HEADER ANTITOXIN 12-DEC-23 8XEO TITLE CRYSTAL STRUCTURE OF MNT ANTITOXIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: MNT; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LEGIONELLA PNEUMOPHILA; SOURCE 3 ORGANISM_TAXID: 446; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ANTITOXIN, NUCLEOTIDYLTRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR C.JIN,C.JEON,D.H.KIM,B.J.LEE REVDAT 1 18-DEC-24 8XEO 0 JRNL AUTH C.JIN,C.JEON,D.H.KIM,B.J.LEE JRNL TITL STRUCTURAL AND FUNCTIONAL STUDY OF HEPN-MNT MODULE FROM JRNL TITL 2 LEGIONELLA PNEUMOPHILA JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.79 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20RC4_4418 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) : 2.79 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.18 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 3 NUMBER OF REFLECTIONS : 11301 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.221 REMARK 3 R VALUE (WORKING SET) : 0.215 REMARK 3 FREE R VALUE : 0.274 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.990 REMARK 3 FREE R VALUE TEST SET COUNT : 1129 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 45.1800 - 5.5800 0.99 1268 151 0.2109 0.2231 REMARK 3 2 5.5800 - 4.4300 0.99 1281 141 0.1804 0.2351 REMARK 3 3 4.4300 - 3.8700 1.00 1284 138 0.1815 0.2929 REMARK 3 4 3.8700 - 3.5200 0.99 1301 135 0.2252 0.2910 REMARK 3 5 3.5100 - 3.2600 0.99 1283 139 0.2328 0.2982 REMARK 3 6 3.2600 - 3.0700 0.99 1270 150 0.2655 0.3335 REMARK 3 7 3.0700 - 2.9200 0.98 1256 132 0.2802 0.3931 REMARK 3 8 2.9200 - 2.7900 0.94 1229 143 0.2994 0.3683 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) : 0.416 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.738 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 64.45 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 68.02 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 : 0.003 1607 REMARK 3 ANGLE : 0.513 2177 REMARK 3 CHIRALITY : 0.038 253 REMARK 3 PLANARITY : 0.004 272 REMARK 3 DIHEDRAL : 4.064 211 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 11.1073 38.8913 35.1413 REMARK 3 T TENSOR REMARK 3 T11: 0.5559 T22: 0.5604 REMARK 3 T33: 0.5357 T12: -0.0197 REMARK 3 T13: 0.0609 T23: 0.0184 REMARK 3 L TENSOR REMARK 3 L11: 0.7767 L22: 1.9679 REMARK 3 L33: 1.1852 L12: 0.7578 REMARK 3 L13: 0.6258 L23: 0.9406 REMARK 3 S TENSOR REMARK 3 S11: -0.1443 S12: 0.1011 S13: -0.0948 REMARK 3 S21: -0.1759 S22: 0.1672 S23: -0.1685 REMARK 3 S31: 0.1050 S32: 0.1056 S33: 0.0185 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 8XEO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-DEC-23. REMARK 100 THE DEPOSITION ID IS D_1300043326. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-NOV-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 : PAL/PLS REMARK 200 BEAMLINE : 11C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97949 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11301 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.790 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 (%) : 99.7 REMARK 200 DATA REDUNDANCY : 6.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.79 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.85 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 (%): 49.49 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.44 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% (W/V) PEG 6000, 0.1 M CITRIC REMARK 280 ACID/SODIUM HYDROXIDE, PH 4.0, 1M LITHIUM CHLORIDE, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 29.08450 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 33.24150 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.79650 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 33.24150 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.08450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 30.79650 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 920 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10430 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 1 REMARK 465 ASN A 2 REMARK 465 GLU A 3 REMARK 465 GLN A 4 REMARK 465 LEU A 5 REMARK 465 ASN A 6 REMARK 465 HIS A 7 REMARK 465 GLU A 107 REMARK 465 SER A 108 REMARK 465 MET B 1 REMARK 465 ASN B 2 REMARK 465 GLU B 3 REMARK 465 GLN B 4 REMARK 465 LEU B 5 REMARK 465 ASN B 6 REMARK 465 GLU B 107 REMARK 465 SER B 108 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 TYR A 35 -168.44 -125.06 REMARK 500 ALA A 39 -4.25 69.71 REMARK 500 HIS A 44 -166.29 -129.74 REMARK 500 TYR B 9 18.71 56.72 REMARK 500 THR B 42 33.01 -89.44 REMARK 500 REMARK 500 REMARK: NULL DBREF 8XEO A 1 108 PDB 8XEO 8XEO 1 108 DBREF 8XEO B 1 108 PDB 8XEO 8XEO 1 108 SEQRES 1 A 108 MET ASN GLU GLN LEU ASN HIS LEU TYR GLY LEU PRO SER SEQRES 2 A 108 HIS ALA ILE GLU ALA LEU LYS CYS VAL PHE LYS GLU TYR SEQRES 3 A 108 SER GLN ILE ASP ASN ALA ILE LEU TYR GLY SER ARG ALA SEQRES 4 A 108 LYS GLY THR TYR HIS GLN GLY SER ASP ILE ASP MET CYS SEQRES 5 A 108 LEU THR GLY ASN LEU LEU GLY ILE THR GLU LEU LEU ALA SEQRES 6 A 108 ILE GLU ASN LYS ILE ASP ASP LEU LEU LEU PRO TRP LYS SEQRES 7 A 108 VAL ASP ILE SER LEU LYS HIS THR ILE ASP ASN PRO ASP SEQRES 8 A 108 LEU LEU GLU HIS ILE GLU ARG ALA GLY ILE LEU PHE TYR SEQRES 9 A 108 THR LYS GLU SER SEQRES 1 B 108 MET ASN GLU GLN LEU ASN HIS LEU TYR GLY LEU PRO SER SEQRES 2 B 108 HIS ALA ILE GLU ALA LEU LYS CYS VAL PHE LYS GLU TYR SEQRES 3 B 108 SER GLN ILE ASP ASN ALA ILE LEU TYR GLY SER ARG ALA SEQRES 4 B 108 LYS GLY THR TYR HIS GLN GLY SER ASP ILE ASP MET CYS SEQRES 5 B 108 LEU THR GLY ASN LEU LEU GLY ILE THR GLU LEU LEU ALA SEQRES 6 B 108 ILE GLU ASN LYS ILE ASP ASP LEU LEU LEU PRO TRP LYS SEQRES 7 B 108 VAL ASP ILE SER LEU LYS HIS THR ILE ASP ASN PRO ASP SEQRES 8 B 108 LEU LEU GLU HIS ILE GLU ARG ALA GLY ILE LEU PHE TYR SEQRES 9 B 108 THR LYS GLU SER FORMUL 3 HOH *17(H2 O) HELIX 1 AA1 PRO A 12 GLU A 25 1 14 HELIX 2 AA2 GLY A 59 ASP A 72 1 14 HELIX 3 AA3 HIS A 85 ILE A 87 5 3 HELIX 4 AA4 ASN A 89 GLY A 100 1 12 HELIX 5 AA5 HIS B 7 LEU B 11 5 5 HELIX 6 AA6 PRO B 12 GLU B 25 1 14 HELIX 7 AA7 GLY B 36 GLY B 41 1 6 HELIX 8 AA8 GLY B 59 LEU B 73 1 15 HELIX 9 AA9 ASN B 89 GLY B 100 1 12 SHEET 1 AA1 4 VAL A 79 LEU A 83 0 SHEET 2 AA1 4 ILE A 49 THR A 54 1 N ILE A 49 O ASP A 80 SHEET 3 AA1 4 ASN A 31 TYR A 35 -1 N ILE A 33 O CYS A 52 SHEET 4 AA1 4 ILE A 101 THR A 105 -1 O PHE A 103 N ALA A 32 SHEET 1 AA2 4 VAL B 79 LEU B 83 0 SHEET 2 AA2 4 ILE B 49 THR B 54 1 N LEU B 53 O SER B 82 SHEET 3 AA2 4 ASN B 31 TYR B 35 -1 N ILE B 33 O CYS B 52 SHEET 4 AA2 4 ILE B 101 THR B 105 -1 O ILE B 101 N LEU B 34 SSBOND 1 CYS A 21 CYS B 21 1555 1555 2.03 CRYST1 58.169 61.593 66.483 90.00 90.00 90.00 P 21 21 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 0.017191 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016236 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015041 0.00000 CONECT 105 899 CONECT 899 105 MASTER 261 0 0 9 8 0 0 6 1593 2 2 18 END