HEADER TOXIN 05-MAR-14 2MLW TITLE NEW CYT-LIKE DELTA-ENDOTOXINS FROM DICKEYA DADANTII - CYTC PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: TYPE-1BA CYTOLYTIC DELTA-ENDOTOXIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CYTC PROTEIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DICKEYA DADANTII; SOURCE 3 ORGANISM_TAXID: 204038; SOURCE 4 GENE: DDA3937_01343; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: NM522; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PGEX KEYWDS CYTOLYSIN FOLD, MODIFIED GREEK KEY TOPOLOGY, TOXIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR K.LOTH,D.COSTECHAREYRE,G.EFFANTIN,Y.RAHBE,G.CONDEMINE,C.LANDON,P.DA AUTHOR 2 SILVA REVDAT 3 14-JUN-23 2MLW 1 REMARK REVDAT 2 18-MAR-15 2MLW 1 JRNL REVDAT 1 18-FEB-15 2MLW 0 JRNL AUTH K.LOTH,D.COSTECHAREYRE,G.EFFANTIN,Y.RAHBE,G.CONDEMINE, JRNL AUTH 2 C.LANDON,P.DA SILVA JRNL TITL NEW CYT-LIKE DELTA-ENDOTOXINS FROM DICKEYA DADANTII: JRNL TITL 2 STRUCTURE AND APHICIDAL ACTIVITY. JRNL REF SCI REP V. 5 8791 2015 JRNL REFN ESSN 2045-2322 JRNL PMID 25740111 JRNL DOI 10.1038/SREP08791 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : VNMRJ, ARIA REMARK 3 AUTHORS : VARIAN (VNMRJ), LINGE, O'DONOGHUE AND NILGES REMARK 3 (ARIA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2MLW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-MAR-14. REMARK 100 THE DEPOSITION ID IS D_1000103770. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 0.1 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.3 MM [U-13C; U-15N] CYTC, 50 REMARK 210 MM TRIS, 100 MM SODIUM CHLORIDE, REMARK 210 1 MM EDTA, 5 MM DTT, 90% H2O/10% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D HNCO; 3D HNCA; 3D HNCACB; 3D REMARK 210 CBCA(CO)NH; 3D C(CO)NH; 3D HCCH- REMARK 210 TOCSY; 3D 1H-15N TOCSY; 3D 1H- REMARK 210 15N NOESY; 3D 1H-13C NOESY; 2D REMARK 210 1H-15N HSQC; 2D 1H-13C HSQC; 3D REMARK 210 HN(CO)CA REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CCPNMR 2.1.5, NMRPIPE, ARIA 2.3 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 500 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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: 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: CLOSE CONTACTS 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 HE22 GLN A 129 H VAL A 136 1.27 REMARK 500 HD22 ASN A 176 H ASP A 179 1.31 REMARK 500 O ILE A 171 HD21 ASN A 176 1.50 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 18 PRO A 122 C - N - CA ANGL. DEV. = 9.1 DEGREES 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 1 SER A 2 -164.17 67.52 REMARK 500 1 ILE A 3 -94.49 -80.41 REMARK 500 1 GLU A 4 91.56 49.60 REMARK 500 1 ILE A 5 -148.80 -123.02 REMARK 500 1 TYR A 6 -58.53 -143.49 REMARK 500 1 ASP A 9 -31.61 -167.91 REMARK 500 1 THR A 12 7.37 -174.03 REMARK 500 1 PHE A 18 -43.94 176.70 REMARK 500 1 LEU A 19 54.55 -154.63 REMARK 500 1 TYR A 26 -19.06 -42.84 REMARK 500 1 ALA A 28 -13.83 -144.56 REMARK 500 1 ASP A 61 -73.51 -116.69 REMARK 500 1 LEU A 62 -147.45 -106.84 REMARK 500 1 ALA A 63 -159.73 -146.10 REMARK 500 1 PHE A 76 29.71 -75.07 REMARK 500 1 SER A 77 -157.58 -84.04 REMARK 500 1 VAL A 95 45.46 -82.18 REMARK 500 1 LEU A 96 -81.96 -94.55 REMARK 500 1 ILE A 98 156.90 -47.58 REMARK 500 1 ASP A 101 -85.46 -107.19 REMARK 500 1 THR A 102 66.82 33.04 REMARK 500 1 TYR A 103 -159.89 -158.94 REMARK 500 1 GLN A 105 -44.65 76.57 REMARK 500 1 ASP A 114 86.25 47.22 REMARK 500 1 LYS A 121 131.32 86.11 REMARK 500 1 PHE A 124 -179.19 -60.41 REMARK 500 1 ASN A 127 -152.42 -106.98 REMARK 500 1 ALA A 128 154.05 -27.55 REMARK 500 1 ASP A 131 -55.40 -140.87 REMARK 500 1 TYR A 141 -139.39 -78.98 REMARK 500 1 SER A 142 102.73 82.22 REMARK 500 1 ALA A 154 -169.43 -79.96 REMARK 500 1 MET A 156 119.62 -162.80 REMARK 500 1 ASP A 173 -129.47 -124.55 REMARK 500 1 LYS A 178 60.24 90.23 REMARK 500 1 PHE A 196 109.69 -29.50 REMARK 500 1 GLN A 197 -72.67 -81.96 REMARK 500 1 THR A 200 -177.25 168.26 REMARK 500 1 PRO A 201 93.87 -47.72 REMARK 500 2 SER A 2 177.47 179.83 REMARK 500 2 ILE A 3 -96.45 -78.08 REMARK 500 2 GLU A 4 88.61 45.20 REMARK 500 2 ILE A 5 -150.42 -121.97 REMARK 500 2 TYR A 6 -54.59 -139.25 REMARK 500 2 PRO A 7 62.76 -64.38 REMARK 500 2 ASP A 8 -66.50 -179.95 REMARK 500 2 ASP A 9 -22.55 -168.00 REMARK 500 2 THR A 12 -5.44 179.56 REMARK 500 2 PHE A 18 -46.79 178.77 REMARK 500 2 LEU A 19 50.13 -143.18 REMARK 500 REMARK 500 THIS ENTRY HAS 810 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ALA A 170 ILE A 171 1 -146.06 REMARK 500 TYR A 141 SER A 142 2 146.31 REMARK 500 THR A 169 ALA A 170 2 -147.79 REMARK 500 TRP A 123 PHE A 124 5 146.12 REMARK 500 ALA A 170 ILE A 171 5 -145.86 REMARK 500 ASN A 176 THR A 177 13 -149.40 REMARK 500 ALA A 170 ILE A 171 14 -149.11 REMARK 500 THR A 169 ALA A 170 17 -145.60 REMARK 500 TYR A 141 SER A 142 18 138.95 REMARK 500 SER A 142 LEU A 143 18 132.93 REMARK 500 ALA A 170 ILE A 171 18 -148.72 REMARK 500 THR A 169 ALA A 170 20 148.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 19834 RELATED DB: BMRB DBREF 2MLW A 1 203 UNP E0SJ33 E0SJ33_DICD3 1 203 SEQRES 1 A 203 MET SER ILE GLU ILE TYR PRO ASP ASP GLY ASN THR LEU SEQRES 2 A 203 PRO TYR GLN VAL PHE LEU ASN LEU GLU ASN GLU HIS TYR SEQRES 3 A 203 TYR ALA GLN ALA ILE GLN LEU ALA GLN LEU PHE ALA HIS SEQRES 4 A 203 GLU VAL ASP ASP ASN GLY GLN LEU ASP LEU ALA LYS ALA SEQRES 5 A 203 LEU LYS LYS ALA GLN ALA GLN PRO ASP LEU ALA ILE ILE SEQRES 6 A 203 ALA THR ASN ASN MET THR LEU LYS LYS SER PHE SER THR SEQRES 7 A 203 LEU SER ALA LEU THR THR THR LEU SER GLU GLN LEU LYS SEQRES 8 A 203 ILE GLU GLY VAL LEU GLY ILE SER GLN ASP THR TYR ILE SEQRES 9 A 203 GLN ASN ILE LEU SER HIS ALA PHE CYS ASP LEU GLU THR SEQRES 10 A 203 GLN LYS ASP LYS PRO TRP PHE HIS ILE ASN ALA GLN PRO SEQRES 11 A 203 ASP ALA GLY HIS SER VAL THR SER TYR SER TYR SER LEU SEQRES 12 A 203 PHE ILE VAL SER GLN GLY GLU GLU THR GLY ALA MET MET SEQRES 13 A 203 ALA ALA GLY PRO LEU ILE ILE THR VAL THR PRO ASN THR SEQRES 14 A 203 ALA ILE SER ASP ILE PHE ASN THR LYS ASP TRP ARG LEU SEQRES 15 A 203 THR LEU GLN LYS GLU GLU ILE THR ILE GLY VAL LYS GLY SEQRES 16 A 203 PHE GLN VAL VAL THR PRO LEU GLY HELIX 1 1 ALA A 28 LEU A 33 1 6 HELIX 2 2 LEU A 33 ALA A 38 1 6 HELIX 3 3 LYS A 51 ALA A 56 1 6 HELIX 4 4 GLN A 57 GLN A 59 5 3 HELIX 5 5 THR A 78 GLN A 89 1 12 SHEET 1 A 4 ILE A 64 LYS A 73 0 SHEET 2 A 4 THR A 183 VAL A 193 -1 O THR A 190 N ALA A 66 SHEET 3 A 4 MET A 155 VAL A 165 -1 N LEU A 161 O GLU A 187 SHEET 4 A 4 SER A 138 SER A 140 -1 N TYR A 139 O THR A 164 SHEET 1 B 4 ILE A 64 LYS A 73 0 SHEET 2 B 4 THR A 183 VAL A 193 -1 O THR A 190 N ALA A 66 SHEET 3 B 4 MET A 155 VAL A 165 -1 N LEU A 161 O GLU A 187 SHEET 4 B 4 ILE A 145 GLN A 148 -1 N ILE A 145 O ALA A 158 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1