HEADER ANTITOXIN 06-APR-24 8YZG TITLE ANTITOXIN PROTEIN FROM S. PNEUMONIAE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ANTITOXIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOCOCCUS PNEUMONIAE TIGR4; SOURCE 3 ORGANISM_TAXID: 170187; SOURCE 4 GENE: SP_1741; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ANTITOXIN PROTEIN, ANTITOXIN EXPDTA X-RAY DIFFRACTION AUTHOR D.H.KIM,S.M.KANG,B.J.LEE REVDAT 1 09-APR-25 8YZG 0 JRNL AUTH D.H.KIM,Y.C.LEE,C.JIN,S.M.KANG,S.J.KANG,H.S.KANG,B.J.LEE JRNL TITL STRUCTURAL AND FUNCTIONAL INSIGHT INTO YEFM-YOEB COMPLEX OF JRNL TITL 2 TOXIN-ANTITOXIN SYSTEM FROM STREPTOCOCCUS PNEUMONIAE. JRNL REF J.CELL.BIOCHEM. V. 126 30672 2025 JRNL REFN ESSN 1097-4644 JRNL PMID 39530329 JRNL DOI 10.1002/JCB.30672 REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.16_3549 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) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.43 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.410 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 13116 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.216 REMARK 3 R VALUE (WORKING SET) : 0.215 REMARK 3 FREE R VALUE : 0.236 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 656 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 34.4300 - 2.3900 1.00 2675 141 0.2311 0.2567 REMARK 3 2 2.3900 - 1.9000 1.00 2514 132 0.2060 0.2348 REMARK 3 3 1.9000 - 1.6600 1.00 2488 132 0.2026 0.2046 REMARK 3 4 1.6600 - 1.5100 1.00 2448 129 0.1956 0.2150 REMARK 3 5 1.5100 - 1.4000 0.95 2335 122 0.1932 0.1948 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.077 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.376 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.84 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.43 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 : 0.006 497 REMARK 3 ANGLE : 0.842 671 REMARK 3 CHIRALITY : 0.074 76 REMARK 3 PLANARITY : 0.005 86 REMARK 3 DIHEDRAL : 3.469 191 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 8YZG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-APR-24. REMARK 100 THE DEPOSITION ID IS D_1300046675. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-OCT-19 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 : SPRING-8 REMARK 200 BEAMLINE : BL44XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.899995 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23751 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 13.03 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 49.8100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.48 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: MOLECULAR REPLACEMENT 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 (%): 44.95 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.23 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 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 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 44.90100 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 18.63650 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 18.63650 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 22.45050 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 18.63650 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 18.63650 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 67.35150 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 18.63650 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 18.63650 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 22.45050 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 18.63650 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 18.63650 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 67.35150 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 44.90100 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: 2280 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7090 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -24.0 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 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 89.80200 DBREF1 8YZG A 1 59 UNP A0A0H2UR92_STRPN DBREF2 8YZG A A0A0H2UR92 1 59 SEQRES 1 A 59 MET GLU ALA VAL LEU TYR SER THR PHE ARG ASN HIS LEU SEQRES 2 A 59 LYS ASP TYR MET LYS LYS VAL ASN ASP GLU PHE GLU PRO SEQRES 3 A 59 LEU THR VAL VAL ASN LYS ASN PRO ASP GLU ASP ILE VAL SEQRES 4 A 59 VAL LEU SER LYS SER GLU TRP ASP SER ILE GLN GLU THR SEQRES 5 A 59 LEU ARG ILE ALA GLN ASN LYS FORMUL 2 HOH *51(H2 O) HELIX 1 AA1 TYR A 6 HIS A 12 1 7 HELIX 2 AA2 HIS A 12 PHE A 24 1 13 HELIX 3 AA3 ASN A 33 ASP A 37 5 5 HELIX 4 AA4 SER A 42 LYS A 59 1 18 SHEET 1 AA1 3 GLU A 2 LEU A 5 0 SHEET 2 AA1 3 LEU A 27 VAL A 30 1 O THR A 28 N GLU A 2 SHEET 3 AA1 3 ILE A 38 VAL A 40 -1 O VAL A 40 N LEU A 27 CRYST1 37.273 37.273 89.802 90.00 90.00 90.00 P 41 21 2 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 0.026829 0.000000 0.000000 0.00000 SCALE2 0.000000 0.026829 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011136 0.00000 TER 490 LYS A 59 HETATM 491 O HOH A 101 -5.007 8.740 50.247 1.00 23.37 O HETATM 492 O HOH A 102 25.640 7.803 40.998 1.00 30.78 O HETATM 493 O HOH A 103 1.584 19.120 40.740 1.00 29.70 O HETATM 494 O HOH A 104 34.518 18.314 47.392 1.00 23.45 O HETATM 495 O HOH A 105 37.640 19.031 43.852 1.00 35.93 O HETATM 496 O HOH A 106 22.479 14.806 35.901 1.00 14.64 O HETATM 497 O HOH A 107 2.675 1.020 30.802 1.00 27.29 O HETATM 498 O HOH A 108 11.777 10.487 37.103 1.00 11.69 O HETATM 499 O HOH A 109 15.365 4.889 34.241 1.00 23.29 O HETATM 500 O HOH A 110 12.644 16.164 35.327 1.00 22.53 O HETATM 501 O HOH A 111 5.601 15.748 35.996 1.00 23.40 O HETATM 502 O HOH A 112 -1.760 -1.489 40.249 1.00 22.12 O HETATM 503 O HOH A 113 15.761 16.590 37.682 1.00 27.11 O HETATM 504 O HOH A 114 8.295 1.266 29.647 1.00 27.27 O HETATM 505 O HOH A 115 2.951 -1.420 33.036 1.00 28.72 O HETATM 506 O HOH A 116 -2.251 10.756 35.393 1.00 13.75 O HETATM 507 O HOH A 117 24.429 14.295 47.078 1.00 27.33 O HETATM 508 O HOH A 118 -9.182 6.558 40.821 1.00 20.79 O HETATM 509 O HOH A 119 10.171 1.736 31.852 1.00 26.98 O HETATM 510 O HOH A 120 -6.657 11.191 47.053 1.00 22.58 O HETATM 511 O HOH A 121 13.309 7.251 28.218 1.00 11.77 O HETATM 512 O HOH A 122 10.538 14.437 29.476 1.00 21.31 O HETATM 513 O HOH A 123 14.619 7.800 34.222 1.00 13.37 O HETATM 514 O HOH A 124 2.188 13.347 31.397 1.00 32.60 O HETATM 515 O HOH A 125 6.256 -2.709 29.299 1.00 32.04 O HETATM 516 O HOH A 126 -0.233 18.893 36.979 1.00 29.20 O HETATM 517 O HOH A 127 5.874 4.946 30.111 1.00 15.32 O HETATM 518 O HOH A 128 -3.681 12.443 37.127 1.00 13.43 O HETATM 519 O HOH A 129 13.227 4.071 31.211 1.00 17.83 O HETATM 520 O HOH A 130 6.142 11.214 34.720 1.00 16.92 O HETATM 521 O HOH A 131 0.406 17.275 51.209 1.00 25.54 O HETATM 522 O HOH A 132 18.336 16.280 37.438 1.00 25.52 O HETATM 523 O HOH A 133 -3.693 16.289 37.715 1.00 22.30 O HETATM 524 O HOH A 134 21.379 6.297 37.950 1.00 28.98 O HETATM 525 O HOH A 135 20.660 8.447 47.393 1.00 26.47 O HETATM 526 O HOH A 136 15.683 4.387 37.504 1.00 12.52 O HETATM 527 O HOH A 137 0.804 14.800 32.372 1.00 28.25 O HETATM 528 O HOH A 138 -0.845 -1.162 31.145 1.00 30.77 O HETATM 529 O HOH A 139 23.933 5.309 41.235 1.00 37.65 O HETATM 530 O HOH A 140 0.172 -1.986 38.348 1.00 18.23 O HETATM 531 O HOH A 141 -1.395 16.316 36.330 1.00 20.56 O HETATM 532 O HOH A 142 -0.194 -0.505 35.867 1.00 15.86 O HETATM 533 O HOH A 143 -7.733 8.983 45.721 1.00 17.36 O HETATM 534 O HOH A 144 -5.605 1.032 49.235 1.00 29.02 O HETATM 535 O HOH A 145 -1.140 14.806 34.028 1.00 27.10 O HETATM 536 O HOH A 146 7.713 18.365 36.806 1.00 30.86 O HETATM 537 O HOH A 147 18.571 3.588 37.707 1.00 26.43 O HETATM 538 O HOH A 148 18.527 14.700 50.201 1.00 32.88 O HETATM 539 O HOH A 149 3.145 19.278 42.964 1.00 30.44 O HETATM 540 O HOH A 150 -8.579 -2.002 45.805 1.00 39.69 O HETATM 541 O HOH A 151 20.931 4.942 47.430 1.00 34.87 O MASTER 215 0 0 4 3 0 0 6 540 1 0 5 END