HEADER SIGNALING PROTEIN 06-OCT-20 7ALK TITLE STRUCTURE OF DROSOPHILA C2-DSL-EGF1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: NEUROGENIC LOCUS PROTEIN DELTA; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DELTA; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DROSOPHILA MELANOGASTER; SOURCE 3 ORGANISM_COMMON: FRUIT FLY; SOURCE 4 ORGANISM_TAXID: 7227; SOURCE 5 GENE: DL, CG3619; SOURCE 6 EXPRESSION_SYSTEM: DROSOPHILA MELANOGASTER; SOURCE 7 EXPRESSION_SYSTEM_COMMON: FRUIT FLY; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 7227; SOURCE 9 EXPRESSION_SYSTEM_CELL_LINE: S2 CELLS KEYWDS DELTA NOTCH LIGAND C2, DSL AND EGF DOMAINS, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR R.SUCKLING,S.JOHNSON,S.M.LEA REVDAT 3 31-JAN-24 7ALK 1 REMARK REVDAT 2 13-OCT-21 7ALK 1 JRNL REMARK REVDAT 1 04-AUG-21 7ALK 0 JRNL AUTH T.MARTINS,Y.MENG,B.KORONA,R.SUCKLING,S.JOHNSON,P.A.HANDFORD, JRNL AUTH 2 S.M.LEA,S.J.BRAY JRNL TITL THE CONSERVED C2 PHOSPHOLIPID-BINDING DOMAIN IN DELTA JRNL TITL 2 CONTRIBUTES TO ROBUST NOTCH SIGNALLING. JRNL REF EMBO REP. V. 22 52729 2021 JRNL REFN ESSN 1469-3178 JRNL PMID 34347930 JRNL DOI 10.15252/EMBR.202152729 REMARK 2 REMARK 2 RESOLUTION. 3.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX DEV_3965 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) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.11 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 5066 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.244 REMARK 3 R VALUE (WORKING SET) : 0.241 REMARK 3 FREE R VALUE : 0.297 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.670 REMARK 3 FREE R VALUE TEST SET COUNT : 287 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 29.1100 - 3.7800 1.00 2418 135 0.2160 0.2696 REMARK 3 2 3.7800 - 3.0000 1.00 2361 152 0.2784 0.3358 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) : 0.505 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.909 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 33.66 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.61 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 1941 REMARK 3 ANGLE : 0.583 2624 REMARK 3 CHIRALITY : 0.053 302 REMARK 3 PLANARITY : 0.003 330 REMARK 3 DIHEDRAL : 14.941 310 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 7ALK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 06-OCT-20. REMARK 100 THE DEPOSITION ID IS D_1292111652. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-JUL-15 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 : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5066 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.000 REMARK 200 RESOLUTION RANGE LOW (A) : 29.110 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 4.5500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.11 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 : 0.850 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: 5MVX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.02 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.41 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS PH 8.5, 0.2M MGCL2, 30% REMARK 280 PEG4K, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 43.36800 REMARK 290 SMTRY3 2 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: MONOMERIC 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 ASP A 101 REMARK 465 ALA A 102 REMARK 465 GLN A 103 REMARK 465 ARG A 104 REMARK 465 PHE A 105 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 SER A 50 OG 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 ASN A 35 70.08 -164.31 REMARK 500 ARG A 44 -178.09 -68.28 REMARK 500 SER A 50 -159.46 -109.39 REMARK 500 THR A 54 -104.62 54.65 REMARK 500 SER A 60 175.65 62.45 REMARK 500 ASN A 95 -121.10 53.95 REMARK 500 ASN A 107 -107.04 -136.44 REMARK 500 ASN A 137 50.32 -158.28 REMARK 500 SER A 171 -140.97 -99.74 REMARK 500 ASP A 201 64.74 -150.31 REMARK 500 SER A 210 -155.34 -84.37 REMARK 500 LYS A 233 97.49 -63.71 REMARK 500 CYS A 235 79.98 60.49 REMARK 500 HIS A 237 -43.28 68.03 REMARK 500 LYS A 253 -159.67 -122.11 REMARK 500 REMARK 500 REMARK: NULL DBREF 7ALK A 23 258 UNP P10041 DL_DROME 23 258 SEQRES 1 A 236 SER GLY SER PHE GLU LEU ARG LEU LYS TYR PHE SER ASN SEQRES 2 A 236 ASP HIS GLY ARG ASP ASN GLU GLY ARG CYS CYS SER GLY SEQRES 3 A 236 GLU SER ASP GLY ALA THR GLY LYS CYS LEU GLY SER CYS SEQRES 4 A 236 LYS THR ARG PHE ARG VAL CYS LEU LYS HIS TYR GLN ALA SEQRES 5 A 236 THR ILE ASP THR THR SER GLN CYS THR TYR GLY ASP VAL SEQRES 6 A 236 ILE THR PRO ILE LEU GLY GLU ASN SER VAL ASN LEU THR SEQRES 7 A 236 ASP ALA GLN ARG PHE GLN ASN LYS GLY PHE THR ASN PRO SEQRES 8 A 236 ILE GLN PHE PRO PHE SER PHE SER TRP PRO GLY THR PHE SEQRES 9 A 236 SER LEU ILE VAL GLU ALA TRP HIS ASP THR ASN ASN SER SEQRES 10 A 236 GLY ASN ALA ARG THR ASN LYS LEU LEU ILE GLN ARG LEU SEQRES 11 A 236 LEU VAL GLN GLN VAL LEU GLU VAL SER SER GLU TRP LYS SEQRES 12 A 236 THR ASN LYS SER GLU SER GLN TYR THR SER LEU GLU TYR SEQRES 13 A 236 ASP PHE ARG VAL THR CYS ASP LEU ASN TYR TYR GLY SER SEQRES 14 A 236 GLY CYS ALA LYS PHE CYS ARG PRO ARG ASP ASP SER PHE SEQRES 15 A 236 GLY HIS SER THR CYS SER GLU THR GLY GLU ILE ILE CYS SEQRES 16 A 236 LEU THR GLY TRP GLN GLY ASP TYR CYS HIS ILE PRO LYS SEQRES 17 A 236 CYS ALA LYS GLY CYS GLU HIS GLY HIS CYS ASP LYS PRO SEQRES 18 A 236 ASN GLN CYS VAL CYS GLN LEU GLY TRP LYS GLY ALA LEU SEQRES 19 A 236 CYS ASN HET NAG B 1 14 HET NAG B 2 14 HET BMA B 3 11 HET MAN B 4 11 HET MAN B 5 11 HET FUC B 6 10 HET NAG A 301 14 HET NAG A 302 14 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM BMA BETA-D-MANNOPYRANOSE HETNAM MAN ALPHA-D-MANNOPYRANOSE HETNAM FUC ALPHA-L-FUCOPYRANOSE HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE HETSYN BMA BETA-D-MANNOSE; D-MANNOSE; MANNOSE HETSYN MAN ALPHA-D-MANNOSE; D-MANNOSE; MANNOSE HETSYN FUC ALPHA-L-FUCOSE; 6-DEOXY-ALPHA-L-GALACTOPYRANOSE; L- HETSYN 2 FUC FUCOSE; FUCOSE FORMUL 2 NAG 4(C8 H15 N O6) FORMUL 2 BMA C6 H12 O6 FORMUL 2 MAN 2(C6 H12 O6) FORMUL 2 FUC C6 H12 O5 FORMUL 5 HOH *2(H2 O) SHEET 1 AA1 3 VAL A 97 ASN A 98 0 SHEET 2 AA1 3 SER A 25 SER A 34 -1 N PHE A 33 O VAL A 97 SHEET 3 AA1 3 ILE A 114 PRO A 117 -1 O ILE A 114 N LEU A 28 SHEET 1 AA2 4 VAL A 97 ASN A 98 0 SHEET 2 AA2 4 SER A 25 SER A 34 -1 N PHE A 33 O VAL A 97 SHEET 3 AA2 4 SER A 175 THR A 183 -1 O SER A 175 N SER A 34 SHEET 4 AA2 4 LYS A 165 GLU A 170 -1 N SER A 169 O LEU A 176 SHEET 1 AA3 3 GLY A 85 ILE A 88 0 SHEET 2 AA3 3 LYS A 62 LYS A 70 -1 N VAL A 67 O VAL A 87 SHEET 3 AA3 3 GLY A 93 GLU A 94 -1 O GLY A 93 N THR A 63 SHEET 1 AA4 4 GLY A 85 ILE A 88 0 SHEET 2 AA4 4 LYS A 62 LYS A 70 -1 N VAL A 67 O VAL A 87 SHEET 3 AA4 4 THR A 125 ASP A 135 -1 O ILE A 129 N CYS A 68 SHEET 4 AA4 4 LYS A 146 VAL A 157 -1 O LEU A 147 N HIS A 134 SHEET 1 AA5 2 TYR A 188 TYR A 189 0 SHEET 2 AA5 2 LYS A 195 PHE A 196 -1 O LYS A 195 N TYR A 189 SHEET 1 AA6 3 ARG A 200 ASP A 202 0 SHEET 2 AA6 3 GLY A 205 CYS A 209 -1 O SER A 207 N ARG A 200 SHEET 3 AA6 3 ILE A 215 CYS A 217 -1 O ILE A 216 N THR A 208 SHEET 1 AA7 2 TRP A 221 GLN A 222 0 SHEET 2 AA7 2 ILE A 228 PRO A 229 -1 O ILE A 228 N GLN A 222 SSBOND 1 CYS A 45 CYS A 57 1555 1555 2.02 SSBOND 2 CYS A 46 CYS A 61 1555 1555 2.03 SSBOND 3 CYS A 68 CYS A 82 1555 1555 2.03 SSBOND 4 CYS A 184 CYS A 193 1555 1555 2.03 SSBOND 5 CYS A 197 CYS A 209 1555 1555 2.03 SSBOND 6 CYS A 217 CYS A 226 1555 1555 2.02 SSBOND 7 CYS A 231 CYS A 240 1555 1555 2.03 SSBOND 8 CYS A 235 CYS A 246 1555 1555 2.02 SSBOND 9 CYS A 248 CYS A 257 1555 1555 2.03 LINK ND2 ASN A 98 C1 NAG A 301 1555 1555 1.45 LINK ND2 ASN A 137 C1 NAG B 1 1555 1555 1.44 LINK ND2 ASN A 167 C1 NAG A 302 1555 1555 1.44 LINK O4 NAG B 1 C1 NAG B 2 1555 1555 1.44 LINK O6 NAG B 1 C1 FUC B 6 1555 1555 1.45 LINK O4 NAG B 2 C1 BMA B 3 1555 1555 1.44 LINK O3 BMA B 3 C1 MAN B 4 1555 1555 1.45 LINK O6 BMA B 3 C1 MAN B 5 1555 1555 1.45 CISPEP 1 ASN A 112 PRO A 113 0 2.97 CRYST1 30.990 86.736 47.558 90.00 94.27 90.00 P 1 21 1 2 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 0.032268 0.000000 0.002410 0.00000 SCALE2 0.000000 0.011529 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021086 0.00000