HEADER SIGNALING PROTEIN 27-MAY-15 5BOW TITLE CRYSTAL STRUCTURE OF IL-38 COMPND MOL_ID: 1; COMPND 2 MOLECULE: INTERLEUKIN-1 FAMILY MEMBER 10; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: IL-1F10,FAMILY OF INTERLEUKIN 1-THETA,FIL1 THETA, COMPND 5 INTERLEUKIN-1 HY2,IL-1HY2,INTERLEUKIN-1 THETA,IL-1 THETA,INTERLEUKIN- COMPND 6 38,IL-38; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: IL1F10, FIL1T, IL1HY2, IL38, FKSG75, UNQ6119/PRO20041; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET30 KEYWDS BETA TREFOIL, INNATE IMMUNE SIGNALING, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.GUENTHER,E.J.SUNDBERG REVDAT 2 22-NOV-17 5BOW 1 REMARK REVDAT 1 01-JUN-16 5BOW 0 JRNL AUTH S.GUENTHER,E.J.SUNDBERG JRNL TITL CRYSTAL STRUCTURE OF INTERLEUKIN-38 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.31 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.1_1168 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) : 1.31 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.27 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 3 NUMBER OF REFLECTIONS : 29422 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.139 REMARK 3 R VALUE (WORKING SET) : 0.138 REMARK 3 FREE R VALUE : 0.160 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.040 REMARK 3 FREE R VALUE TEST SET COUNT : 1484 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 31.2839 - 2.9142 1.00 2769 159 0.1581 0.1603 REMARK 3 2 2.9142 - 2.3133 0.99 2650 157 0.1597 0.1533 REMARK 3 3 2.3133 - 2.0209 0.99 2570 154 0.1303 0.1592 REMARK 3 4 2.0209 - 1.8362 0.99 2545 127 0.1251 0.1445 REMARK 3 5 1.8362 - 1.7046 0.97 2542 133 0.1182 0.1618 REMARK 3 6 1.7046 - 1.6041 0.98 2546 133 0.1147 0.1448 REMARK 3 7 1.6041 - 1.5237 0.97 2478 129 0.1098 0.1599 REMARK 3 8 1.5237 - 1.4574 0.97 2522 119 0.1134 0.1415 REMARK 3 9 1.4574 - 1.4013 0.97 2503 119 0.1205 0.2014 REMARK 3 10 1.4013 - 1.3530 0.96 2455 142 0.1232 0.2135 REMARK 3 11 1.3530 - 1.3100 0.91 2358 112 0.1411 0.1974 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) : 0.100 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 15.480 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.31 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 : 0.006 1341 REMARK 3 ANGLE : 1.145 1823 REMARK 3 CHIRALITY : 0.076 189 REMARK 3 PLANARITY : 0.004 246 REMARK 3 DIHEDRAL : 12.864 508 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 5BOW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-MAY-15. REMARK 100 THE DEPOSITION ID IS D_1000210295. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-NOV-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X25 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.1 REMARK 200 MONOCHROMATOR : DOUBLE SILICON(111) CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS, DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29448 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.310 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 200 DATA REDUNDANCY : 11.40 REMARK 200 R MERGE (I) : 0.09800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.31 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.33 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.1 REMARK 200 DATA REDUNDANCY IN SHELL : 7.50 REMARK 200 R MERGE FOR SHELL (I) : 0.40300 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: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 32.21 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.81 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, NAACETATE, PH 5.5, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,-Y,-Z+1/2 REMARK 290 4555 -X+1/2,-Y,Z+1/2 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 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 15.63200 REMARK 290 SMTRY2 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 31.27500 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 15.63200 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 31.27500 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2140 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16430 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 1.0 KCAL/MOL 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 31.26400 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -62.55000 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 308 O HOH A 413 2.11 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 TYR A 14 -163.36 -119.87 REMARK 500 LYS A 54 -163.20 -116.58 REMARK 500 SER A 138 -78.04 -88.99 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 EDO A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 206 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4IZE RELATED DB: PDB REMARK 900 RELATED ID: 1MD6 RELATED DB: PDB REMARK 900 RELATED ID: 1ILR RELATED DB: PDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 AUTHORS STATE THAT THESE ARE NATURAL OCCURRING VARIANTS. DBREF 5BOW A 3 152 UNP Q8WWZ1 IL1FA_HUMAN 3 152 SEQADV 5BOW SER A 2 UNP Q8WWZ1 EXPRESSION TAG SEQADV 5BOW THR A 44 UNP Q8WWZ1 ILE 44 ENGINEERED MUTATION SEQADV 5BOW ASP A 51 UNP Q8WWZ1 ALA 51 ENGINEERED MUTATION SEQRES 1 A 151 SER SER LEU PRO MET ALA ARG TYR TYR ILE ILE LYS TYR SEQRES 2 A 151 ALA ASP GLN LYS ALA LEU TYR THR ARG ASP GLY GLN LEU SEQRES 3 A 151 LEU VAL GLY ASP PRO VAL ALA ASP ASN CYS CYS ALA GLU SEQRES 4 A 151 LYS ILE CYS THR LEU PRO ASN ARG GLY LEU ASP ARG THR SEQRES 5 A 151 LYS VAL PRO ILE PHE LEU GLY ILE GLN GLY GLY SER ARG SEQRES 6 A 151 CYS LEU ALA CYS VAL GLU THR GLU GLU GLY PRO SER LEU SEQRES 7 A 151 GLN LEU GLU ASP VAL ASN ILE GLU GLU LEU TYR LYS GLY SEQRES 8 A 151 GLY GLU GLU ALA THR ARG PHE THR PHE PHE GLN SER SER SEQRES 9 A 151 SER GLY SER ALA PHE ARG LEU GLU ALA ALA ALA TRP PRO SEQRES 10 A 151 GLY TRP PHE LEU CYS GLY PRO ALA GLU PRO GLN GLN PRO SEQRES 11 A 151 VAL GLN LEU THR LYS GLU SER GLU PRO SER ALA ARG THR SEQRES 12 A 151 LYS PHE TYR PHE GLU GLN SER TRP HET EDO A 201 4 HET EDO A 202 4 HET EDO A 203 4 HET EDO A 204 4 HET EDO A 205 4 HET EDO A 206 4 HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 EDO 6(C2 H6 O2) FORMUL 8 HOH *152(H2 O) HELIX 1 AA1 TYR A 14 LYS A 18 5 5 HELIX 2 AA2 PRO A 32 ASN A 36 5 5 HELIX 3 AA3 ASN A 85 LYS A 91 1 7 HELIX 4 AA4 GLY A 93 PHE A 99 5 7 HELIX 5 AA5 SER A 141 LYS A 145 5 5 SHEET 1 AA1 5 SER A 78 GLU A 82 0 SHEET 2 AA1 5 ARG A 66 VAL A 71 -1 N ALA A 69 O GLN A 80 SHEET 3 AA1 5 PRO A 56 ILE A 61 -1 N ILE A 61 O ARG A 66 SHEET 4 AA1 5 PHE A 101 SER A 106 -1 O PHE A 101 N ILE A 57 SHEET 5 AA1 5 ALA A 109 ALA A 114 -1 O GLU A 113 N PHE A 102 SHEET 1 AA2 6 SER A 78 GLU A 82 0 SHEET 2 AA2 6 ARG A 66 VAL A 71 -1 N ALA A 69 O GLN A 80 SHEET 3 AA2 6 PRO A 56 ILE A 61 -1 N ILE A 61 O ARG A 66 SHEET 4 AA2 6 ILE A 42 PRO A 46 -1 N CYS A 43 O GLY A 60 SHEET 5 AA2 6 ARG A 8 LYS A 13 -1 N ARG A 8 O THR A 44 SHEET 6 AA2 6 TYR A 147 GLN A 150 -1 O TYR A 147 N LYS A 13 SHEET 1 AA3 2 ALA A 19 ARG A 23 0 SHEET 2 AA3 2 GLN A 26 GLY A 30 -1 O LEU A 28 N TYR A 21 SHEET 1 AA4 2 TRP A 120 CYS A 123 0 SHEET 2 AA4 2 GLN A 133 LYS A 136 -1 O THR A 135 N PHE A 121 SSBOND 1 CYS A 38 CYS A 38 1555 2554 2.93 SITE 1 AC1 3 THR A 135 LYS A 136 HOH A 328 SITE 1 AC2 8 ALA A 34 ASN A 36 GLN A 150 SER A 151 SITE 2 AC2 8 TRP A 152 HOH A 308 HOH A 310 HOH A 373 SITE 1 AC3 4 TYR A 9 GLY A 63 GLU A 87 HOH A 317 SITE 1 AC4 6 THR A 53 GLU A 75 PRO A 77 LEU A 134 SITE 2 AC4 6 HOH A 337 HOH A 341 SITE 1 AC5 7 TYR A 21 VAL A 29 PRO A 128 GLN A 129 SITE 2 AC5 7 HOH A 307 HOH A 345 HOH A 361 SITE 1 AC6 5 LYS A 13 ALA A 19 GLY A 107 SER A 108 SITE 2 AC6 5 HOH A 302 CRYST1 31.264 62.514 62.550 90.00 90.00 90.00 P 21 2 21 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 0.031986 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015996 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015987 0.00000