HEADER IMMUNOSUPPRESSANT 19-AUG-24 9J7J TITLE THE CRYSTAL STRUCTURE OF RIPG4 LRR DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: GALA PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: GALA4 TYPE III EFFECTOR; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RALSTONIA SOLANACEARUM UW551; SOURCE 3 ORGANISM_TAXID: 342110; SOURCE 4 GENE: QQO21_16795; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS BACTERIA TYPE3 SECRETION SYSTEM, BACTERIA EFFECTOR PROTEIN, GALA KEYWDS 2 FAMILY, RALSTONIA SOLANACEARUM EFFECTOR. LRR DOMAIN, KEYWDS 3 IMMUNOSUPPRESSANT EXPDTA X-RAY DIFFRACTION AUTHOR E.H.JUNG,M.S.KIM REVDAT 1 03-SEP-25 9J7J 0 JRNL AUTH E.H.JUNG,M.S.KIM JRNL TITL THE CRYSTAL STRUCTURE OF RIPG4 LRR DOMAIN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1-4487 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) : 3.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.25 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 16806 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.226 REMARK 3 R VALUE (WORKING SET) : 0.224 REMARK 3 FREE R VALUE : 0.264 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 833 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 38.2500 - 6.0800 0.99 2796 148 0.1841 0.2325 REMARK 3 2 6.0800 - 4.8300 0.99 2664 141 0.2509 0.2602 REMARK 3 3 4.8300 - 4.2200 1.00 2635 138 0.2162 0.2678 REMARK 3 4 4.2200 - 3.8300 0.99 2599 138 0.2445 0.2795 REMARK 3 5 3.8300 - 3.5600 0.99 2583 135 0.2688 0.3142 REMARK 3 6 3.5600 - 3.3500 0.98 2531 133 0.3094 0.3499 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.510 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.450 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 9J7J COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-AUG-24. REMARK 100 THE DEPOSITION ID IS D_1300048678. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-FEB-24 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 : PAL/PLS REMARK 200 BEAMLINE : 5C (4A) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16806 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.350 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 19.90 REMARK 200 R MERGE (I) : 0.09700 REMARK 200 R SYM (I) : 0.04100 REMARK 200 FOR THE DATA SET : 28.7800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.41 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 : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX 1.20.1-4487 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 83.56 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 7.48 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M BIS-TRIS PROPANE PH 7.5, 1.5M REMARK 280 AMMONIUM TARTRATE DIBASIC, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 277.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+1/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+5/6 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 72.15933 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 36.07967 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 54.11950 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 18.03983 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 90.19917 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 72.15933 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 36.07967 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 18.03983 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 54.11950 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 90.19917 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 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 102 136.04 178.83 REMARK 500 THR A 106 57.32 -140.07 REMARK 500 SER A 111 118.76 -164.16 REMARK 500 ARG A 139 27.45 -79.59 REMARK 500 CYS A 177 57.21 -151.66 REMARK 500 LEU A 193 107.56 -58.89 REMARK 500 LEU A 198 28.72 -145.28 REMARK 500 THR A 240 -29.72 -146.06 REMARK 500 THR A 263 51.81 -143.40 REMARK 500 ALA A 264 -39.32 -142.27 REMARK 500 LEU A 294 49.47 -103.57 REMARK 500 ALA A 298 35.76 71.34 REMARK 500 ASN A 380 17.11 56.98 REMARK 500 ASN A 391 -154.51 -106.30 REMARK 500 VAL A 412 36.28 -144.32 REMARK 500 SER A 414 45.09 37.74 REMARK 500 ASN A 415 -149.67 -120.54 REMARK 500 ASN A 439 -156.78 -114.20 REMARK 500 REMARK 500 REMARK: NULL DBREF 9J7J A 101 460 UNP F5CT18 F5CT18_RALSL 101 460 SEQRES 1 A 360 GLN GLN LEU THR ILE THR ASN ARG LYS GLY SER GLY GLY SEQRES 2 A 360 ILE PRO SER PRO ASP ASP TYR PRO ALA LEU ARG LYS LEU SEQRES 3 A 360 THR LEU VAL GLY PRO PHE THR ASP ALA ASP LEU GLN ARG SEQRES 4 A 360 LEU PRO PRO SER LEU ARG GLU LEU ASP LEU SER LEU CYS SEQRES 5 A 360 GLU GLY PRO ILE THR ALA VAL GLY ILE ALA HIS LEU LEU SEQRES 6 A 360 ALA LEU PRO LEU ASP ARG LEU ASP VAL SER GLY CYS GLU SEQRES 7 A 360 LEU ASN ALA ASP SER ALA ARG LEU LEU ALA GLY HIS PRO SEQRES 8 A 360 THR LEU THR THR LEU ASN LEU ARG ARG ASN ALA ILE GLY SEQRES 9 A 360 ASP ALA GLY VAL ALA ALA PHE ALA ARG ASN LYS LYS LEU SEQRES 10 A 360 THR THR LEU ASN VAL SER SER ASN GLY ILE GLY PRO VAL SEQRES 11 A 360 GLY VAL ARG ALA LEU ALA ALA ASN THR THR ILE THR THR SEQRES 12 A 360 LEU ASP ILE SER ASN ASN GLU ILE GLY ASP GLU GLY ALA SEQRES 13 A 360 ARG ALA LEU ALA SER ASN THR ALA LEU THR ARG LEU ASP SEQRES 14 A 360 ALA SER ASP CYS GLY ILE GLY PRO GLU GLY THR GLN ALA SEQRES 15 A 360 LEU ALA THR SER THR THR LEU THR SER LEU ASP LEU SER SEQRES 16 A 360 TYR ASN ALA ILE GLU ALA GLU GLY VAL GLU ALA LEU GLY SEQRES 17 A 360 ARG ASN THR THR LEU ARG THR LEU HIS ALA CYS GLY ASN SEQRES 18 A 360 GLU LEU GLY HIS ARG GLU ALA GLU LEU LEU ALA ALA ASN SEQRES 19 A 360 THR THR LEU THR VAL LEU ASN LEU SER SER ASN ALA ILE SEQRES 20 A 360 GLY ASN ALA GLY ALA ARG ALA PHE GLY ALA ASN THR THR SEQRES 21 A 360 LEU VAL GLU LEU ASN LEU SER ASN ASN GLY ILE GLU ARG SEQRES 22 A 360 VAL PRO GLU TRP ALA ASP ASN GLY LYS LEU THR THR LEU SEQRES 23 A 360 ASP LEU SER ASN ASN GLN ILE GLY ASP THR ALA ALA GLN SEQRES 24 A 360 VAL LEU ALA ALA SER HIS THR LEU THR THR LEU ASN VAL SEQRES 25 A 360 GLY SER ASN ARG ILE GLY ASP THR GLY ALA CYS ALA LEU SEQRES 26 A 360 ALA GLY ASN THR THR LEU THR THR LEU ASN VAL SER LEU SEQRES 27 A 360 ASN ARG ILE GLY LYS ALA GLY MET LEU ALA LEU ALA THR SEQRES 28 A 360 ASN THR THR LEU GLU LYS LEU GLU ARG HELIX 1 AA1 THR A 133 ARG A 139 1 7 HELIX 2 AA2 THR A 157 ALA A 166 1 10 HELIX 3 AA3 ASN A 180 GLY A 189 1 10 HELIX 4 AA4 GLY A 204 ALA A 212 1 9 HELIX 5 AA5 GLY A 228 ALA A 236 1 9 HELIX 6 AA6 ILE A 251 ASN A 262 1 12 HELIX 7 AA7 GLY A 276 THR A 285 1 10 HELIX 8 AA8 GLU A 300 ASN A 310 1 11 HELIX 9 AA9 GLY A 324 ASN A 334 1 11 HELIX 10 AB1 ILE A 347 ASN A 358 1 12 HELIX 11 AB2 GLY A 394 ALA A 403 1 10 HELIX 12 AB3 GLY A 418 GLY A 427 1 10 HELIX 13 AB4 GLY A 442 THR A 451 1 10 SHEET 1 AA1 2 GLN A 102 THR A 106 0 SHEET 2 AA1 2 LYS A 125 VAL A 129 1 O THR A 127 N LEU A 103 SHEET 1 AA212 THR A 195 ASN A 197 0 SHEET 2 AA212 THR A 219 ASN A 221 1 O THR A 219 N LEU A 196 SHEET 3 AA212 THR A 243 ASP A 245 1 O THR A 243 N LEU A 220 SHEET 4 AA212 ARG A 267 ASP A 269 1 O ARG A 267 N LEU A 244 SHEET 5 AA212 SER A 291 ASP A 293 1 O ASP A 293 N LEU A 268 SHEET 6 AA212 THR A 315 HIS A 317 1 O THR A 315 N LEU A 292 SHEET 7 AA212 VAL A 339 ASN A 341 1 O VAL A 339 N LEU A 316 SHEET 8 AA212 GLU A 363 ASN A 365 1 O ASN A 365 N LEU A 340 SHEET 9 AA212 THR A 385 ASP A 387 1 O THR A 385 N LEU A 364 SHEET 10 AA212 THR A 409 ASN A 411 1 O ASN A 411 N LEU A 386 SHEET 11 AA212 THR A 433 ASN A 435 1 O THR A 433 N LEU A 410 SHEET 12 AA212 LYS A 457 GLU A 459 1 O LYS A 457 N LEU A 434 CRYST1 188.846 188.846 108.239 90.00 90.00 120.00 P 65 2 2 12 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 0.005295 0.003057 0.000000 0.00000 SCALE2 0.000000 0.006115 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009239 0.00000 TER 2609 ARG A 460 MASTER 260 0 0 13 14 0 0 6 2608 1 0 28 END