADER HYDROLASE/DNA/RNA 09-JUN-18 6DOF 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 540 S TITLE 3 AT 21 C COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBONUCLEASE H; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CATALYTIC DOMAIN; COMPND 5 SYNONYM: RNASE H; COMPND 6 EC: 3.1.26.4; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: RNA (5'-R(*AP*CP*AP*U)-3'); COMPND 10 CHAIN: B; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: RNA (5'-R(P*CP*G)-3'); COMPND 14 CHAIN: b; COMPND 15 ENGINEERED: YES; COMPND 16 MOL_ID: 4; COMPND 17 MOLECULE: DNA (5'-D(*CP*GP*AP*TP*GP*T)-3'); COMPND 18 CHAIN: C; COMPND 19 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS HALODURANS; SOURCE 3 ORGANISM_TAXID: 272558; SOURCE 4 STRAIN: ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125; SOURCE 5 GENE: RNHA, BH0863; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET15B; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 14 ORGANISM_TAXID: 32630; SOURCE 15 MOL_ID: 3; SOURCE 16 SYNTHETIC: YES; SOURCE 17 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 18 ORGANISM_TAXID: 32630; SOURCE 19 MOL_ID: 4; SOURCE 20 SYNTHETIC: YES; SOURCE 21 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 22 ORGANISM_TAXID: 32630 KEYWDS PROTEIN-RNA-DNA COMPLEX, DOUBLE HELIX, RNA HYDROLYSIS, IN CRYSTALLO KEYWDS 2 CATALYSIS, METAL DEPENDENT CATALYSIS, MONOVALENT CATIONS, DIVALENT KEYWDS 3 CATIONS, HYDROLASE, HYDROLASE-DNA-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR N.L.SAMARA,W.YANG REVDAT 2 13-MAR-24 6DOF 1 LINK REVDAT 1 15-AUG-18 6DOF 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. 1.43 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) : 1.43 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.06 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 34641 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.162 REMARK 3 R VALUE (WORKING SET) : 0.161 REMARK 3 FREE R VALUE : 0.187 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.860 REMARK 3 FREE R VALUE TEST SET COUNT : 1684 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 31.0681 - 3.2800 0.93 2689 143 0.1431 0.1789 REMARK 3 2 3.2800 - 2.6039 0.98 2770 146 0.1567 0.1810 REMARK 3 3 2.6039 - 2.2749 0.99 2757 158 0.1586 0.1726 REMARK 3 4 2.2749 - 2.0669 0.99 2811 118 0.1518 0.1867 REMARK 3 5 2.0669 - 1.9188 1.00 2795 136 0.1584 0.1675 REMARK 3 6 1.9188 - 1.8057 1.00 2755 133 0.1661 0.1751 REMARK 3 7 1.8057 - 1.7152 1.00 2776 146 0.1683 0.1969 REMARK 3 8 1.7152 - 1.6406 1.00 2789 130 0.1782 0.2269 REMARK 3 9 1.6406 - 1.5774 1.00 2771 153 0.1850 0.1972 REMARK 3 10 1.5774 - 1.5230 1.00 2735 156 0.1997 0.2182 REMARK 3 11 1.5230 - 1.4754 1.00 2809 138 0.2325 0.2489 REMARK 3 12 1.4754 - 1.4332 0.91 2500 127 0.2765 0.3004 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) : 0.140 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.200 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.13 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 1514 REMARK 3 ANGLE : 1.126 2062 REMARK 3 CHIRALITY : 0.077 225 REMARK 3 PLANARITY : 0.007 213 REMARK 3 DIHEDRAL : 23.902 593 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 9 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ( CHAIN A AND RESID 61:87 ) REMARK 3 ORIGIN FOR THE GROUP (A): 25.635 -5.582 17.561 REMARK 3 T TENSOR REMARK 3 T11: 0.1440 T22: 0.0868 REMARK 3 T33: 0.1425 T12: 0.0182 REMARK 3 T13: 0.0126 T23: 0.0090 REMARK 3 L TENSOR REMARK 3 L11: 5.9598 L22: 1.5238 REMARK 3 L33: 3.4683 L12: -1.3759 REMARK 3 L13: 1.4194 L23: -0.3187 REMARK 3 S TENSOR REMARK 3 S11: 0.2646 S12: 0.2412 S13: -0.1995 REMARK 3 S21: -0.1902 S22: -0.1533 S23: -0.1078 REMARK 3 S31: 0.3243 S32: 0.1376 S33: -0.0793 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: ( CHAIN A AND RESID 88:96 ) REMARK 3 ORIGIN FOR THE GROUP (A): 28.336 -11.545 24.151 REMARK 3 T TENSOR REMARK 3 T11: 0.2051 T22: 0.1334 REMARK 3 T33: 0.2682 T12: 0.0581 REMARK 3 T13: 0.0028 T23: 0.0271 REMARK 3 L TENSOR REMARK 3 L11: 8.5207 L22: 4.8502 REMARK 3 L33: 5.7200 L12: -2.2141 REMARK 3 L13: -3.9895 L23: 0.3199 REMARK 3 S TENSOR REMARK 3 S11: -0.1277 S12: -0.2344 S13: -1.2214 REMARK 3 S21: -0.0467 S22: 0.0577 S23: -0.4249 REMARK 3 S31: 0.7217 S32: 0.4472 S33: 0.0488 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: ( CHAIN A AND RESID 97:133 ) REMARK 3 ORIGIN FOR THE GROUP (A): 21.774 -1.209 23.578 REMARK 3 T TENSOR REMARK 3 T11: 0.0813 T22: 0.0735 REMARK 3 T33: 0.1000 T12: 0.0105 REMARK 3 T13: 0.0155 T23: 0.0046 REMARK 3 L TENSOR REMARK 3 L11: 3.4093 L22: 1.0205 REMARK 3 L33: 2.9100 L12: -0.1421 REMARK 3 L13: 1.3037 L23: 0.3286 REMARK 3 S TENSOR REMARK 3 S11: 0.0836 S12: -0.1833 S13: -0.1126 REMARK 3 S21: -0.0269 S22: -0.0812 S23: 0.0373 REMARK 3 S31: 0.0390 S32: -0.2713 S33: 0.0005 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: ( CHAIN A AND RESID 134:142 ) REMARK 3 ORIGIN FOR THE GROUP (A): 23.876 9.406 16.749 REMARK 3 T TENSOR REMARK 3 T11: 0.2508 T22: 0.0876 REMARK 3 T33: 0.1613 T12: 0.0104 REMARK 3 T13: 0.0385 T23: 0.0361 REMARK 3 L TENSOR REMARK 3 L11: 3.2155 L22: 5.2530 REMARK 3 L33: 5.1747 L12: -3.0709 REMARK 3 L13: -0.5199 L23: -0.3803 REMARK 3 S TENSOR REMARK 3 S11: 0.2659 S12: 0.1071 S13: 0.4583 REMARK 3 S21: -0.0964 S22: -0.1614 S23: -0.2056 REMARK 3 S31: -0.9572 S32: 0.0165 S33: -0.0628 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: ( CHAIN A AND RESID 143:155 ) REMARK 3 ORIGIN FOR THE GROUP (A): 8.477 7.301 16.335 REMARK 3 T TENSOR REMARK 3 T11: 0.3418 T22: 0.4262 REMARK 3 T33: 0.2186 T12: 0.2368 REMARK 3 T13: -0.0291 T23: -0.0932 REMARK 3 L TENSOR REMARK 3 L11: 5.3517 L22: 2.3192 REMARK 3 L33: 2.0840 L12: 0.2304 REMARK 3 L13: 2.1290 L23: -0.3270 REMARK 3 S TENSOR REMARK 3 S11: 0.1964 S12: 0.0360 S13: 0.4766 REMARK 3 S21: -0.1341 S22: -0.3220 S23: 0.3880 REMARK 3 S31: -0.4587 S32: -0.7492 S33: 0.2240 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: ( CHAIN A AND RESID 156:169 ) REMARK 3 ORIGIN FOR THE GROUP (A): 12.433 5.645 25.052 REMARK 3 T TENSOR REMARK 3 T11: 0.1438 T22: 0.2238 REMARK 3 T33: 0.1422 T12: 0.0749 REMARK 3 T13: 0.0254 T23: -0.0302 REMARK 3 L TENSOR REMARK 3 L11: 8.3798 L22: 2.4283 REMARK 3 L33: 6.8281 L12: 0.7194 REMARK 3 L13: 6.4032 L23: 1.5690 REMARK 3 S TENSOR REMARK 3 S11: 0.1749 S12: -0.2343 S13: 0.0633 REMARK 3 S21: -0.0440 S22: -0.2888 S23: 0.1995 REMARK 3 S31: -0.1130 S32: -0.7059 S33: 0.1018 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: ( CHAIN A AND RESID 170:196 ) REMARK 3 ORIGIN FOR THE GROUP (A): 28.999 -0.783 17.941 REMARK 3 T TENSOR REMARK 3 T11: 0.1160 T22: 0.1086 REMARK 3 T33: 0.0906 T12: 0.0388 REMARK 3 T13: 0.0017 T23: 0.0275 REMARK 3 L TENSOR REMARK 3 L11: 3.1867 L22: 2.8337 REMARK 3 L33: 5.0131 L12: -0.3083 REMARK 3 L13: -0.7039 L23: 1.1060 REMARK 3 S TENSOR REMARK 3 S11: 0.0723 S12: 0.3123 S13: -0.1155 REMARK 3 S21: -0.3605 S22: -0.0123 S23: -0.1768 REMARK 3 S31: 0.0524 S32: 0.1711 S33: -0.0915 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: ( CHAIN B AND RESID 1:4 ) OR ( CHAIN B AND RESID 5:6 REMARK 3 ) REMARK 3 ORIGIN FOR THE GROUP (A): 23.776 0.764 5.256 REMARK 3 T TENSOR REMARK 3 T11: 0.3095 T22: 0.2525 REMARK 3 T33: 0.1475 T12: 0.0514 REMARK 3 T13: 0.0219 T23: 0.0189 REMARK 3 L TENSOR REMARK 3 L11: 3.7284 L22: 7.0339 REMARK 3 L33: 0.4481 L12: 1.4477 REMARK 3 L13: 1.1679 L23: -0.1487 REMARK 3 S TENSOR REMARK 3 S11: -0.2099 S12: 0.0783 S13: -0.1826 REMARK 3 S21: -0.7375 S22: -0.0578 S23: -0.2733 REMARK 3 S31: 0.1123 S32: -0.0332 S33: 0.2892 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: ( CHAIN C AND RESID 1:6 ) REMARK 3 ORIGIN FOR THE GROUP (A): 16.443 3.464 3.366 REMARK 3 T TENSOR REMARK 3 T11: 0.4251 T22: 0.2424 REMARK 3 T33: 0.1564 T12: 0.0716 REMARK 3 T13: -0.0400 T23: 0.0006 REMARK 3 L TENSOR REMARK 3 L11: 3.3747 L22: 2.7440 REMARK 3 L33: 4.3987 L12: -1.0868 REMARK 3 L13: -2.4955 L23: 1.4737 REMARK 3 S TENSOR REMARK 3 S11: -0.2291 S12: 0.3807 S13: -0.1970 REMARK 3 S21: -0.9671 S22: -0.2426 S23: 0.2278 REMARK 3 S31: -0.3802 S32: -0.2150 S33: 0.4692 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 6DOF 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_1000234963. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-JUL-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.31 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34647 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.430 REMARK 200 RESOLUTION RANGE LOW (A) : 31.060 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 200 DATA REDUNDANCY : 1.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.43 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.46 REMARK 200 COMPLETENESS FOR SHELL (%) : 86.5 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: 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 (%): 50.41 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 40.91950 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.94450 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 40.91950 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 18.94450 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6970 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7480 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -28.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, b, C REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A 55 REMARK 465 SER A 56 REMARK 465 HIS A 57 REMARK 465 MET A 58 REMARK 465 ALA A 59 REMARK 465 LYS A 60 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 A B 1 O2' REMARK 470 G b 6 O2' REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O2 EDO A 211 O1 GOL A 215 1.26 REMARK 500 OE2 GLU A 175 O HOH A 301 2.12 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 301 O HOH A 301 2656 1.61 REMARK 500 O HOH A 410 O HOH A 410 2656 1.84 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 C b 5 P C b 5 OP3 -0.130 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. = -5.9 DEGREES REMARK 500 DG C 2 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 458 DISTANCE = 6.23 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 104.4 REMARK 620 3 HOH A 302 O 175.9 75.6 REMARK 620 4 HOH A 305 O 89.1 92.9 86.8 REMARK 620 5 HOH A 318 O 87.4 87.5 96.7 176.5 REMARK 620 6 C b 5 OP3 163.1 92.5 17.7 91.1 92.4 REMARK 620 7 C b 5 OP1 98.3 156.3 82.3 94.3 86.7 64.8 REMARK 620 8 C b 5 OP1 99.9 153.7 81.0 97.6 83.6 63.4 3.6 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 97.0 REMARK 620 3 ASP A 132 OD1 126.3 98.9 REMARK 620 4 ASP A 132 OD2 98.6 151.5 52.8 REMARK 620 5 U B 4 O3' 152.6 91.1 77.7 85.9 REMARK 620 6 C b 5 OP1 90.6 109.3 130.2 94.3 62.1 REMARK 620 7 C b 5 OP1 90.0 114.5 127.3 89.2 62.9 5.2 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 217 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 132 OD2 REMARK 620 2 HOH A 318 O 45.0 REMARK 620 3 HOH A 361 O 54.8 60.9 REMARK 620 4 HOH B 208 O 157.6 154.2 116.7 REMARK 620 5 C b 5 OP2 84.6 71.0 130.9 110.8 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 203 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 192 OD1 REMARK 620 2 ASP A 192 OD2 40.0 REMARK 620 3 HOH A 302 O 50.2 82.4 REMARK 620 4 HOH A 305 O 58.5 96.3 52.3 REMARK 620 5 HOH A 324 O 75.5 50.8 82.1 128.9 REMARK 620 6 G b 6 OP2 100.6 140.3 60.8 50.2 129.5 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 431 O REMARK 620 2 DT C 4 O4 93.4 REMARK 620 3 DG C 5 O6 161.0 70.5 REMARK 620 4 HOH C 208 O 83.6 83.2 84.6 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 206 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 208 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 209 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 210 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 211 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 212 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 213 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 214 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 215 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PGE A 216 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K A 217 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K C 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL C 102 DBREF 6DOF A 59 196 UNP Q9KEI9 RNH1_BACHD 59 196 DBREF 6DOF B 1 4 PDB 6DOF 6DOF 1 4 DBREF 6DOF b 5 6 PDB 6DOF 6DOF 5 6 DBREF 6DOF C 1 6 PDB 6DOF 6DOF 1 6 SEQADV 6DOF GLY A 55 UNP Q9KEI9 EXPRESSION TAG SEQADV 6DOF SER A 56 UNP Q9KEI9 EXPRESSION TAG SEQADV 6DOF HIS A 57 UNP Q9KEI9 EXPRESSION TAG SEQADV 6DOF MET A 58 UNP Q9KEI9 EXPRESSION TAG SEQRES 1 A 142 GLY SER HIS MET ALA LYS GLU GLU ILE ILE TRP GLU SER SEQRES 2 A 142 LEU SER VAL ASP VAL GLY SER GLN GLY ASN PRO GLY ILE SEQRES 3 A 142 VAL GLU TYR LYS GLY VAL ASP THR LYS THR GLY GLU VAL SEQRES 4 A 142 LEU PHE GLU ARG GLU PRO ILE PRO ILE GLY THR ASN ASN SEQRES 5 A 142 MET GLY GLU PHE LEU ALA ILE VAL HIS GLY LEU ARG TYR SEQRES 6 A 142 LEU LYS GLU ARG ASN SER ARG LYS PRO ILE TYR SER ASP SEQRES 7 A 142 SER GLN THR ALA ILE LYS TRP VAL LYS ASP LYS LYS ALA SEQRES 8 A 142 LYS SER THR LEU VAL ARG ASN GLU GLU THR ALA LEU ILE SEQRES 9 A 142 TRP LYS LEU VAL ASP GLU ALA GLU GLU TRP LEU ASN THR SEQRES 10 A 142 HIS THR TYR GLU THR PRO ILE LEU LYS TRP GLN THR ASP SEQRES 11 A 142 LYS TRP GLY GLU ILE LYS ALA ASP TYR GLY ARG LYS SEQRES 1 B 4 A C A U SEQRES 1 b 2 C G SEQRES 1 C 6 DC DG DA DT DG DT HET MG A 201 1 HET MG A 202 1 HET K A 203 1 HET IOD A 204 1 HET IOD A 205 1 HET IOD A 206 1 HET IOD A 207 1 HET EDO A 208 4 HET EDO A 209 4 HET EDO A 210 4 HET EDO A 211 4 HET GOL A 212 6 HET GOL A 213 6 HET GOL A 214 6 HET GOL A 215 6 HET PGE A 216 10 HET K A 217 1 HET K C 101 1 HET GOL C 102 6 HETNAM MG MAGNESIUM ION HETNAM K POTASSIUM ION HETNAM IOD IODIDE ION HETNAM EDO 1,2-ETHANEDIOL HETNAM GOL GLYCEROL HETNAM PGE TRIETHYLENE GLYCOL HETSYN EDO ETHYLENE GLYCOL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 5 MG 2(MG 2+) FORMUL 7 K 3(K 1+) FORMUL 8 IOD 4(I 1-) FORMUL 12 EDO 4(C2 H6 O2) FORMUL 16 GOL 5(C3 H8 O3) FORMUL 20 PGE C6 H14 O4 FORMUL 24 HOH *196(H2 O) HELIX 1 AA1 THR A 104 ARG A 123 1 20 HELIX 2 AA2 SER A 133 LYS A 143 1 11 HELIX 3 AA3 THR A 155 ASN A 170 1 16 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 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 2.04 LINK OE1 GLU A 109 MG MG A 202 1555 1555 2.04 LINK OD1 ASP A 132 MG MG A 202 1555 1555 2.09 LINK OD2 ASP A 132 MG MG A 202 1555 1555 2.66 LINK OD2 ASP A 132 K B K A 217 1555 1555 3.31 LINK OD1 ASP A 192 MG MG A 201 1555 1555 2.08 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 3.36 LINK MG MG A 201 O CHOH A 302 1555 1555 2.02 LINK MG MG A 201 O HOH A 305 1555 1555 2.09 LINK MG MG A 201 O HOH A 318 1555 1555 2.11 LINK MG MG A 201 OP3B C b 5 1555 1555 2.02 LINK MG MG A 201 OP1B C b 5 1555 1555 2.39 LINK MG MG A 201 OP1C C b 5 1555 1555 2.25 LINK MG MG A 202 O3'C U B 4 1555 1555 2.61 LINK MG MG A 202 OP1B C b 5 1555 1555 2.07 LINK MG MG A 202 OP1C C b 5 1555 1555 2.13 LINK K C K A 203 O CHOH A 302 1555 1555 3.08 LINK K C K A 203 O HOH A 305 1555 1555 3.31 LINK K C K A 203 O HOH A 324 1555 1555 2.61 LINK K C K A 203 OP2 G b 6 1555 1555 2.86 LINK K B K A 217 O HOH A 318 1555 1555 3.49 LINK K B K A 217 O HOH A 361 1555 1555 3.36 LINK K B K A 217 O HOH B 208 1555 1555 2.60 LINK K B K A 217 OP2B C b 5 1555 1555 2.56 LINK O HOH A 431 K A K C 101 4555 1555 3.44 LINK O4 DT C 4 K A K C 101 1555 1555 3.44 LINK O6 DG C 5 K A K C 101 1555 1555 2.58 LINK K A K C 101 O HOH C 208 1555 1555 3.11 CISPEP 1 ASN A 77 PRO A 78 0 -1.31 SITE 1 AC1 6 ASP A 71 ASP A 192 HOH A 302 HOH A 305 SITE 2 AC1 6 HOH A 318 C b 5 SITE 1 AC2 5 ASP A 71 GLU A 109 ASP A 132 U B 4 SITE 2 AC2 5 C b 5 SITE 1 AC3 8 ASP A 192 GLY A 194 ARG A 195 LYS A 196 SITE 2 AC3 8 HOH A 302 HOH A 324 C b 5 G b 6 SITE 1 AC4 1 TYR A 83 SITE 1 AC5 1 PGE A 216 SITE 1 AC6 3 ILE A 64 HOH A 426 HOH A 458 SITE 1 AC7 5 LYS A 143 THR A 173 TYR A 174 HOH A 303 SITE 2 AC7 5 HOH A 396 SITE 1 AC8 5 THR A 148 HOH A 312 DT C 4 DG C 5 SITE 2 AC8 5 HOH C 202 SITE 1 AC9 4 ILE A 80 PRO A 99 HOH A 355 HOH A 359 SITE 1 AD1 6 TRP A 65 GLU A 66 SER A 67 ASP A 87 SITE 2 AD1 6 LYS A 127 GOL A 215 SITE 1 AD2 5 HIS A 115 ARG A 118 ASN A 170 GOL A 213 SITE 2 AD2 5 HOH A 306 SITE 1 AD3 9 HIS A 115 TYR A 119 GLU A 122 ARG A 123 SITE 2 AD3 9 GLU A 167 ASN A 170 GOL A 212 HOH A 389 SITE 3 AD3 9 HOH A 401 SITE 1 AD4 7 PRO A 78 ILE A 102 VAL A 150 ASN A 152 SITE 2 AD4 7 GLU A 154 HOH A 313 HOH C 209 SITE 1 AD5 5 GLU A 66 SER A 125 LYS A 127 EDO A 211 SITE 2 AD5 5 HOH A 325 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 411 SITE 3 AD6 11 A B 3 U B 4 HOH B 204 SITE 1 AD7 5 ASP A 132 HOH A 316 U B 4 HOH B 208 SITE 2 AD7 5 C b 5 SITE 1 AD8 3 DT C 4 DG C 5 HOH C 212 SITE 1 AD9 7 GLY A 76 ASN A 77 HOH B 207 DG C 2 SITE 2 AD9 7 DA C 3 HOH C 211 HOH C 215 CRYST1 81.839 37.889 62.494 90.00 96.26 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 0.012219 0.000000 0.001340 0.00000 SCALE2 0.000000 0.026393 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016097 0.00000