HEADER HYDROLASE 28-MAY-25 9OUF TITLE CRYSTAL STRUCTURE OF AN ADP-RIBOSYL HYDROLASE FROM STREPTOCOCCUS TITLE 2 PARASANGUINIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBONUCLEASE; COMPND 3 CHAIN: A; COMPND 4 EC: 3.1.-.-; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOCOCCUS PARASANGUINIS; SOURCE 3 ORGANISM_TAXID: 1318; SOURCE 4 GENE: SPLFYP13_01488; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS ADP-RIBOSYL CYCLASE/HYDROLASE, TOXIN, ANTIBACTERIAL, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR J.COLAUTTI,Y.KIM,J.C.WHITNEY REVDAT 1 30-JUL-25 9OUF 0 JRNL AUTH J.COLAUTTI,Y.KIM,J.C.WHITNEY JRNL TITL ANTIBACTERIAL ADP-RIBOSYL CYCLASE TOXINS INHIBIT BACTERIAL JRNL TITL 2 GROWTH BY RAPIDLY DEPLETING NAD(P). JRNL REF J.BIOL.CHEM. 10491 2025 JRNL REFN ESSN 1083-351X JRNL PMID 40680842 JRNL DOI 10.1016/J.JBC.2025.110491 REMARK 2 REMARK 2 RESOLUTION. 1.39 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.21.2_5419 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.39 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.18 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 28109 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.171 REMARK 3 R VALUE (WORKING SET) : 0.170 REMARK 3 FREE R VALUE : 0.197 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1378 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 33.1800 - 2.9800 1.00 2829 185 0.1649 0.1763 REMARK 3 2 2.9800 - 2.3700 1.00 2735 134 0.1709 0.1851 REMARK 3 3 2.3700 - 2.0700 1.00 2732 131 0.1511 0.1908 REMARK 3 4 2.0700 - 1.8800 1.00 2697 114 0.1391 0.1761 REMARK 3 5 1.8800 - 1.7500 1.00 2696 94 0.1533 0.2015 REMARK 3 6 1.7500 - 1.6400 1.00 2672 144 0.1645 0.2241 REMARK 3 7 1.6400 - 1.5600 1.00 2636 151 0.1662 0.2258 REMARK 3 8 1.5600 - 1.4900 1.00 2634 148 0.1940 0.2415 REMARK 3 9 1.4900 - 1.4400 1.00 2631 152 0.2531 0.3031 REMARK 3 10 1.4300 - 1.3900 0.94 2469 125 0.3210 0.3453 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.184 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.041 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.33 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.45 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 1232 REMARK 3 ANGLE : 0.943 1676 REMARK 3 CHIRALITY : 0.095 186 REMARK 3 PLANARITY : 0.008 222 REMARK 3 DIHEDRAL : 12.191 462 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 9OUF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-MAY-25. REMARK 100 THE DEPOSITION ID IS D_1000296242. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-MAR-25 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS-II REMARK 200 BEAMLINE : 17-ID-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97934 REMARK 200 MONOCHROMATOR : HORIZONTAL BOUNCE SI(111) DOUBLE REMARK 200 CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : AUTOPROC REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28170 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.390 REMARK 200 RESOLUTION RANGE LOW (A) : 33.180 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 11.20 REMARK 200 R MERGE (I) : 0.11700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.39 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.46 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.8 REMARK 200 DATA REDUNDANCY IN SHELL : 8.60 REMARK 200 R MERGE FOR SHELL (I) : 1.27100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP, HKL-3000 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.38 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M AMMONIUM ACETATE, 0.1 M REMARK 280 BISTRISHCL PH 5.5, 17 % PEG 10,000, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 28.59250 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.57550 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.59250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.57550 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: MONOMERIC 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 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 MET A 241 REMARK 465 GLY A 242 REMARK 465 SER A 243 REMARK 465 SER A 244 REMARK 465 HIS A 245 REMARK 465 HIS A 246 REMARK 465 HIS A 247 REMARK 465 HIS A 248 REMARK 465 HIS A 249 REMARK 465 HIS A 250 REMARK 465 SER A 251 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 GLN A 252 CG CD OE1 NE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ILE A 369 -58.36 -127.04 REMARK 500 REMARK 500 REMARK: NULL DBREF1 9OUF A 255 399 UNP A0A6N3DPK9_STRPA DBREF2 9OUF A A0A6N3DPK9 458 602 SEQADV 9OUF MET A 241 UNP A0A6N3DPK INITIATING METHIONINE SEQADV 9OUF GLY A 242 UNP A0A6N3DPK EXPRESSION TAG SEQADV 9OUF SER A 243 UNP A0A6N3DPK EXPRESSION TAG SEQADV 9OUF SER A 244 UNP A0A6N3DPK EXPRESSION TAG SEQADV 9OUF HIS A 245 UNP A0A6N3DPK EXPRESSION TAG SEQADV 9OUF HIS A 246 UNP A0A6N3DPK EXPRESSION TAG SEQADV 9OUF HIS A 247 UNP A0A6N3DPK EXPRESSION TAG SEQADV 9OUF HIS A 248 UNP A0A6N3DPK EXPRESSION TAG SEQADV 9OUF HIS A 249 UNP A0A6N3DPK EXPRESSION TAG SEQADV 9OUF HIS A 250 UNP A0A6N3DPK EXPRESSION TAG SEQADV 9OUF SER A 251 UNP A0A6N3DPK EXPRESSION TAG SEQADV 9OUF GLN A 252 UNP A0A6N3DPK EXPRESSION TAG SEQADV 9OUF ASP A 253 UNP A0A6N3DPK EXPRESSION TAG SEQADV 9OUF PRO A 254 UNP A0A6N3DPK EXPRESSION TAG SEQRES 1 A 159 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER GLN ASP SEQRES 2 A 159 PRO SER ASN ARG TYR SER LYS ILE ASP PHE THR GLN THR SEQRES 3 A 159 ASP PHE ASP VAL GLU LEU ILE ARG GLY ARG LEU LYS THR SEQRES 4 A 159 ASP PRO ASP THR ALA PHE PHE TRP SER GLY ARG THR ASP SEQRES 5 A 159 GLY ILE GLY GLY MET ASP VAL ALA LYS LYS ILE ALA LYS SEQRES 6 A 159 ASN LYS GLY GLY VAL THR LEU GLU SER THR ILE ASP ASP SEQRES 7 A 159 THR ASN ILE VAL MET PRO GLU TRP ASP PHE ASN THR PRO SEQRES 8 A 159 SER SER VAL THR ALA TRP GLU GLU ALA SER ASN VAL TYR SEQRES 9 A 159 ALA GLU GLN VAL SER GLY GLU ILE ARG ALA VAL VAL GLY SEQRES 10 A 159 SER GLU LEU ARG PRO GLY ASN ILE TRP GLU ASN ILE GLU SEQRES 11 A 159 LEU PRO ARG LEU LYS ALA ASN PRO ASN VAL THR LYS VAL SEQRES 12 A 159 THR THR ILE ASP PRO LYS THR GLY VAL GLU LYS ILE ILE SEQRES 13 A 159 PHE GLU ARG HET EDO A 401 8 HET CL A 402 1 HET CL A 403 1 HET CL A 404 1 HETNAM EDO 1,2-ETHANEDIOL HETNAM CL CHLORIDE ION HETSYN EDO ETHYLENE GLYCOL FORMUL 2 EDO C2 H6 O2 FORMUL 3 CL 3(CL 1-) FORMUL 6 HOH *96(H2 O) HELIX 1 AA1 ASP A 269 ILE A 273 5 5 HELIX 2 AA2 ARG A 274 LYS A 278 5 5 HELIX 3 AA3 GLY A 296 LYS A 307 1 12 HELIX 4 AA4 THR A 311 THR A 319 1 9 HELIX 5 AA5 THR A 330 GLN A 347 1 18 HELIX 6 AA6 ASN A 364 ILE A 369 1 6 HELIX 7 AA7 ILE A 369 ALA A 376 1 8 SHEET 1 AA1 2 ILE A 261 ASP A 262 0 SHEET 2 AA1 2 ILE A 321 VAL A 322 1 O VAL A 322 N ILE A 261 SHEET 1 AA2 4 PHE A 285 SER A 288 0 SHEET 2 AA2 4 GLY A 350 VAL A 356 1 O VAL A 355 N PHE A 286 SHEET 3 AA2 4 VAL A 380 ILE A 386 1 O LYS A 382 N ILE A 352 SHEET 4 AA2 4 GLU A 393 GLU A 398 -1 O LYS A 394 N THR A 385 SHEET 1 AA3 2 ARG A 290 THR A 291 0 SHEET 2 AA3 2 ILE A 294 GLY A 295 -1 O ILE A 294 N THR A 291 CRYST1 57.185 59.151 40.075 90.00 90.00 90.00 P 21 21 2 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 0.017487 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016906 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024953 0.00000 CONECT 1200 1202 1204 CONECT 1201 1203 1205 CONECT 1202 1200 CONECT 1203 1201 CONECT 1204 1200 1206 CONECT 1205 1201 1207 CONECT 1206 1204 CONECT 1207 1205 MASTER 241 0 4 7 8 0 0 6 1262 1 8 13 END