HEADER ANTITOXIN 10-JAN-22 7TH0 TITLE ESCHERICHIA COLI RPNA-S COMPND MOL_ID: 1; COMPND 2 MOLECULE: RECOMBINATION-PROMOTING NUCLEASE RPNA; COMPND 3 CHAIN: A; COMPND 4 EC: 3.1.21.-; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI STR. K-12 SUBSTR. MG1655; SOURCE 3 ORGANISM_TAXID: 511145; SOURCE 4 STRAIN: K-12; SOURCE 5 GENE: RPNA, YHGA, B3411, JW3374; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TOXIN-ANTITOXIN PHAGE DEFENSE ENDONUCLEASE ABORTIVE INFECTION, KEYWDS 2 ANTITOXIN EXPDTA X-RAY DIFFRACTION AUTHOR A.ZHONG,A.B.HICKMAN,G.STORZ,F.DYDA REVDAT 3 15-NOV-23 7TH0 1 REMARK REVDAT 2 25-OCT-23 7TH0 1 JRNL REVDAT 1 29-MAR-23 7TH0 0 JRNL AUTH A.ZHONG,X.JIANG,A.B.HICKMAN,K.KLIER,G.I.C.TEODORO,F.DYDA, JRNL AUTH 2 M.T.LAUB,G.STORZ JRNL TITL TOXIC ANTIPHAGE DEFENSE PROTEINS INHIBITED BY INTRAGENIC JRNL TITL 2 ANTITOXIN PROTEINS. JRNL REF PROC.NATL.ACAD.SCI.USA V. 120 82120 2023 JRNL REFN ESSN 1091-6490 JRNL PMID 37487082 JRNL DOI 10.1073/PNAS.2307382120 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2_3874 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.36 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.020 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 3573 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.226 REMARK 3 R VALUE (WORKING SET) : 0.225 REMARK 3 FREE R VALUE : 0.247 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.020 REMARK 3 FREE R VALUE TEST SET COUNT : 108 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 19.3600 - 1.9000 1.00 3465 108 0.2250 0.2470 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.20 REMARK 3 SHRINKAGE RADIUS : 1.00 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.000 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.290 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 55.08 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 244 THROUGH 268 ) REMARK 3 ORIGIN FOR THE GROUP (A): 15.2467 33.8748 9.7278 REMARK 3 T TENSOR REMARK 3 T11: 0.3153 T22: 0.3907 REMARK 3 T33: 0.4119 T12: -0.0100 REMARK 3 T13: 0.0264 T23: -0.0180 REMARK 3 L TENSOR REMARK 3 L11: 4.9404 L22: 5.3501 REMARK 3 L33: 4.4457 L12: 0.7732 REMARK 3 L13: 1.1809 L23: -2.8503 REMARK 3 S TENSOR REMARK 3 S11: 0.0750 S12: -0.1881 S13: 0.1439 REMARK 3 S21: 0.6074 S22: -0.1818 S23: 0.6817 REMARK 3 S31: 0.0185 S32: -0.3370 S33: 0.4585 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 269 THROUGH 280 ) REMARK 3 ORIGIN FOR THE GROUP (A): 13.2035 18.2997 12.1006 REMARK 3 T TENSOR REMARK 3 T11: 0.6222 T22: 0.2783 REMARK 3 T33: 0.5104 T12: -0.2883 REMARK 3 T13: -0.1021 T23: 0.1251 REMARK 3 L TENSOR REMARK 3 L11: 5.9678 L22: 3.1568 REMARK 3 L33: 1.4194 L12: 3.0600 REMARK 3 L13: 1.8249 L23: 2.1090 REMARK 3 S TENSOR REMARK 3 S11: 0.8535 S12: -1.6290 S13: -1.4248 REMARK 3 S21: 0.4262 S22: -0.4496 S23: 0.3889 REMARK 3 S31: 1.9266 S32: -1.0468 S33: 0.2342 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 281 THROUGH 289 ) REMARK 3 ORIGIN FOR THE GROUP (A): 5.5850 26.0801 11.7981 REMARK 3 T TENSOR REMARK 3 T11: 0.6392 T22: 0.5113 REMARK 3 T33: 1.1114 T12: -0.0794 REMARK 3 T13: 0.2139 T23: -0.0457 REMARK 3 L TENSOR REMARK 3 L11: 5.1904 L22: 6.5332 REMARK 3 L33: 4.0765 L12: 1.2454 REMARK 3 L13: -0.6832 L23: 0.9431 REMARK 3 S TENSOR REMARK 3 S11: 0.6007 S12: -1.9258 S13: 0.6763 REMARK 3 S21: 1.0966 S22: -0.3103 S23: 3.5175 REMARK 3 S31: 0.3064 S32: -1.2312 S33: -0.1623 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7TH0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-JAN-22. REMARK 100 THE DEPOSITION ID IS D_1000262188. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-JUN-21 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : 8.3-9.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU FR-X REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 S 4M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 3582 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 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 (%) : 99.8 REMARK 200 DATA REDUNDANCY : 13.48 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 43.4600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.91 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.95 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL 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: SAD 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 (%): 38.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.99 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.5M LICL 0.1M TRIS HCL 30% PEG 6K 5 REMARK 280 MM FE(III)CL, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 19.35500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 19.35500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 19.01000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 29.13500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 19.01000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 29.13500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 19.35500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 19.01000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 29.13500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 19.35500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 19.01000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 29.13500 REMARK 290 SMTRY3 8 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1570 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5950 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 38.02000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 19.35500 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 ALA A 290 REMARK 465 SER A 291 REMARK 465 GLN A 292 DBREF 7TH0 A 244 292 UNP P31667 RPNA_ECOLI 244 292 SEQRES 1 A 49 MSE THR ILE ALA GLU ARG LEU ARG GLN GLU GLY GLU GLN SEQRES 2 A 49 SER LYS ALA LEU HIS ILE ALA LYS ILE MSE LEU GLU SER SEQRES 3 A 49 GLY VAL PRO LEU ALA ASP ILE MSE ARG PHE THR GLY LEU SEQRES 4 A 49 SER GLU GLU GLU LEU ALA ALA ALA SER GLN MODRES 7TH0 MSE A 244 MET MODIFIED RESIDUE MODRES 7TH0 MSE A 266 MET MODIFIED RESIDUE MODRES 7TH0 MSE A 277 MET MODIFIED RESIDUE HET MSE A 244 8 HET MSE A 266 8 HET MSE A 277 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 3(C5 H11 N O2 SE) FORMUL 2 HOH *8(H2 O) HELIX 1 AA1 THR A 245 SER A 269 1 25 HELIX 2 AA2 PRO A 272 GLY A 281 1 10 HELIX 3 AA3 SER A 283 ALA A 289 1 7 LINK C MSE A 244 N THR A 245 1555 1555 1.33 LINK C ILE A 265 N MSE A 266 1555 1555 1.33 LINK C MSE A 266 N LEU A 267 1555 1555 1.34 LINK C ILE A 276 N MSE A 277 1555 1555 1.33 LINK C MSE A 277 N ARG A 278 1555 1555 1.34 CRYST1 38.020 58.270 38.710 90.00 90.00 90.00 C 2 2 21 8 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 0.026302 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017161 0.000000 0.00000 SCALE3 0.000000 0.000000 0.025833 0.00000 HETATM 1 N MSE A 244 13.670 46.621 21.237 1.00 90.69 N ANISOU 1 N MSE A 244 14857 9445 10155 774 1960 -3268 N HETATM 2 CA MSE A 244 14.978 46.493 20.602 1.00 88.44 C ANISOU 2 CA MSE A 244 14535 9146 9922 440 1343 -2965 C HETATM 3 C MSE A 244 15.207 47.573 19.537 1.00 85.16 C ANISOU 3 C MSE A 244 13961 8380 10017 533 1011 -2904 C HETATM 4 O MSE A 244 14.371 48.456 19.348 1.00 87.33 O ANISOU 4 O MSE A 244 14196 8379 10606 856 1234 -3115 O HETATM 5 CB MSE A 244 15.142 45.094 19.999 1.00 81.62 C ANISOU 5 CB MSE A 244 13194 8700 9119 290 1281 -2553 C HETATM 6 CG MSE A 244 14.153 44.766 18.886 1.00 78.89 C ANISOU 6 CG MSE A 244 12221 8478 9278 536 1483 -2380 C HETATM 7 SE MSE A 244 14.048 42.854 18.464 1.00 88.87 SE ANISOU 7 SE MSE A 244 13016 10236 10514 371 1539 -1986 SE HETATM 8 CE MSE A 244 12.969 42.263 19.981 1.00 81.09 C ANISOU 8 CE MSE A 244 12231 9466 9114 449 2174 -2201 C