HEADER SIGNALING PROTEIN 09-AUG-19 6TYY TITLE HEDGEHOG AUTOPROCESSING MUTANT D46H COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN HEDGEHOG; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: 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: HH, CG4637; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HEDGEHOG AUTOPROCESSING DOAMIN, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR H.LI,Z.LI,C.WANG,B.P.CALLAHAN REVDAT 3 11-OCT-23 6TYY 1 REMARK REVDAT 2 04-DEC-19 6TYY 1 JRNL REVDAT 1 20-NOV-19 6TYY 0 JRNL AUTH J.ZHAO,D.A.CIULLA,J.XIE,A.G.WAGNER,D.A.CASTILLO,A.S.ZWARYCZ, JRNL AUTH 2 Z.LIN,S.BEADLE,J.L.GINER,Z.LI,H.LI,N.BANAVALI,B.P.CALLAHAN, JRNL AUTH 3 C.WANG JRNL TITL GENERAL BASE SWAP PRESERVES ACTIVITY AND EXPANDS SUBSTRATE JRNL TITL 2 TOLERANCE IN HEDGEHOG AUTOPROCESSING. JRNL REF J.AM.CHEM.SOC. V. 141 18380 2019 JRNL REFN ESSN 1520-5126 JRNL PMID 31682419 JRNL DOI 10.1021/JACS.9B08914 REMARK 2 REMARK 2 RESOLUTION. 1.36 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.36 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.66 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 28172 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.172 REMARK 3 R VALUE (WORKING SET) : 0.171 REMARK 3 FREE R VALUE : 0.195 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.080 REMARK 3 FREE R VALUE TEST SET COUNT : 1994 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 25.6560 - 3.2765 1.00 1941 149 0.1382 0.1549 REMARK 3 2 3.2765 - 2.6015 1.00 1901 147 0.1539 0.1779 REMARK 3 3 2.6015 - 2.2729 1.00 1889 141 0.1660 0.1595 REMARK 3 4 2.2729 - 2.0652 1.00 1858 139 0.1512 0.1764 REMARK 3 5 2.0652 - 1.9172 1.00 1881 147 0.1574 0.1937 REMARK 3 6 1.9172 - 1.8042 1.00 1868 141 0.1776 0.1944 REMARK 3 7 1.8042 - 1.7138 1.00 1881 143 0.1744 0.2320 REMARK 3 8 1.7138 - 1.6393 1.00 1850 139 0.1880 0.2007 REMARK 3 9 1.6393 - 1.5762 1.00 1869 142 0.1931 0.2097 REMARK 3 10 1.5762 - 1.5218 1.00 1864 141 0.2071 0.2519 REMARK 3 11 1.5218 - 1.4742 1.00 1869 141 0.2282 0.2984 REMARK 3 12 1.4742 - 1.4321 1.00 1858 142 0.2836 0.3695 REMARK 3 13 1.4321 - 1.3944 1.00 1842 142 0.3544 0.4015 REMARK 3 14 1.3944 - 1.3603 0.96 1807 140 0.4232 0.4362 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.720 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.53 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 6TYY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-AUG-19. REMARK 100 THE DEPOSITION ID IS D_1000243544. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JUN-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL14-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.1271 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 : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28219 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.360 REMARK 200 RESOLUTION RANGE LOW (A) : 100.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 4.700 REMARK 200 R MERGE (I) : 0.05800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.36 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.3 REMARK 200 DATA REDUNDANCY IN SHELL : 2.90 REMARK 200 R MERGE FOR SHELL (I) : 0.92400 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: PHENIX REMARK 200 STARTING MODEL: 1AT0 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.58 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES, PH 7.5, 3.4 M SODIUM REMARK 280 FORMATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 12.45033 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 24.90067 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 18.67550 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 31.12583 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 6.22517 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 O HOH A 570 O HOH A 613 1.77 REMARK 500 O HOH A 501 O HOH A 548 1.85 REMARK 500 O HOH A 607 O HOH A 655 1.95 REMARK 500 O HOH A 566 O HOH A 593 1.97 REMARK 500 O HOH A 575 O HOH A 609 2.09 REMARK 500 O HOH A 635 O HOH A 653 2.10 REMARK 500 O HOH A 594 O HOH A 659 2.10 REMARK 500 O HOH A 509 O HOH A 568 2.11 REMARK 500 NZ LYS A 352 O HOH A 501 2.15 REMARK 500 OE1 GLU A 351 O HOH A 501 2.19 REMARK 500 O HOH A 619 O HOH A 637 2.19 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 LYS A 352 -15.94 77.80 REMARK 500 REMARK 500 REMARK: NULL DBREF 6TYY A 258 403 UNP Q02936 HH_DROME 258 403 SEQADV 6TYY HIS A 303 UNP Q02936 ASP 303 ENGINEERED MUTATION SEQRES 1 A 146 CSD PHE THR PRO GLU SER THR ALA LEU LEU GLU SER GLY SEQRES 2 A 146 VAL ARG LYS PRO LEU GLY GLU LEU SER ILE GLY ASP ARG SEQRES 3 A 146 VAL LEU SER MET THR ALA ASN GLY GLN ALA VAL TYR SER SEQRES 4 A 146 GLU VAL ILE LEU PHE MET HIS ARG ASN LEU GLU GLN MET SEQRES 5 A 146 GLN ASN PHE VAL GLN LEU HIS THR ASP GLY GLY ALA VAL SEQRES 6 A 146 LEU THR VAL THR PRO ALA HIS LEU VAL SER VAL TRP GLN SEQRES 7 A 146 PRO GLU SER GLN LYS LEU THR PHE VAL PHE ALA ASP ARG SEQRES 8 A 146 ILE GLU GLU LYS ASN GLN VAL LEU VAL ARG ASP VAL GLU SEQRES 9 A 146 THR GLY GLU LEU ARG PRO GLN ARG VAL VAL LYS VAL GLY SEQRES 10 A 146 SER VAL ARG SER LYS GLY VAL VAL ALA PRO LEU THR ARG SEQRES 11 A 146 GLU GLY THR ILE VAL VAL ASN SER VAL ALA ALA SER CYS SEQRES 12 A 146 TYR ALA VAL MODRES 6TYY CSD A 258 CYS MODIFIED RESIDUE HET CSD A 258 8 HETNAM CSD 3-SULFINOALANINE HETSYN CSD S-CYSTEINESULFINIC ACID; S-SULFINOCYSTEINE FORMUL 1 CSD C3 H7 N O4 S FORMUL 2 HOH *161(H2 O) HELIX 1 AA1 ASP A 347 ILE A 349 5 3 SHEET 1 AA1 2 THR A 264 LEU A 266 0 SHEET 2 AA1 2 ARG A 272 PRO A 274 -1 O LYS A 273 N ALA A 265 SHEET 1 AA2 6 ARG A 283 MET A 287 0 SHEET 2 AA2 6 ALA A 293 THR A 317 -1 O SER A 296 N VAL A 284 SHEET 3 AA2 6 LEU A 365 THR A 386 -1 O LEU A 385 N LEU A 300 SHEET 4 AA2 6 GLN A 354 ARG A 358 -1 N VAL A 357 O ARG A 366 SHEET 5 AA2 6 VAL A 396 ALA A 402 -1 O ALA A 397 N LEU A 356 SHEET 6 AA2 6 THR A 390 VAL A 393 -1 N ILE A 391 O ALA A 398 SHEET 1 AA3 4 LYS A 340 PHE A 345 0 SHEET 2 AA3 4 HIS A 329 GLN A 335 -1 N VAL A 331 O VAL A 344 SHEET 3 AA3 4 VAL A 396 ALA A 402 -1 O SER A 399 N LEU A 330 SHEET 4 AA3 4 THR A 390 VAL A 393 -1 N ILE A 391 O ALA A 398 SHEET 1 AA4 6 VAL A 322 VAL A 325 0 SHEET 2 AA4 6 ALA A 293 THR A 317 -1 N VAL A 313 O VAL A 325 SHEET 3 AA4 6 LEU A 365 THR A 386 -1 O LEU A 385 N LEU A 300 SHEET 4 AA4 6 GLN A 354 ARG A 358 -1 N VAL A 357 O ARG A 366 SHEET 5 AA4 6 HIS A 329 GLN A 335 -1 N TRP A 334 O GLN A 354 SHEET 6 AA4 6 LYS A 340 PHE A 345 -1 O VAL A 344 N VAL A 331 LINK C CSD A 258 N PHE A 259 1555 1555 1.34 CRYST1 78.381 78.381 37.351 90.00 90.00 120.00 P 61 6 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 0.012758 0.007366 0.000000 0.00000 SCALE2 0.000000 0.014732 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026773 0.00000 HETATM 1 N CSD A 258 23.340 -31.304 -2.039 1.00 13.02 N HETATM 2 CA CSD A 258 24.781 -31.332 -1.918 1.00 11.98 C HETATM 3 CB CSD A 258 25.356 -32.578 -2.596 1.00 15.56 C HETATM 4 SG CSD A 258 24.928 -34.036 -1.694 1.00 19.61 S HETATM 5 C CSD A 258 25.432 -30.092 -2.523 1.00 11.61 C HETATM 6 O CSD A 258 24.855 -29.419 -3.390 1.00 12.81 O HETATM 7 OD1 CSD A 258 23.492 -33.961 -1.455 1.00 25.71 O HETATM 8 OD2 CSD A 258 24.897 -35.156 -2.970 1.00 31.47 O