HEADER SIGNALING PROTEIN 05-MAR-20 6Y8I TITLE FRAGMENT KCL_I013 IN COMPLEX WITH IL-1-BETA COMPND MOL_ID: 1; COMPND 2 MOLECULE: INTERLEUKIN-1 BETA; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: IL-1 BETA,CATABOLIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: IL1B, IL1F2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS FBDD, FRAGMENT BASED DRUG DESIGN, XCHEM, IL1B, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR G.F.DE NICOLA,C.E.NICHOLS REVDAT 2 24-JAN-24 6Y8I 1 REMARK REVDAT 1 17-JUN-20 6Y8I 0 JRNL AUTH G.F.DE NICOLA,C.E.NICHOLS JRNL TITL FRAGMENT KCL_I013 IN COMPLEX WITH IL-1-BETA JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.46 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.16_3549 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) : 1.46 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.50 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.310 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.7 REMARK 3 NUMBER OF REFLECTIONS : 37594 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.240 REMARK 3 R VALUE (WORKING SET) : 0.239 REMARK 3 FREE R VALUE : 0.263 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.910 REMARK 3 FREE R VALUE TEST SET COUNT : 3587 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 24.5000 - 4.3200 0.64 1806 75 0.2366 0.2849 REMARK 3 2 4.3200 - 3.4300 0.92 2547 143 0.2057 0.2182 REMARK 3 3 3.4300 - 3.0000 0.99 2753 144 0.2305 0.2262 REMARK 3 4 3.0000 - 2.7200 0.99 2808 110 0.2483 0.2977 REMARK 3 5 2.7200 - 2.5300 0.99 2766 133 0.2504 0.2634 REMARK 3 6 2.5300 - 2.3800 0.98 2709 150 0.2479 0.2975 REMARK 3 7 2.3800 - 2.2600 0.98 2708 160 0.2414 0.3180 REMARK 3 8 2.2600 - 2.1600 0.98 2745 130 0.2403 0.2666 REMARK 3 9 2.1600 - 2.0800 0.97 2713 165 0.2365 0.2716 REMARK 3 10 2.0800 - 2.0100 0.98 2789 111 0.2450 0.2873 REMARK 3 11 2.0100 - 1.9400 0.98 2661 159 0.2536 0.2407 REMARK 3 12 1.9400 - 1.8900 0.98 2744 107 0.2449 0.3258 REMARK 3 13 1.8900 - 1.8400 0.98 2767 129 0.2394 0.3121 REMARK 3 14 1.8400 - 1.7900 0.98 2693 169 0.2506 0.2882 REMARK 3 15 1.7900 - 1.7500 0.97 2681 144 0.2517 0.2378 REMARK 3 16 1.7500 - 1.7200 0.97 2730 133 0.2465 0.2281 REMARK 3 17 1.7200 - 1.6800 0.97 2755 134 0.2562 0.2612 REMARK 3 18 1.6800 - 1.6500 0.97 2646 171 0.2639 0.2746 REMARK 3 19 1.6500 - 1.6200 0.97 2656 147 0.2807 0.3171 REMARK 3 20 1.6200 - 1.5900 0.97 2751 125 0.2869 0.2933 REMARK 3 21 1.5900 - 1.5700 0.96 2674 122 0.3024 0.2834 REMARK 3 22 1.5700 - 1.5400 0.97 2638 198 0.3244 0.3612 REMARK 3 23 1.5400 - 1.5200 0.96 2680 138 0.3264 0.3536 REMARK 3 24 1.5200 - 1.5000 0.96 2651 150 0.3362 0.3501 REMARK 3 25 1.5000 - 1.4800 0.96 2691 126 0.3323 0.3482 REMARK 3 26 1.4800 - 1.4600 0.95 2715 114 0.3492 0.3977 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) : 0.201 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.747 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 31.27 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.51 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 : 0.005 1200 REMARK 3 ANGLE : 0.822 1629 REMARK 3 CHIRALITY : 0.094 182 REMARK 3 PLANARITY : 0.005 221 REMARK 3 DIHEDRAL : 2.986 940 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 6Y8I COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 05-MAR-20. REMARK 100 THE DEPOSITION ID IS D_1292107127. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-SEP-19 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 : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9763 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 37604 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.460 REMARK 200 RESOLUTION RANGE LOW (A) : 37.790 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.46 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.49 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 : 1.100 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: 5R85 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.27 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.26 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.8M AMMONIUM SULPHATE AND 0.1M TRIS REMARK 280 PH7.9, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 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 -Y,X,Z+3/4 REMARK 290 4555 Y,-X,Z+1/4 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 37.78500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 56.67750 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 18.89250 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 ALA A 1 REMARK 465 PRO A 2 REMARK 465 THR A 137 REMARK 465 LYS A 138 REMARK 465 GLY A 139 REMARK 465 SER A 153 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 GLN A 14 CD OE1 NE2 REMARK 470 GLN A 34 CG CD OE1 NE2 REMARK 470 ASP A 35 CG OD1 OD2 REMARK 470 GLU A 37 CG CD OE1 OE2 REMARK 470 GLN A 38 CG CD OE1 NE2 REMARK 470 GLN A 48 CG CD OE1 NE2 REMARK 470 GLU A 50 CG CD OE1 OE2 REMARK 470 LYS A 55 CD CE NZ REMARK 470 LYS A 63 CD CE NZ REMARK 470 GLU A 64 CD OE1 OE2 REMARK 470 LYS A 74 CG CD CE NZ REMARK 470 ASP A 75 CG OD1 OD2 REMARK 470 LYS A 77 CE NZ REMARK 470 LYS A 88 CG CD CE NZ REMARK 470 LYS A 93 CE NZ REMARK 470 LYS A 94 CD CE NZ REMARK 470 LYS A 97 CD CE NZ REMARK 470 GLU A 105 CG CD OE1 OE2 REMARK 470 GLN A 141 CG CD OE1 NE2 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 94 77.72 -102.20 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue OGE A 202 DBREF 6Y8I A 1 153 UNP P01584 IL1B_HUMAN 117 269 SEQRES 1 A 153 ALA PRO VAL ARG SER LEU ASN CYS THR LEU ARG ASP SER SEQRES 2 A 153 GLN GLN LYS SER LEU VAL MET SER GLY PRO TYR GLU LEU SEQRES 3 A 153 LYS ALA LEU HIS LEU GLN GLY GLN ASP MET GLU GLN GLN SEQRES 4 A 153 VAL VAL PHE SER MET SER PHE VAL GLN GLY GLU GLU SER SEQRES 5 A 153 ASN ASP LYS ILE PRO VAL ALA LEU GLY LEU LYS GLU LYS SEQRES 6 A 153 ASN LEU TYR LEU SER CYS VAL LEU LYS ASP ASP LYS PRO SEQRES 7 A 153 THR LEU GLN LEU GLU SER VAL ASP PRO LYS ASN TYR PRO SEQRES 8 A 153 LYS LYS LYS MET GLU LYS ARG PHE VAL PHE ASN LYS ILE SEQRES 9 A 153 GLU ILE ASN ASN LYS LEU GLU PHE GLU SER ALA GLN PHE SEQRES 10 A 153 PRO ASN TRP TYR ILE SER THR SER GLN ALA GLU ASN MET SEQRES 11 A 153 PRO VAL PHE LEU GLY GLY THR LYS GLY GLY GLN ASP ILE SEQRES 12 A 153 THR ASP PHE THR MET GLN PHE VAL SER SER HET SO4 A 201 5 HET OGE A 202 14 HETNAM SO4 SULFATE ION HETNAM OGE 1-(5-BROMANYLPYRIDIN-2-YL)-3-(2-HYDROXYETHYL)UREA FORMUL 2 SO4 O4 S 2- FORMUL 3 OGE C8 H10 BR N3 O2 FORMUL 4 HOH *22(H2 O) HELIX 1 AA1 GLN A 32 GLN A 39 5 8 HELIX 2 AA2 GLU A 96 PHE A 99 5 4 SHEET 1 AA1 7 SER A 5 ASP A 12 0 SHEET 2 AA1 7 PHE A 42 PHE A 46 -1 O PHE A 42 N CYS A 8 SHEET 3 AA1 7 LYS A 55 LEU A 62 -1 O GLY A 61 N SER A 43 SHEET 4 AA1 7 PHE A 101 ILE A 106 -1 O LYS A 103 N ILE A 56 SHEET 5 AA1 7 LYS A 109 SER A 114 -1 O GLU A 113 N ASN A 102 SHEET 6 AA1 7 PHE A 146 PHE A 150 -1 O PHE A 146 N LEU A 110 SHEET 7 AA1 7 SER A 5 ASP A 12 -1 N ARG A 11 O THR A 147 SHEET 1 AA2 3 SER A 17 MET A 20 0 SHEET 2 AA2 3 LEU A 26 LEU A 29 -1 O LYS A 27 N VAL A 19 SHEET 3 AA2 3 MET A 130 PRO A 131 -1 O MET A 130 N ALA A 28 SHEET 1 AA3 2 LEU A 67 LYS A 74 0 SHEET 2 AA3 2 LYS A 77 SER A 84 -1 O GLU A 83 N TYR A 68 SHEET 1 AA4 2 TYR A 121 SER A 123 0 SHEET 2 AA4 2 PHE A 133 GLY A 135 -1 O PHE A 133 N SER A 123 CISPEP 1 TYR A 90 PRO A 91 0 0.60 SITE 1 AC1 1 ARG A 98 SITE 1 AC2 5 ASN A 108 LYS A 109 THR A 147 MET A 148 SITE 2 AC2 5 GLN A 149 CRYST1 54.790 54.790 75.570 90.00 90.00 90.00 P 43 4 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 0.018252 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018252 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013233 0.00000