HEADER CYTOKINE 22-NOV-10 3POK TITLE INTERLEUKIN-1-BETA LBT L3 MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: INTERLEUKIN-1 BETA; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: MATURE FORM (UNP RESIDUES 117-269); COMPND 5 SYNONYM: IL-1 BETA, CATABOLIN; COMPND 6 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: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)-RIL KEYWDS LANTHANIDE TAG, BETA TREFOIL, INTERLEUKIN, SIGNALING, RECEPTOR, KEYWDS 2 EXTRACELLULAR MEMBRANE, CYTOKINE EXPDTA X-RAY DIFFRACTION AUTHOR K.BARTHELMES,A.M.REYNOLDS,E.PEISACH,H.R.A.JONKER,N.J.DENUNZIO, AUTHOR 2 K.N.ALLEN,B.IMPERIALI,H.SCHWALBE REVDAT 3 26-JUL-17 3POK 1 SOURCE REMARK REVDAT 2 09-MAR-11 3POK 1 JRNL REVDAT 1 19-JAN-11 3POK 0 JRNL AUTH K.BARTHELMES,A.M.REYNOLDS,E.PEISACH,H.R.JONKER,N.J.DENUNZIO, JRNL AUTH 2 K.N.ALLEN,B.IMPERIALI,H.SCHWALBE JRNL TITL ENGINEERING ENCODABLE LANTHANIDE-BINDING TAGS INTO LOOP JRNL TITL 2 REGIONS OF PROTEINS. JRNL REF J.AM.CHEM.SOC. V. 133 808 2011 JRNL REFN ISSN 0002-7863 JRNL PMID 21182275 JRNL DOI 10.1021/JA104983T REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.5_2) 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.17 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.020 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 3 NUMBER OF REFLECTIONS : 33108 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.175 REMARK 3 FREE R VALUE : 0.212 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.130 REMARK 3 FREE R VALUE TEST SET COUNT : 3355 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 19.1712 - 3.6558 1.00 3061 333 0.1531 0.1777 REMARK 3 2 3.6558 - 2.9049 1.00 3057 370 0.1658 0.2037 REMARK 3 3 2.9049 - 2.5387 1.00 3024 356 0.1805 0.2236 REMARK 3 4 2.5387 - 2.3070 1.00 3061 336 0.1788 0.2076 REMARK 3 5 2.3070 - 2.1419 0.99 2985 336 0.1658 0.2136 REMARK 3 6 2.1419 - 2.0157 0.98 3002 340 0.1701 0.2170 REMARK 3 7 2.0157 - 1.9149 0.97 2989 327 0.1703 0.1808 REMARK 3 8 1.9149 - 1.8316 0.95 2915 320 0.1912 0.2539 REMARK 3 9 1.8316 - 1.7611 0.94 2896 324 0.2132 0.2529 REMARK 3 10 1.7611 - 1.7004 0.91 2763 313 0.2418 0.2664 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 : 0.38 REMARK 3 B_SOL : 52.72 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.230 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) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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 : 0.007 1333 REMARK 3 ANGLE : 1.145 1806 REMARK 3 CHIRALITY : 0.079 198 REMARK 3 PLANARITY : 0.005 238 REMARK 3 DIHEDRAL : 17.708 503 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A REMARK 3 ORIGIN FOR THE GROUP (A): -15.8574 -5.2276 -9.2840 REMARK 3 T TENSOR REMARK 3 T11: 0.1300 T22: 0.1099 REMARK 3 T33: 0.1025 T12: 0.0033 REMARK 3 T13: 0.0252 T23: -0.0079 REMARK 3 L TENSOR REMARK 3 L11: 1.3357 L22: 3.2902 REMARK 3 L33: 2.5145 L12: 0.8786 REMARK 3 L13: -0.3851 L23: -1.8013 REMARK 3 S TENSOR REMARK 3 S11: 0.0068 S12: -0.1250 S13: 0.0683 REMARK 3 S21: -0.0856 S22: 0.0868 S23: 0.0132 REMARK 3 S31: -0.1926 S32: -0.0169 S33: 0.0026 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 3POK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-NOV-10. REMARK 100 THE DEPOSITION ID IS D_1000062627. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JAN-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.5 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 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NICKEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33108 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 19.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 200 DATA REDUNDANCY : 9.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.03900 REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.48000 REMARK 200 FOR SHELL : 4.770 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.43 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM SODIUM ACETATE TRIHYDRATE PH REMARK 280 4.5, 3.0 M NACL, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 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+1/4 REMARK 290 4555 Y,-X,Z+3/4 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 44.00100 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 22.00050 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 66.00150 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 MET A 0 REMARK 465 ASN A 80 REMARK 465 ASP A 81 REMARK 465 GLY A 82 REMARK 465 TRP A 83 REMARK 465 ILE A 84 REMARK 465 GLU A 85 REMARK 465 GLY A 86 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 ASP A 54 46.95 -142.61 REMARK 500 GLU A 64 -2.79 71.61 REMARK 500 THR A 78 -16.44 110.86 REMARK 500 ASN A 121 32.09 -97.06 REMARK 500 ASN A 132 1.65 84.43 REMARK 500 REMARK 500 REMARK: NULL REMARK 999 REMARK 999 SEQUENCE REMARK 999 AUTHORS HAVE REMOVED NATIVE SEQUENCE KDDK AND INSERTED ENGINEERED REMARK 999 SEQUENCE GYIDTNNDGWIEGDELY. THIS INSERTION REPRESENTS A LANTHANIDE REMARK 999 BINDING TAG (LBT) THAT WAS INSERTED AT THE END OF A LOOP. DBREF 3POK A 1 73 UNP P01584 IL1B_HUMAN 117 189 DBREF 3POK A 91 166 UNP P01584 IL1B_HUMAN 194 269 SEQADV 3POK MET A 0 UNP P01584 EXPRESSION TAG SEQADV 3POK GLY A 74 UNP P01584 INSERTION SEQADV 3POK TYR A 75 UNP P01584 INSERTION SEQADV 3POK ILE A 76 UNP P01584 INSERTION SEQADV 3POK ASP A 77 UNP P01584 INSERTION SEQADV 3POK THR A 78 UNP P01584 INSERTION SEQADV 3POK ASN A 79 UNP P01584 INSERTION SEQADV 3POK ASN A 80 UNP P01584 INSERTION SEQADV 3POK ASP A 81 UNP P01584 INSERTION SEQADV 3POK GLY A 82 UNP P01584 INSERTION SEQADV 3POK TRP A 83 UNP P01584 INSERTION SEQADV 3POK ILE A 84 UNP P01584 INSERTION SEQADV 3POK GLU A 85 UNP P01584 INSERTION SEQADV 3POK GLY A 86 UNP P01584 INSERTION SEQADV 3POK ASP A 87 UNP P01584 INSERTION SEQADV 3POK GLU A 88 UNP P01584 INSERTION SEQADV 3POK LEU A 89 UNP P01584 INSERTION SEQADV 3POK TYR A 90 UNP P01584 INSERTION SEQRES 1 A 167 MET ALA PRO VAL ARG SER LEU ASN CYS THR LEU ARG ASP SEQRES 2 A 167 SER GLN GLN LYS SER LEU VAL MET SER GLY PRO TYR GLU SEQRES 3 A 167 LEU LYS ALA LEU HIS LEU GLN GLY GLN ASP MET GLU GLN SEQRES 4 A 167 GLN VAL VAL PHE SER MET SER PHE VAL GLN GLY GLU GLU SEQRES 5 A 167 SER ASN ASP LYS ILE PRO VAL ALA LEU GLY LEU LYS GLU SEQRES 6 A 167 LYS ASN LEU TYR LEU SER CYS VAL LEU GLY TYR ILE ASP SEQRES 7 A 167 THR ASN ASN ASP GLY TRP ILE GLU GLY ASP GLU LEU TYR SEQRES 8 A 167 PRO THR LEU GLN LEU GLU SER VAL ASP PRO LYS ASN TYR SEQRES 9 A 167 PRO LYS LYS LYS MET GLU LYS ARG PHE VAL PHE ASN LYS SEQRES 10 A 167 ILE GLU ILE ASN ASN LYS LEU GLU PHE GLU SER ALA GLN SEQRES 11 A 167 PHE PRO ASN TRP TYR ILE SER THR SER GLN ALA GLU ASN SEQRES 12 A 167 MET PRO VAL PHE LEU GLY GLY THR LYS GLY GLY GLN ASP SEQRES 13 A 167 ILE THR ASP PHE THR MET GLN PHE VAL SER SER FORMUL 2 HOH *106(H2 O) HELIX 1 1 GLN A 32 GLN A 39 5 8 HELIX 2 2 GLU A 109 PHE A 112 5 4 SHEET 1 A 9 TYR A 90 SER A 97 0 SHEET 2 A 9 LEU A 67 GLY A 74 -1 N TYR A 68 O GLU A 96 SHEET 3 A 9 ILE A 56 LEU A 62 -1 N LEU A 62 O LEU A 67 SHEET 4 A 9 PHE A 114 ILE A 119 -1 O PHE A 114 N VAL A 58 SHEET 5 A 9 LYS A 122 SER A 127 -1 O GLU A 126 N ASN A 115 SHEET 6 A 9 PHE A 159 SER A 165 -1 O PHE A 159 N LEU A 123 SHEET 7 A 9 SER A 5 ASP A 12 -1 N ASN A 7 O SER A 165 SHEET 8 A 9 PHE A 42 PHE A 46 -1 O PHE A 42 N CYS A 8 SHEET 9 A 9 ILE A 56 LEU A 62 -1 O GLY A 61 N SER A 43 SHEET 1 B 3 SER A 17 MET A 20 0 SHEET 2 B 3 LEU A 26 LEU A 29 -1 O LEU A 29 N SER A 17 SHEET 3 B 3 MET A 143 PRO A 144 -1 O MET A 143 N ALA A 28 SHEET 1 C 2 TYR A 134 SER A 136 0 SHEET 2 C 2 PHE A 146 GLY A 148 -1 O GLY A 148 N TYR A 134 CISPEP 1 ALA A 1 PRO A 2 0 -9.41 CISPEP 2 TYR A 103 PRO A 104 0 2.40 CISPEP 3 ASN A 120 ASN A 121 0 -1.15 CRYST1 42.595 42.595 88.002 90.00 90.00 90.00 P 41 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 0.023477 0.000000 0.000000 0.00000 SCALE2 0.000000 0.023477 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011363 0.00000 MASTER 255 0 0 2 14 0 0 6 0 0 0 13 END