HEADER TOXIN 04-JAN-12 4AE0 TITLE CRYSTAL STRUCTURE OF DIPHTHERIA TOXIN MUTANT CRM197 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIPHTHERIA TOXIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DT, NAD(+)--DIPHTHAMIDE ADP-RIBOSYLTRANSFERASE, DIPHTHERIA COMPND 5 TOXIN FRAGMENT A, DIPHTHERIA TOXIN FRAGMENT B, CRM197; COMPND 6 EC: 2.4.2.36; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CORYNEBACTERIUM DIPHTHERIAE; SOURCE 3 ORGANISM_TAXID: 1717 KEYWDS TOXIN EXPDTA X-RAY DIFFRACTION AUTHOR E.MALITO,G.SPRAGGON REVDAT 3 20-DEC-23 4AE0 1 REMARK REVDAT 2 18-APR-12 4AE0 1 JRNL REVDAT 1 28-MAR-12 4AE0 0 JRNL AUTH E.MALITO,B.BURSULAYA,C.CHEN,P.L.SURDO,M.PICCHIANTI, JRNL AUTH 2 E.BALDUCCI,M.BIANCUCCI,A.BROCK,F.BERTI,M.J.BOTTOMLEY, JRNL AUTH 3 M.NISSUM,P.COSTANTINO,R.RAPPUOLI,G.SPRAGGON JRNL TITL STRUCTURAL BASIS FOR LACK OF TOXICITY OF THE DIPHTHERIA JRNL TITL 2 TOXIN MUTANT CRM197. JRNL REF PROC.NATL.ACAD.SCI.USA V. 109 5229 2012 JRNL REFN ISSN 0027-8424 JRNL PMID 22431623 JRNL DOI 10.1073/PNAS.1201964109 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.34 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.210 REMARK 3 COMPLETENESS FOR RANGE (%) : 88.5 REMARK 3 NUMBER OF REFLECTIONS : 36533 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.211 REMARK 3 R VALUE (WORKING SET) : 0.210 REMARK 3 FREE R VALUE : 0.241 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1837 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 41.3437 - 4.2984 0.97 3848 226 0.1927 0.2216 REMARK 3 2 4.2984 - 3.4123 0.99 3906 211 0.1885 0.2122 REMARK 3 3 3.4123 - 2.9811 0.99 3870 212 0.2202 0.2435 REMARK 3 4 2.9811 - 2.7086 0.97 3829 190 0.2175 0.2735 REMARK 3 5 2.7086 - 2.5145 0.95 3735 204 0.2135 0.2586 REMARK 3 6 2.5145 - 2.3662 0.92 3605 186 0.2149 0.2843 REMARK 3 7 2.3662 - 2.2477 0.89 3463 176 0.2123 0.2433 REMARK 3 8 2.2477 - 2.1499 0.85 3318 173 0.2238 0.2805 REMARK 3 9 2.1499 - 2.0671 0.77 2985 163 0.2466 0.3065 REMARK 3 10 2.0671 - 1.9958 0.55 2137 96 0.2699 0.3050 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 : 0.30 REMARK 3 B_SOL : 49.67 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.290 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.360 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 38.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 56.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -8.26490 REMARK 3 B22 (A**2) : 15.48350 REMARK 3 B33 (A**2) : -7.21870 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -9.50350 REMARK 3 B23 (A**2) : 0.00000 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 : 0.007 3735 REMARK 3 ANGLE : 0.961 5082 REMARK 3 CHIRALITY : 0.067 590 REMARK 3 PLANARITY : 0.004 664 REMARK 3 DIHEDRAL : 12.271 1287 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): -15.9226 24.0845 27.3640 REMARK 3 T TENSOR REMARK 3 T11: 0.2790 T22: 0.3515 REMARK 3 T33: 0.2620 T12: -0.0234 REMARK 3 T13: 0.0243 T23: 0.0245 REMARK 3 L TENSOR REMARK 3 L11: 1.1370 L22: 1.0249 REMARK 3 L33: 0.4686 L12: 0.1770 REMARK 3 L13: -0.0665 L23: 0.1043 REMARK 3 S TENSOR REMARK 3 S11: -0.1805 S12: 0.1049 S13: 0.0038 REMARK 3 S21: -0.1289 S22: 0.1524 S23: 0.1927 REMARK 3 S31: -0.0506 S32: -0.1535 S33: 0.0253 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: RESIDUES 1-4, 38-49, 188-200, 349-352, REMARK 3 AND 517-519, ARE DISORDERED. DISORDERED SIDE CHAINS WERE MODELED REMARK 3 UP TO THE BACKBONE CBETA ATOMS, AND RESIDUE NAMES WERE KEPT REMARK 3 CONSISTENT WITH SEQUENCE OF THE PROTEIN. REMARK 4 REMARK 4 4AE0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 04-JAN-12. REMARK 100 THE DEPOSITION ID IS D_1290050861. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-MAY-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.3 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 : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39541 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 24.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.5 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 0.62000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 1SGK REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.86 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.9 M AMMONIUM SULFATE, 100 MM BICINE REMARK 280 [PH 9.0] REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 52.92050 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 45.69400 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 52.92050 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 45.69400 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: 7190 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 40480 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -23.7 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 -1.000000 0.000000 0.000000 -1.90497 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 63.80957 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A2054 LIES ON A SPECIAL POSITION. REMARK 400 REMARK 400 COMPOUND REMARK 400 ENGINEERED RESIDUE IN CHAIN A, GLY 53 TO GLU 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 GLY A 1 REMARK 465 ALA A 2 REMARK 465 ASP A 3 REMARK 465 ASP A 4 REMARK 465 PRO A 38 REMARK 465 LYS A 39 REMARK 465 SER A 40 REMARK 465 GLY A 41 REMARK 465 THR A 42 REMARK 465 GLN A 43 REMARK 465 GLY A 44 REMARK 465 ASN A 45 REMARK 465 TYR A 46 REMARK 465 ASP A 47 REMARK 465 ASP A 48 REMARK 465 ASP A 49 REMARK 465 GLY A 188 REMARK 465 ASN A 189 REMARK 465 ARG A 190 REMARK 465 VAL A 191 REMARK 465 ARG A 192 REMARK 465 ARG A 193 REMARK 465 SER A 194 REMARK 465 VAL A 195 REMARK 465 GLY A 196 REMARK 465 SER A 197 REMARK 465 SER A 198 REMARK 465 LEU A 199 REMARK 465 SER A 200 REMARK 465 GLU A 349 REMARK 465 LEU A 350 REMARK 465 VAL A 351 REMARK 465 ASP A 352 REMARK 465 THR A 517 REMARK 465 VAL A 518 REMARK 465 ASP A 519 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 LYS A 10 CG CD CE NZ REMARK 470 LYS A 33 CG CD CE NZ REMARK 470 GLN A 36 CG CD OE1 NE2 REMARK 470 LYS A 37 CG CD CE NZ REMARK 470 TRP A 50 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP A 50 CZ3 CH2 REMARK 470 LYS A 51 CG CD CE NZ REMARK 470 GLU A 100 CG CD OE1 OE2 REMARK 470 LYS A 103 CG CD CE NZ REMARK 470 LYS A 104 CG CD CE NZ REMARK 470 GLU A 105 CG CD OE1 OE2 REMARK 470 LEU A 108 CG CD1 CD2 REMARK 470 LEU A 110 CG CD1 CD2 REMARK 470 THR A 111 OG1 CG2 REMARK 470 GLU A 112 CG CD OE1 OE2 REMARK 470 GLU A 116 CG CD OE1 OE2 REMARK 470 GLU A 121 CG CD OE1 OE2 REMARK 470 LYS A 125 CG CD CE NZ REMARK 470 GLU A 154 CG CD OE1 OE2 REMARK 470 LYS A 172 CG CD CE NZ REMARK 470 LYS A 214 CG CD CE NZ REMARK 470 GLU A 218 CG CD OE1 OE2 REMARK 470 LYS A 227 CG CD CE NZ REMARK 470 LYS A 229 CG CD CE NZ REMARK 470 GLU A 232 CG CD OE1 OE2 REMARK 470 LYS A 236 CG CD CE NZ REMARK 470 THR A 237 OG1 CG2 REMARK 470 GLU A 241 CG CD OE1 OE2 REMARK 470 LYS A 242 CG CD CE NZ REMARK 470 LYS A 244 CG CD CE NZ REMARK 470 GLN A 245 CG CD OE1 NE2 REMARK 470 LEU A 338 CG CD1 CD2 REMARK 470 ILE A 344 CG1 CG2 CD1 REMARK 470 LEU A 346 CG CD1 CD2 REMARK 470 VAL A 347 CG1 CG2 REMARK 470 ILE A 353 CG1 CG2 CD1 REMARK 470 TYR A 358 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 GLN A 411 CG CD OE1 NE2 REMARK 470 LYS A 440 CG CD CE NZ REMARK 470 ARG A 460 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 465 CG OD1 OD2 REMARK 470 ASP A 467 CG OD1 OD2 REMARK 470 SER A 496 OG REMARK 470 GLU A 497 CG CD OE1 OE2 REMARK 470 LYS A 498 CG CD CE NZ REMARK 470 HIS A 500 CG ND1 CD2 CE1 NE2 REMARK 470 LYS A 516 CG CD CE NZ REMARK 470 HIS A 520 CG ND1 CD2 CE1 NE2 REMARK 470 LYS A 522 CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 NH2 ARG A 170 O HOH A 2053 2.11 REMARK 500 REMARK 500 REMARK: NULL 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 GLN A 36 -75.26 -110.89 REMARK 500 THR A 111 -74.21 -96.14 REMARK 500 TYR A 358 -94.19 -107.08 REMARK 500 LYS A 385 -134.45 46.19 REMARK 500 ASN A 424 -96.36 -147.07 REMARK 500 LEU A 441 84.02 -173.38 REMARK 500 SER A 501 -0.48 -58.12 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1F0L RELATED DB: PDB REMARK 900 1.55 ANGSTROM CRYSTAL STRUCTURE OF WILD TYPE DIPHTHERIA TOXIN REMARK 900 RELATED ID: 4AE1 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF DIPHTHERIA TOXIN MUTANT CRM197 IN COMPLEX WITH REMARK 900 NICOTINAMIDE REMARK 900 RELATED ID: 1SGK RELATED DB: PDB REMARK 900 NUCLEOTIDE-FREE DIPHTHERIA TOXIN REMARK 900 RELATED ID: 1DTP RELATED DB: PDB REMARK 900 DIPHTHERIA TOXIN CATALYTIC DOMAIN (RESIDUES 1 - 190) COMPLEXED WITH REMARK 900 ADENYLYL(3'->5')URIDINE 3'-MONOPHOSPHATE (APUP) REMARK 900 RELATED ID: 1DDT RELATED DB: PDB REMARK 900 DIPHTHERIA TOXIN (DIMERIC) REMARK 900 RELATED ID: 1MDT RELATED DB: PDB REMARK 900 MONOMERIC DIPHTHERIA TOXIN REMARK 900 RELATED ID: 1TOX RELATED DB: PDB REMARK 900 DIPHTHERIA TOXIN DIMER COMPLEXED WITH NAD REMARK 900 RELATED ID: 1XDT RELATED DB: PDB REMARK 900 COMPLEX OF DIPHTHERIA TOXIN AND HEPARIN-BINDING EPIDERMAL GROWTH REMARK 900 FACTOR REMARK 999 REMARK 999 SEQUENCE REMARK 999 COORDINATES USE STANDARD RESIDUE NUMBERING FOR CONSISTENCY REMARK 999 WITH PREVIOUS WORK RESULTING IN THE NATURAL GLY TO GLU MUTATION REMARK 999 AT POSITION 52 INSTEAD OF 53. RESIDUES 1-32 IN THE UNIPROT REMARK 999 SEQUENCE ARE THE SIGNAL PEPTIDE. DBREF 4AE0 A 1 535 UNP P00588 DTX_CORBE 33 567 SEQADV 4AE0 GLU A 52 UNP P00588 GLY 53 ENGINEERED MUTATION SEQRES 1 A 535 GLY ALA ASP ASP VAL VAL ASP SER SER LYS SER PHE VAL SEQRES 2 A 535 MET GLU ASN PHE SER SER TYR HIS GLY THR LYS PRO GLY SEQRES 3 A 535 TYR VAL ASP SER ILE GLN LYS GLY ILE GLN LYS PRO LYS SEQRES 4 A 535 SER GLY THR GLN GLY ASN TYR ASP ASP ASP TRP LYS GLU SEQRES 5 A 535 PHE TYR SER THR ASP ASN LYS TYR ASP ALA ALA GLY TYR SEQRES 6 A 535 SER VAL ASP ASN GLU ASN PRO LEU SER GLY LYS ALA GLY SEQRES 7 A 535 GLY VAL VAL LYS VAL THR TYR PRO GLY LEU THR LYS VAL SEQRES 8 A 535 LEU ALA LEU LYS VAL ASP ASN ALA GLU THR ILE LYS LYS SEQRES 9 A 535 GLU LEU GLY LEU SER LEU THR GLU PRO LEU MET GLU GLN SEQRES 10 A 535 VAL GLY THR GLU GLU PHE ILE LYS ARG PHE GLY ASP GLY SEQRES 11 A 535 ALA SER ARG VAL VAL LEU SER LEU PRO PHE ALA GLU GLY SEQRES 12 A 535 SER SER SER VAL GLU TYR ILE ASN ASN TRP GLU GLN ALA SEQRES 13 A 535 LYS ALA LEU SER VAL GLU LEU GLU ILE ASN PHE GLU THR SEQRES 14 A 535 ARG GLY LYS ARG GLY GLN ASP ALA MET TYR GLU TYR MET SEQRES 15 A 535 ALA GLN ALA CYS ALA GLY ASN ARG VAL ARG ARG SER VAL SEQRES 16 A 535 GLY SER SER LEU SER CYS ILE ASN LEU ASP TRP ASP VAL SEQRES 17 A 535 ILE ARG ASP LYS THR LYS THR LYS ILE GLU SER LEU LYS SEQRES 18 A 535 GLU HIS GLY PRO ILE LYS ASN LYS MET SER GLU SER PRO SEQRES 19 A 535 ASN LYS THR VAL SER GLU GLU LYS ALA LYS GLN TYR LEU SEQRES 20 A 535 GLU GLU PHE HIS GLN THR ALA LEU GLU HIS PRO GLU LEU SEQRES 21 A 535 SER GLU LEU LYS THR VAL THR GLY THR ASN PRO VAL PHE SEQRES 22 A 535 ALA GLY ALA ASN TYR ALA ALA TRP ALA VAL ASN VAL ALA SEQRES 23 A 535 GLN VAL ILE ASP SER GLU THR ALA ASP ASN LEU GLU LYS SEQRES 24 A 535 THR THR ALA ALA LEU SER ILE LEU PRO GLY ILE GLY SER SEQRES 25 A 535 VAL MET GLY ILE ALA ASP GLY ALA VAL HIS HIS ASN THR SEQRES 26 A 535 GLU GLU ILE VAL ALA GLN SER ILE ALA LEU SER SER LEU SEQRES 27 A 535 MET VAL ALA GLN ALA ILE PRO LEU VAL GLY GLU LEU VAL SEQRES 28 A 535 ASP ILE GLY PHE ALA ALA TYR ASN PHE VAL GLU SER ILE SEQRES 29 A 535 ILE ASN LEU PHE GLN VAL VAL HIS ASN SER TYR ASN ARG SEQRES 30 A 535 PRO ALA TYR SER PRO GLY HIS LYS THR GLN PRO PHE LEU SEQRES 31 A 535 HIS ASP GLY TYR ALA VAL SER TRP ASN THR VAL GLU ASP SEQRES 32 A 535 SER ILE ILE ARG THR GLY PHE GLN GLY GLU SER GLY HIS SEQRES 33 A 535 ASP ILE LYS ILE THR ALA GLU ASN THR PRO LEU PRO ILE SEQRES 34 A 535 ALA GLY VAL LEU LEU PRO THR ILE PRO GLY LYS LEU ASP SEQRES 35 A 535 VAL ASN LYS SER LYS THR HIS ILE SER VAL ASN GLY ARG SEQRES 36 A 535 LYS ILE ARG MET ARG CYS ARG ALA ILE ASP GLY ASP VAL SEQRES 37 A 535 THR PHE CYS ARG PRO LYS SER PRO VAL TYR VAL GLY ASN SEQRES 38 A 535 GLY VAL HIS ALA ASN LEU HIS VAL ALA PHE HIS ARG SER SEQRES 39 A 535 SER SER GLU LYS ILE HIS SER ASN GLU ILE SER SER ASP SEQRES 40 A 535 SER ILE GLY VAL LEU GLY TYR GLN LYS THR VAL ASP HIS SEQRES 41 A 535 THR LYS VAL ASN SER LYS LEU SER LEU PHE PHE GLU ILE SEQRES 42 A 535 LYS SER FORMUL 2 HOH *169(H2 O) HELIX 1 1 ASP A 7 SER A 11 5 5 HELIX 2 2 TYR A 27 GLN A 32 1 6 HELIX 3 3 ASN A 58 GLY A 64 1 7 HELIX 4 4 ASN A 98 LEU A 106 1 9 HELIX 5 5 PRO A 113 GLY A 119 1 7 HELIX 6 6 THR A 120 GLY A 128 1 9 HELIX 7 7 GLU A 154 LEU A 159 5 6 HELIX 8 8 GLU A 168 GLY A 171 5 4 HELIX 9 9 GLN A 175 ALA A 183 1 9 HELIX 10 10 GLN A 184 ALA A 187 5 4 HELIX 11 11 ASP A 205 HIS A 223 1 19 HELIX 12 12 HIS A 223 SER A 231 1 9 HELIX 13 13 SER A 239 LEU A 255 1 17 HELIX 14 14 GLU A 256 GLU A 259 5 4 HELIX 15 15 LEU A 260 THR A 267 1 8 HELIX 16 16 ASN A 270 PHE A 273 5 4 HELIX 17 17 ALA A 274 ILE A 289 1 16 HELIX 18 18 ASP A 290 ASP A 295 1 6 HELIX 19 19 ASN A 296 SER A 305 1 10 HELIX 20 20 ILE A 310 GLY A 315 1 6 HELIX 21 21 THR A 325 GLY A 348 1 24 HELIX 22 22 ILE A 353 ALA A 357 5 5 HELIX 23 23 TYR A 358 ARG A 377 1 20 HELIX 24 24 VAL A 401 ASP A 403 5 3 SHEET 1 AA 5 PHE A 12 GLU A 15 0 SHEET 2 AA 5 LEU A 88 ALA A 93 -1 O THR A 89 N MET A 14 SHEET 3 AA 5 ARG A 133 PRO A 139 1 O ARG A 133 N LYS A 90 SHEET 4 AA 5 VAL A 147 ASN A 151 -1 O GLU A 148 N LEU A 138 SHEET 5 AA 5 PHE A 53 THR A 56 -1 O PHE A 53 N ASN A 151 SHEET 1 AB 3 SER A 18 THR A 23 0 SHEET 2 AB 3 GLY A 79 THR A 84 -1 O GLY A 79 N THR A 23 SHEET 3 AB 3 SER A 160 ASN A 166 -1 O SER A 160 N THR A 84 SHEET 1 AC 2 ILE A 316 ALA A 317 0 SHEET 2 AC 2 ALA A 320 VAL A 321 -1 O ALA A 320 N ALA A 317 SHEET 1 AD10 PHE A 389 HIS A 391 0 SHEET 2 AD10 TYR A 394 TRP A 398 -1 O TYR A 394 N HIS A 391 SHEET 3 AD10 GLY A 412 ALA A 422 -1 O LYS A 419 N SER A 397 SHEET 4 AD10 ALA A 485 ARG A 493 -1 O ALA A 485 N ILE A 420 SHEET 5 AD10 HIS A 449 VAL A 452 -1 O HIS A 449 N HIS A 488 SHEET 6 AD10 ARG A 455 ILE A 464 -1 O ARG A 455 N VAL A 452 SHEET 7 AD10 VAL A 468 PRO A 473 -1 O VAL A 468 N ILE A 464 SHEET 8 AD10 GLY A 431 PRO A 435 -1 O VAL A 432 N CYS A 471 SHEET 9 AD10 SER A 508 LYS A 516 -1 O GLY A 510 N LEU A 433 SHEET 10 AD10 VAL A 523 PHE A 530 -1 O VAL A 523 N LYS A 516 SHEET 1 AE 5 PHE A 389 HIS A 391 0 SHEET 2 AE 5 TYR A 394 TRP A 398 -1 O TYR A 394 N HIS A 391 SHEET 3 AE 5 GLY A 412 ALA A 422 -1 O LYS A 419 N SER A 397 SHEET 4 AE 5 ALA A 485 ARG A 493 -1 O ALA A 485 N ILE A 420 SHEET 5 AE 5 ASP A 442 VAL A 443 -1 O ASP A 442 N HIS A 492 SHEET 1 AF 2 ILE A 405 ARG A 407 0 SHEET 2 AF 2 GLU A 532 LYS A 534 1 O GLU A 532 N ILE A 406 SHEET 1 AG 2 LEU A 427 PRO A 428 0 SHEET 2 AG 2 TYR A 478 VAL A 479 -1 O VAL A 479 N LEU A 427 SSBOND 1 CYS A 186 CYS A 201 1555 1555 2.04 SSBOND 2 CYS A 461 CYS A 471 1555 1555 2.06 CRYST1 105.841 91.388 63.838 90.00 91.71 90.00 C 1 2 1 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 0.009448 0.000000 0.000282 0.00000 SCALE2 0.000000 0.010942 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015672 0.00000