HEADER SIGNALING PROTEIN 06-APR-21 7ME5 TITLE STRUCTURE OF THE EXTRACELLULAR WNT-BINDING MODULE IN DRL-2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: TYROSINE-PROTEIN KINASE TRANSMEMBRANE RECEPTOR DRL-2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: EXTRACELLULAR DOMAIN, UNP RESIDUES 26-183; COMPND 5 SYNONYM: DERAILED 2; COMPND 6 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: DRL-2, CG12463, DMEL\CG3915, DNL, DNT-LIKE, DRL-2, DRL-2, SOURCE 6 DRL2, CG3915, DMEL_CG3915; SOURCE 7 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 7108 KEYWDS WNT SIGNALING, RECEPTOR TYROSINE KINASES, ACYLATION, GROWTH FACTOR KEYWDS 2 SIGNALING, CO-RECEPTOR, PSEUDOKINASES, LIGAND, RECEPTOR, CANCER, KEYWDS 3 SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR F.SHI,J.M.MENDROLA,K.PERRY,S.E.STAYROOK,M.A.LEMMON REVDAT 3 18-OCT-23 7ME5 1 REMARK REVDAT 2 24-NOV-21 7ME5 1 JRNL REVDAT 1 13-OCT-21 7ME5 0 JRNL AUTH F.SHI,J.M.MENDROLA,J.B.SHEETZ,N.WU,A.SOMMER,K.F.SPEER, JRNL AUTH 2 J.N.NOORDERMEER,Z.Y.KAN,K.PERRY,S.W.ENGLANDER,S.E.STAYROOK, JRNL AUTH 3 L.G.FRADKIN,M.A.LEMMON JRNL TITL ROR AND RYK EXTRACELLULAR REGION STRUCTURES SUGGEST THAT JRNL TITL 2 RECEPTOR TYROSINE KINASES HAVE DISTINCT WNT-RECOGNITION JRNL TITL 3 MODES. JRNL REF CELL REP V. 37 09834 2021 JRNL REFN ESSN 2211-1247 JRNL PMID 34686333 JRNL DOI 10.1016/J.CELREP.2021.109834 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX DEV_3915 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) : 29.97 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 13748 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.232 REMARK 3 R VALUE (WORKING SET) : 0.230 REMARK 3 FREE R VALUE : 0.253 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.630 REMARK 3 FREE R VALUE TEST SET COUNT : 636 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 29.9700 - 3.4200 1.00 2727 155 0.1826 0.2046 REMARK 3 2 3.4200 - 2.7100 1.00 2600 158 0.2484 0.2796 REMARK 3 3 2.7100 - 2.3700 1.00 2623 127 0.2872 0.3469 REMARK 3 4 2.3700 - 2.1500 1.00 2608 106 0.2913 0.3445 REMARK 3 5 2.1500 - 2.0000 0.97 2554 90 0.3536 0.3651 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) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 35.920 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 46.01 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 1262 REMARK 3 ANGLE : 0.625 1727 REMARK 3 CHIRALITY : 0.063 193 REMARK 3 PLANARITY : 0.005 225 REMARK 3 DIHEDRAL : 6.526 169 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 7ME5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-APR-21. REMARK 100 THE DEPOSITION ID IS D_1000256062. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-JAN-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 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 MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : OSMIC MIRRORS REMARK 200 OPTICS : OSMIC MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944+ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13786 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 45.790 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : 0.06700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.1000 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) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.89800 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: PHASER REMARK 200 STARTING MODEL: 2YGN REMARK 200 REMARK 200 REMARK: BAR REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.93 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 12 MG/ML PROTEIN, 100MM TRIS (PH 8.5), REMARK 280 100 MM SODIUM ACETATE, 25% PEG 6000, 15% GLYCEROL, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 294.15K 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 38.18100 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 38.18100 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 28.48900 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 45.79150 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 28.48900 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 45.79150 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 38.18100 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 28.48900 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 45.79150 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 38.18100 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 28.48900 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 45.79150 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: 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 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 SER A 179 REMARK 465 GLN A 180 REMARK 465 GLY A 181 REMARK 465 PRO A 182 REMARK 465 ALA A 183 REMARK 465 ILE A 184 REMARK 465 GLU A 185 REMARK 465 GLY A 186 REMARK 465 ARG A 187 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 LEU A 131 149.72 -173.68 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 383 DISTANCE = 6.01 ANGSTROMS REMARK 525 HOH A 384 DISTANCE = 6.29 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7ME4 RELATED DB: PDB DBREF 7ME5 A 26 183 UNP Q7JQT0 Q7JQT0_DROME 26 183 SEQADV 7ME5 ILE A 184 UNP Q7JQT0 EXPRESSION TAG SEQADV 7ME5 GLU A 185 UNP Q7JQT0 EXPRESSION TAG SEQADV 7ME5 GLY A 186 UNP Q7JQT0 EXPRESSION TAG SEQADV 7ME5 ARG A 187 UNP Q7JQT0 EXPRESSION TAG SEQRES 1 A 162 TYR LEU ASN ILE PHE ILE SER HIS HIS GLU VAL MET LYS SEQRES 2 A 162 LEU MET GLY LEU GLU ALA ASP LEU PHE TYR VAL HIS GLU SEQRES 3 A 162 GLY ALA ILE ASN THR TYR ALA MET HIS PHE THR VAL PRO SEQRES 4 A 162 VAL PRO ALA ASP VAL HIS GLU LEU GLU PHE SER TRP GLN SEQRES 5 A 162 SER LEU ILE ALA TYR PRO LEU PRO TYR ALA ILE SER ILE SEQRES 6 A 162 GLU TYR ASN ASN ASP GLN GLU ALA LEU GLY THR PRO THR SEQRES 7 A 162 LEU SER ILE PRO HIS LYS GLY LEU VAL PRO GLN GLU ILE SEQRES 8 A 162 GLU SER PHE LEU VAL TYR LEU PRO CYS THR GLY ASN ALA SEQRES 9 A 162 SER LEU GLN MET PRO VAL ASN VAL ASN MET VAL VAL ARG SEQRES 10 A 162 ALA PRO PRO ARG PHE ASN ASP THR ARG LEU HIS PHE LYS SEQRES 11 A 162 ARG ASN LYS ILE CYS ALA LYS GLY ILE SER PRO GLU PRO SEQRES 12 A 162 ASN GLN SER PRO ALA PRO ALA HIS ALA PRO SER GLN GLY SEQRES 13 A 162 PRO ALA ILE GLU GLY ARG HET NAG A 201 14 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE 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 FORMUL 2 NAG C8 H15 N O6 FORMUL 3 HOH *84(H2 O) HELIX 1 AA1 SER A 32 GLY A 41 1 10 HELIX 2 AA2 ASN A 55 PHE A 61 1 7 SHEET 1 AA1 6 ALA A 53 ILE A 54 0 SHEET 2 AA1 6 LEU A 46 HIS A 50 -1 N HIS A 50 O ALA A 53 SHEET 3 AA1 6 LEU A 27 ILE A 31 -1 N ILE A 29 O VAL A 49 SHEET 4 AA1 6 GLU A 71 SER A 78 -1 O SER A 75 N PHE A 30 SHEET 5 AA1 6 GLU A 117 TYR A 122 -1 O PHE A 119 N PHE A 74 SHEET 6 AA1 6 THR A 103 LEU A 104 -1 N THR A 103 O TYR A 122 SHEET 1 AA2 5 THR A 62 VAL A 65 0 SHEET 2 AA2 5 THR A 150 CYS A 160 1 O ILE A 159 N VAL A 65 SHEET 3 AA2 5 LEU A 131 VAL A 141 -1 N MET A 139 O LEU A 152 SHEET 4 AA2 5 PRO A 85 GLU A 91 -1 N SER A 89 O ASN A 138 SHEET 5 AA2 5 LYS A 109 LEU A 111 -1 O GLY A 110 N TYR A 86 SSBOND 1 CYS A 125 CYS A 160 1555 1555 2.03 LINK ND2 ASN A 169 C1 NAG A 201 1555 1555 1.45 CRYST1 56.978 91.583 76.362 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 0.017551 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010919 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013096 0.00000