HEADER CYTOKINE 21-FEB-14 4P0L TITLE CRYSTAL STRUCTURE OF DOUBLE LOOP-SWAPPED INTERLEUKIN-36RA WITH TITLE 2 ADDITIONAL POINT MUTATIONS COMPND MOL_ID: 1; COMPND 2 MOLECULE: INTERLEUKIN-36 RECEPTOR ANTAGONIST/INTERLEUKIN-36 GAMMA COMPND 3 CHIMERA PROTEIN; COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET30 KEYWDS CHIMERA PROTEIN, INTERLEUKIN, CYTOKINE EXPDTA X-RAY DIFFRACTION AUTHOR S.GUENTHER,E.J.SUNDBERG REVDAT 4 27-SEP-23 4P0L 1 REMARK REVDAT 3 22-NOV-17 4P0L 1 SOURCE KEYWDS REMARK CRYST1 REVDAT 2 16-JUL-14 4P0L 1 JRNL REVDAT 1 25-JUN-14 4P0L 0 JRNL AUTH S.GUNTHER,E.J.SUNDBERG JRNL TITL MOLECULAR DETERMINANTS OF AGONIST AND ANTAGONIST SIGNALING JRNL TITL 2 THROUGH THE IL-36 RECEPTOR. JRNL REF J IMMUNOL. V. 193 921 2014 JRNL REFN ESSN 1550-6606 JRNL PMID 24935927 JRNL DOI 10.4049/JIMMUNOL.1400538 REMARK 2 REMARK 2 RESOLUTION. 1.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.4_1496) 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) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 19214 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.182 REMARK 3 R VALUE (WORKING SET) : 0.181 REMARK 3 FREE R VALUE : 0.215 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 961 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 37.0000 - 2.9630 1.00 2791 145 0.1664 0.1971 REMARK 3 2 2.9630 - 2.3520 1.00 2630 134 0.1880 0.2236 REMARK 3 3 2.3520 - 2.0547 1.00 2589 138 0.1796 0.1993 REMARK 3 4 2.0547 - 1.8668 1.00 2590 135 0.1789 0.2194 REMARK 3 5 1.8668 - 1.7330 1.00 2571 139 0.1877 0.2316 REMARK 3 6 1.7330 - 1.6309 1.00 2549 137 0.2093 0.2874 REMARK 3 7 1.6309 - 1.5500 1.00 2533 133 0.2364 0.2671 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) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.580 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.12 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.62 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 : 0.013 1190 REMARK 3 ANGLE : 1.436 1621 REMARK 3 CHIRALITY : 0.079 176 REMARK 3 PLANARITY : 0.008 214 REMARK 3 DIHEDRAL : 15.431 442 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 4P0L COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-FEB-14. REMARK 100 THE DEPOSITION ID IS D_1000200422. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-DEC-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.3 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL11-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : 0.97945 REMARK 200 MONOCHROMATOR : SI DOUBLE CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XSCALE REMARK 200 DATA SCALING SOFTWARE : XDS, AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19268 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.550 REMARK 200 RESOLUTION RANGE LOW (A) : 37.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 9.500 REMARK 200 R MERGE (I) : 0.06500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.58 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.8 REMARK 200 DATA REDUNDANCY IN SHELL : 9.40 REMARK 200 R MERGE FOR SHELL (I) : 0.73500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.800 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: 1MD6 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.89 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% (W/V) PEG5000MME, 0.1 M NAACETATE, REMARK 280 PH 5.3, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 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 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 39.93133 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 79.86267 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 79.86267 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 39.93133 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 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 2 REMARK 465 LEU A 3 REMARK 465 SER A 4 REMARK 465 GLY A 5 REMARK 465 ALA A 6 REMARK 465 HIS A 32 REMARK 465 ALA A 33 REMARK 465 GLY A 34 REMARK 465 LYS A 35 REMARK 465 VAL A 36 REMARK 465 ASP A 155 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 143 -134.87 -100.93 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4P0J RELATED DB: PDB REMARK 900 RELATED ID: 4P0K RELATED DB: PDB DBREF 4P0L A 2 49 UNP Q9UBH0 I36RA_HUMAN 2 49 DBREF 4P0L A 50 58 UNP Q9NZH8 IL36G_HUMAN 64 72 DBREF 4P0L A 59 139 UNP Q9UBH0 I36RA_HUMAN 55 135 DBREF 4P0L A 140 146 UNP Q9NZH8 IL36G_HUMAN 154 160 DBREF 4P0L A 147 155 UNP Q9UBH0 I36RA_HUMAN 147 155 SEQADV 4P0L SER A 2 UNP Q9UBH0 VAL 2 ENGINEERED MUTATION SEQADV 4P0L ALA A 107 UNP Q9UBH0 ARG 103 ENGINEERED MUTATION SEQADV 4P0L ALA A 109 UNP Q9UBH0 MET 105 ENGINEERED MUTATION SEQRES 1 A 154 SER LEU SER GLY ALA LEU CYS PHE ARG MET LYS ASP SER SEQRES 2 A 154 ALA LEU LYS VAL LEU TYR LEU HIS ASN ASN GLN LEU LEU SEQRES 3 A 154 ALA GLY GLY LEU HIS ALA GLY LYS VAL ILE LYS GLY GLU SEQRES 4 A 154 GLU ILE SER VAL VAL PRO ASN ARG TRP PRO GLU ALA LEU SEQRES 5 A 154 GLU GLN GLY ARG GLY SER PRO VAL ILE LEU GLY VAL GLN SEQRES 6 A 154 GLY GLY SER GLN CYS LEU SER CYS GLY VAL GLY GLN GLU SEQRES 7 A 154 PRO THR LEU THR LEU GLU PRO VAL ASN ILE MET GLU LEU SEQRES 8 A 154 TYR LEU GLY ALA LYS GLU SER LYS SER PHE THR PHE TYR SEQRES 9 A 154 ARG ALA ASP ALA GLY LEU THR SER SER PHE GLU SER ALA SEQRES 10 A 154 ALA TYR PRO GLY TRP PHE LEU CYS THR VAL PRO GLU ALA SEQRES 11 A 154 ASP GLN PRO VAL ARG LEU THR GLN GLU LEU GLY LYS SER SEQRES 12 A 154 TYR ASN THR ASP PHE TYR PHE GLN GLN CYS ASP FORMUL 2 HOH *139(H2 O) HELIX 1 AA1 TRP A 49 LEU A 53 5 5 HELIX 2 AA2 GLU A 54 GLY A 58 5 5 HELIX 3 AA3 ASN A 88 LEU A 94 1 7 HELIX 4 AA4 SER A 99 SER A 101 5 3 SHEET 1 AA1 2 PHE A 9 ASP A 13 0 SHEET 2 AA1 2 PHE A 149 GLN A 153 -1 O GLN A 152 N ARG A 10 SHEET 1 AA2 3 VAL A 18 HIS A 22 0 SHEET 2 AA2 3 GLN A 25 GLY A 29 -1 O LEU A 27 N TYR A 20 SHEET 3 AA2 3 GLN A 133 PRO A 134 -1 O GLN A 133 N ALA A 28 SHEET 1 AA3 4 SER A 43 PRO A 46 0 SHEET 2 AA3 4 SER A 59 VAL A 65 -1 O ILE A 62 N VAL A 45 SHEET 3 AA3 4 GLN A 70 SER A 73 -1 O LEU A 72 N LEU A 63 SHEET 4 AA3 4 THR A 83 GLU A 85 -1 O THR A 83 N SER A 73 SHEET 1 AA4 4 SER A 43 PRO A 46 0 SHEET 2 AA4 4 SER A 59 VAL A 65 -1 O ILE A 62 N VAL A 45 SHEET 3 AA4 4 THR A 103 ASP A 108 -1 O ARG A 106 N SER A 59 SHEET 4 AA4 4 SER A 113 SER A 117 -1 O GLU A 116 N TYR A 105 SHEET 1 AA5 2 PHE A 124 CYS A 126 0 SHEET 2 AA5 2 ARG A 136 THR A 138 -1 O THR A 138 N PHE A 124 CRYST1 42.773 42.773 119.794 90.00 90.00 120.00 P 31 2 1 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 0.023379 0.013498 0.000000 0.00000 SCALE2 0.000000 0.026996 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008348 0.00000