HEADER TRANSFERASE 25-JUN-25 9VLF TITLE STRUCTURAL STUDIES ON THE CONFORMATION CHANGES INDUCED BY LIGAND TITLE 2 BINDING IN AN ADENINE PHOSPHORIBOSYLTRANSFERASE (FNAPRT) FROM TITLE 3 FUSOBACTERIUM NUCLEATUM COMPND MOL_ID: 1; COMPND 2 MOLECULE: ADENINE PHOSPHORIBOSYLTRANSFERASE; COMPND 3 CHAIN: B; COMPND 4 SYNONYM: APRT; COMPND 5 EC: 2.4.2.7; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: FUSOBACTERIUM NUCLEATUM; SOURCE 3 ORGANISM_TAXID: 851; SOURCE 4 GENE: APT, FN1483; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS FUSOBACTERIUM NUCLEATUM, ADENINE PHOSPHORIBOSYLTRANSFERASE, LIGAND KEYWDS 2 BINDING, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR B.KIM,J.HWANG,H.DO,J.H.LEE REVDAT 1 11-FEB-26 9VLF 0 JRNL AUTH B.KIM,J.HWANG,H.DO,Y.S.SHIM,J.H.LEE JRNL TITL STRUCTURAL INSIGHTS INTO LIGAND-INDUCED CONFORMATIONAL JRNL TITL 2 CHANGES IN ADENINE PHOSPHORIBOSYL TRANSFERASE FROM JRNL TITL 3 FUSOBACTERIUM NUCLEATUM. JRNL REF PROTEIN PEPT.LETT. 2026 JRNL REFN ISSN 0929-8665 JRNL PMID 41588988 JRNL DOI 10.2174/0109298665403166251021110505 REMARK 2 REMARK 2 RESOLUTION. 1.61 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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) : 1.61 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.02 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 24557 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.206 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 1226 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 4.0000 - 3.3500 1.00 2708 160 0.1570 0.1635 REMARK 3 2 3.3500 - 2.6600 1.00 2639 123 0.2187 0.2640 REMARK 3 3 2.6600 - 2.3200 1.00 2614 135 0.2215 0.2241 REMARK 3 4 2.3200 - 2.1100 1.00 2575 135 0.2054 0.2054 REMARK 3 5 2.1100 - 1.9600 1.00 2561 136 0.2094 0.2276 REMARK 3 6 1.9600 - 1.8400 1.00 2577 127 0.2021 0.2333 REMARK 3 7 1.8400 - 1.7500 1.00 2558 135 0.2354 0.2447 REMARK 3 8 1.7500 - 1.6700 1.00 2546 136 0.2588 0.2636 REMARK 3 9 1.6700 - 1.6100 1.00 2553 139 0.2408 0.2691 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) : 0.142 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.008 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 26.43 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.83 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 1387 REMARK 3 ANGLE : 1.240 1881 REMARK 3 CHIRALITY : 0.069 212 REMARK 3 PLANARITY : 0.007 235 REMARK 3 DIHEDRAL : 13.512 520 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 9VLF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-JUL-25. REMARK 100 THE DEPOSITION ID IS D_1300060978. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-MAR-24 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 : 7A (6B, 6C1) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 S 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24571 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.610 REMARK 200 RESOLUTION RANGE LOW (A) : 29.020 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 13.10 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 2.9100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.61 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.66 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: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.92 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.46 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 8.2, 1.8M NAH2PO4/K2HPO4, VAPOR REMARK 280 DIFFUSION, SITTING 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 23.90350 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 23.90350 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 36.52400 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 53.26150 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 36.52400 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 53.26150 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 23.90350 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 36.52400 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 53.26150 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 23.90350 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 36.52400 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 53.26150 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: 4670 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14200 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -37.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 73.04800 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 23.90350 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 LYS B 15 -118.07 -125.74 REMARK 500 ALA B 122 -95.81 -116.46 REMARK 500 REMARK 500 REMARK: NULL DBREF 9VLF B 1 170 UNP Q8RDM9 APT_FUSNN 1 170 SEQRES 1 B 170 MET ASP LEU LYS ASN TYR VAL ALA SER ILE GLU ASN TYR SEQRES 2 B 170 PRO LYS GLU GLY ILE ILE PHE ARG ASP ILE THR PRO LEU SEQRES 3 B 170 MET ASN ASP GLY GLU ALA TYR LYS TYR ALA THR GLU LYS SEQRES 4 B 170 ILE VAL GLU PHE ALA LYS ASP HIS HIS ILE ASP ILE VAL SEQRES 5 B 170 VAL GLY PRO GLU ALA ARG GLY PHE ILE PHE GLY CYS PRO SEQRES 6 B 170 VAL SER TYR ALA LEU GLY VAL GLY PHE VAL PRO VAL ARG SEQRES 7 B 170 LYS PRO GLY LYS LEU PRO ARG GLU VAL ILE GLU TYR ALA SEQRES 8 B 170 TYR ASP LEU GLU TYR GLY SER ASN LYS LEU CYS LEU HIS SEQRES 9 B 170 LYS ASP SER ILE LYS PRO GLY GLN LYS VAL LEU VAL VAL SEQRES 10 B 170 ASP ASP LEU LEU ALA THR GLY GLY THR VAL GLU ALA THR SEQRES 11 B 170 ILE LYS LEU VAL GLU GLU LEU GLY GLY VAL VAL ALA GLY SEQRES 12 B 170 LEU ALA PHE LEU ILE GLU LEU VAL ASP LEU LYS GLY ARG SEQRES 13 B 170 GLU ARG LEU ASP LYS TYR PRO MET ILE THR LEU MET GLN SEQRES 14 B 170 TYR HET PO4 B 201 5 HET AMP B 202 23 HETNAM PO4 PHOSPHATE ION HETNAM AMP ADENOSINE MONOPHOSPHATE FORMUL 2 PO4 O4 P 3- FORMUL 3 AMP C10 H14 N5 O7 P FORMUL 4 HOH *54(H2 O) HELIX 1 AA1 ASP B 2 VAL B 7 5 6 HELIX 2 AA2 ILE B 23 ASP B 29 1 7 HELIX 3 AA3 ASP B 29 HIS B 47 1 19 HELIX 4 AA4 ALA B 57A GLY B 71 1 15 HELIX 5 AA5 GLY B 124 LEU B 137 1 14 HELIX 6 AA6 LYS B 154 ASP B 160 1 7 SHEET 1 AA1 2 ALA B 8 GLU B 11 0 SHEET 2 AA1 2 ILE B 19 ASP B 22 -1 O ASP B 22 N ALA B 8 SHEET 1 AA2 5 GLY B 73 VAL B 77 0 SHEET 2 AA2 5 ILE B 51 PRO B 55 1 N VAL B 52 O VAL B 75 SHEET 3 AA2 5 LYS B 113 LEU B 121 1 O LEU B 115 N VAL B 53 SHEET 4 AA2 5 VAL B 140 LEU B 150 1 O VAL B 140 N VAL B 114 SHEET 5 AA2 5 MET B 164 TYR B 170 1 O TYR B 170 N GLU B 149 SHEET 1 AA3 2 VAL B 87 ASP B 93 0 SHEET 2 AA3 2 SER B 98 HIS B 104 -1 O ASN B 99 N TYR B 92 CISPEP 1 TYR B 13 PRO B 14 0 2.18 CISPEP 2 GLU B 56 ALA B 57A 0 -7.65 CRYST1 73.048 106.523 47.807 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 0.013690 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009388 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020917 0.00000 CONECT 1333 1334 1335 1336 1337 CONECT 1334 1333 CONECT 1335 1333 CONECT 1336 1333 CONECT 1337 1333 CONECT 1338 1339 1340 1341 1342 CONECT 1339 1338 CONECT 1340 1338 CONECT 1341 1338 CONECT 1342 1338 1343 CONECT 1343 1342 1344 CONECT 1344 1343 1345 1346 CONECT 1345 1344 1350 CONECT 1346 1344 1347 1348 CONECT 1347 1346 CONECT 1348 1346 1349 1350 CONECT 1349 1348 CONECT 1350 1345 1348 1351 CONECT 1351 1350 1352 1360 CONECT 1352 1351 1353 CONECT 1353 1352 1354 CONECT 1354 1353 1355 1360 CONECT 1355 1354 1356 1357 CONECT 1356 1355 CONECT 1357 1355 1358 CONECT 1358 1357 1359 CONECT 1359 1358 1360 CONECT 1360 1351 1354 1359 MASTER 238 0 2 6 9 0 0 6 1413 1 28 14 END