HEADER TOXIN 25-JUN-99 1QS2 TITLE CRYSTAL STRUCTURE OF VIP2 WITH NAD COMPND MOL_ID: 1; COMPND 2 MOLECULE: ADP-RIBOSYLTRANSFERASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: MATURE VIP2; COMPND 5 EC: 2.4.2.30; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 OTHER_DETAILS: COMPLEXED WITH NAD SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS CEREUS; SOURCE 3 ORGANISM_TAXID: 1396; SOURCE 4 EXPRESSION_SYSTEM: BACILLUS CEREUS; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 1396 KEYWDS ALPHA-BETA PROTEIN, PROTEIN-NAD COMPLEX, BINARY TOXIN, TOXIN EXPDTA X-RAY DIFFRACTION AUTHOR S.HAN,J.A.CRAIG,C.D.PUTNAM,N.B.CAROZZI,J.A.TAINER REVDAT 3 14-FEB-24 1QS2 1 REMARK REVDAT 2 24-FEB-09 1QS2 1 VERSN REVDAT 1 29-DEC-99 1QS2 0 JRNL AUTH S.HAN,J.A.CRAIG,C.D.PUTNAM,N.B.CAROZZI,J.A.TAINER JRNL TITL EVOLUTION AND MECHANISM FROM STRUCTURES OF AN JRNL TITL 2 ADP-RIBOSYLATING TOXIN AND NAD COMPLEX. JRNL REF NAT.STRUCT.BIOL. V. 6 932 1999 JRNL REFN ISSN 1072-8368 JRNL PMID 10504727 JRNL DOI 10.1038/13300 REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 15323 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.207 REMARK 3 FREE R VALUE : 0.266 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1508 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.82 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.40 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1626 REMARK 3 BIN R VALUE (WORKING SET) : 0.3240 REMARK 3 BIN FREE R VALUE : 0.3840 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3200 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 44 REMARK 3 SOLVENT ATOMS : 145 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 61.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.05 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.66600 REMARK 3 B22 (A**2) : -2.17700 REMARK 3 B33 (A**2) : -0.48900 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.41 REMARK 3 ESD FROM SIGMAA (A) : 0.21 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.49 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.45 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.450 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 21.26 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.140 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1QS2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-DEC-99. REMARK 100 THE DEPOSITION ID IS D_1000009231. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-MAR-98 REMARK 200 TEMPERATURE (KELVIN) : 103.0 REMARK 200 PH : 8.0 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 RU200 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 : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15370 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 200 DATA REDUNDANCY : 7.700 REMARK 200 R MERGE (I) : 0.09800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 7.80 REMARK 200 R MERGE FOR SHELL (I) : 0.30900 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: NULL REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.49 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.96 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG200, 2-METHYL 2,4-PENTANEDIOL, NAD, REMARK 280 BIS-TRIS, PH 8.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 298.0K 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 26.83650 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 71.30600 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.28200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 71.30600 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.83650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 35.28200 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 300 REMARK: THE BIOLOGICAL ASSEMBLY IS A MONOMER 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 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 ASP A 65 98.80 -179.47 REMARK 500 LYS A 67 -99.11 47.30 REMARK 500 ASN A 137 57.64 -117.80 REMARK 500 SER A 167 -51.21 111.46 REMARK 500 ALA A 194 144.04 -39.29 REMARK 500 SER A 198 -165.54 -78.86 REMARK 500 SER A 199 -95.86 -38.81 REMARK 500 LYS A 213 -70.87 -69.98 REMARK 500 THR A 216 -77.32 -46.75 REMARK 500 LYS A 220 69.54 -67.77 REMARK 500 SER A 265 111.79 -167.01 REMARK 500 LYS A 269 -139.20 50.76 REMARK 500 ASN A 270 20.41 -78.30 REMARK 500 GLN A 305 -34.05 -150.31 REMARK 500 ASN A 376 -0.30 76.24 REMARK 500 PHE A 397 36.87 -149.85 REMARK 500 ALA A 424 165.28 -43.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAD A 500 DBREF 1QS2 A 62 462 PDB 1QS2 1QS2 62 462 SEQRES 1 A 401 LYS VAL GLU ASP PHE LYS GLU ASP LYS GLU LYS ALA LYS SEQRES 2 A 401 GLU TRP GLY LYS GLU LYS GLU LYS GLU TRP LYS LEU THR SEQRES 3 A 401 ALA THR GLU LYS GLY LYS MET ASN ASN PHE LEU ASP ASN SEQRES 4 A 401 LYS ASN ASP ILE LYS THR ASN TYR LYS GLU ILE THR PHE SEQRES 5 A 401 SER MET ALA GLY SER PHE GLU ASP GLU ILE LYS ASP LEU SEQRES 6 A 401 LYS GLU ILE ASP LYS MET PHE ASP LYS THR ASN LEU SER SEQRES 7 A 401 ASN SER ILE ILE THR TYR LYS ASN VAL GLU PRO THR THR SEQRES 8 A 401 ILE GLY PHE ASN LYS SER LEU THR GLU GLY ASN THR ILE SEQRES 9 A 401 ASN SER ASP ALA MET ALA GLN PHE LYS GLU GLN PHE LEU SEQRES 10 A 401 ASP ARG ASP ILE LYS PHE ASP SER TYR LEU ASP THR HIS SEQRES 11 A 401 LEU THR ALA GLN GLN VAL SER SER LYS GLU ARG VAL ILE SEQRES 12 A 401 LEU LYS VAL THR VAL PRO SER GLY LYS GLY SER THR THR SEQRES 13 A 401 PRO THR LYS ALA GLY VAL ILE LEU ASN ASN SER GLU TYR SEQRES 14 A 401 LYS MET LEU ILE ASP ASN GLY TYR MET VAL HIS VAL ASP SEQRES 15 A 401 LYS VAL SER LYS VAL VAL LYS LYS GLY VAL GLU CYS LEU SEQRES 16 A 401 GLN ILE GLU GLY THR LEU LYS LYS SER LEU ASP PHE LYS SEQRES 17 A 401 ASN ASP ILE ASN ALA GLU ALA HIS SER TRP GLY MET LYS SEQRES 18 A 401 ASN TYR GLU GLU TRP ALA LYS ASP LEU THR ASP SER GLN SEQRES 19 A 401 ARG GLU ALA LEU ASP GLY TYR ALA ARG GLN ASP TYR LYS SEQRES 20 A 401 GLU ILE ASN ASN TYR LEU ARG ASN GLN GLY GLY SER GLY SEQRES 21 A 401 ASN GLU LYS LEU ASP ALA GLN ILE LYS ASN ILE SER ASP SEQRES 22 A 401 ALA LEU GLY LYS LYS PRO ILE PRO GLU ASN ILE THR VAL SEQRES 23 A 401 TYR ARG TRP CYS GLY MET PRO GLU PHE GLY TYR GLN ILE SEQRES 24 A 401 SER ASP PRO LEU PRO SER LEU LYS ASP PHE GLU GLU GLN SEQRES 25 A 401 PHE LEU ASN THR ILE LYS GLU ASP LYS GLY TYR MET SER SEQRES 26 A 401 THR SER LEU SER SER GLU ARG LEU ALA ALA PHE GLY SER SEQRES 27 A 401 ARG LYS ILE ILE LEU ARG LEU GLN VAL PRO LYS GLY SER SEQRES 28 A 401 THR GLY ALA TYR LEU SER ALA ILE GLY GLY PHE ALA SER SEQRES 29 A 401 GLU LYS GLU ILE LEU LEU ASP LYS ASP SER LYS TYR HIS SEQRES 30 A 401 ILE ASP LYS VAL THR GLU VAL ILE ILE LYS GLY VAL LYS SEQRES 31 A 401 ARG TYR VAL VAL ASP ALA THR LEU LEU THR ASN HET NAD A 500 44 HETNAM NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE FORMUL 2 NAD C21 H27 N7 O14 P2 FORMUL 3 HOH *145(H2 O) HELIX 1 1 ASP A 69 TRP A 84 1 16 HELIX 2 2 THR A 87 ASP A 99 1 13 HELIX 3 3 ASN A 100 ASN A 102 5 3 HELIX 4 4 ASP A 103 PHE A 113 1 11 HELIX 5 5 PHE A 119 ASP A 134 1 16 HELIX 6 6 GLU A 149 GLY A 154 5 6 HELIX 7 7 SER A 167 LEU A 178 1 12 HELIX 8 8 GLU A 275 ASP A 290 1 16 HELIX 9 9 THR A 292 GLN A 305 1 14 HELIX 10 10 ASP A 306 GLN A 317 1 12 HELIX 11 11 ASN A 322 LYS A 338 1 17 HELIX 12 12 GLY A 352 GLY A 357 5 6 HELIX 13 13 SER A 366 LEU A 375 1 10 HELIX 14 14 LEU A 394 GLY A 398 5 5 HELIX 15 15 SER A 418 GLY A 421 5 4 SHEET 1 A 6 VAL A 63 GLU A 64 0 SHEET 2 A 6 SER A 141 VAL A 148 1 O SER A 141 N GLU A 64 SHEET 3 A 6 VAL A 203 VAL A 209 -1 N VAL A 203 O VAL A 148 SHEET 4 A 6 VAL A 253 LYS A 264 1 O LEU A 256 N ILE A 204 SHEET 5 A 6 TYR A 238 LYS A 250 -1 N MET A 239 O LYS A 263 SHEET 6 A 6 ASP A 181 ILE A 182 -1 O ILE A 182 N VAL A 240 SHEET 1 B 2 THR A 160 GLU A 161 0 SHEET 2 B 2 THR A 164 ILE A 165 -1 O THR A 164 N GLU A 161 SHEET 1 C 3 LEU A 188 THR A 190 0 SHEET 2 C 3 GLU A 229 ILE A 234 -1 N MET A 232 O THR A 190 SHEET 3 C 3 ALA A 221 ASN A 226 -1 O GLY A 222 N LEU A 233 SHEET 1 D 5 ILE A 345 CYS A 351 0 SHEET 2 D 5 ILE A 402 VAL A 408 -1 O ILE A 402 N CYS A 351 SHEET 3 D 5 VAL A 450 LEU A 459 1 O TYR A 453 N ILE A 403 SHEET 4 D 5 SER A 435 ILE A 447 -1 N HIS A 438 O THR A 458 SHEET 5 D 5 ILE A 378 ASP A 381 -1 O LYS A 379 N TYR A 437 SHEET 1 E 3 MET A 385 SER A 388 0 SHEET 2 E 3 GLU A 428 LEU A 431 -1 N ILE A 429 O THR A 387 SHEET 3 E 3 GLY A 414 TYR A 416 -1 O ALA A 415 N LEU A 430 SITE 1 AC1 14 TYR A 307 ARG A 315 ARG A 349 TRP A 350 SITE 2 AC1 14 PRO A 354 GLU A 355 ASP A 381 THR A 387 SITE 3 AC1 14 PHE A 397 ARG A 400 SER A 425 GLU A 428 SITE 4 AC1 14 HOH A1033 HOH A1089 CRYST1 53.673 70.564 142.612 90.00 90.00 90.00 P 21 21 21 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 0.018631 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014172 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007012 0.00000