HEADER CYTOKINE 17-JUL-22 8DPW TITLE THE STRUCTURE OF INTERLEUKIN-11 MUTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: INTERLEUKIN-11; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: IL-11,ADIPOGENESIS INHIBITORY FACTOR,AGIF; 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 GENE: IL11; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 KEYWDS COMPLEX, CYTOKINE, IL-6 FAMILY CYTOKINE EXPDTA X-RAY DIFFRACTION AUTHOR R.D.METCALFE,M.D.W.GRIFFIN REVDAT 2 01-MAY-24 8DPW 1 JRNL REVDAT 1 29-NOV-23 8DPW 0 JRNL AUTH R.D.METCALFE,E.HANSSEN,K.Y.FUNG,K.AIZEL,C.C.KOSASIH, JRNL AUTH 2 C.O.ZLATIC,L.DOUGHTY,C.J.MORTON,A.P.LEIS,M.W.PARKER, JRNL AUTH 3 P.R.GOOLEY,T.L.PUTOCZKI,M.D.W.GRIFFIN JRNL TITL STRUCTURES OF THE INTERLEUKIN 11 SIGNALLING COMPLEX REVEAL JRNL TITL 2 GP130 DYNAMICS AND THE INHIBITORY MECHANISM OF A CYTOKINE JRNL TITL 3 VARIANT. JRNL REF NAT COMMUN V. 14 7543 2023 JRNL REFN ESSN 2041-1723 JRNL PMID 37985757 JRNL DOI 10.1038/S41467-023-42754-W REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2_3874 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.60 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.410 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 12623 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.197 REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.670 REMARK 3 FREE R VALUE TEST SET COUNT : 590 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 33.6000 - 2.8600 1.00 3064 161 0.1796 0.2127 REMARK 3 2 2.8600 - 2.2700 1.00 2993 144 0.2040 0.2287 REMARK 3 3 2.2700 - 1.9800 1.00 2994 150 0.2101 0.2594 REMARK 3 4 1.9800 - 1.8000 1.00 2982 135 0.2708 0.3019 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) : 0.263 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.720 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 32.06 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 46.65 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 : 0.003 1321 REMARK 3 ANGLE : 0.630 1805 REMARK 3 CHIRALITY : 0.031 214 REMARK 3 PLANARITY : 0.004 235 REMARK 3 DIHEDRAL : 20.288 507 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN 'A' AND RESID 31 THROUGH 178) REMARK 3 ORIGIN FOR THE GROUP (A): -6.7466 7.6317 -17.8513 REMARK 3 T TENSOR REMARK 3 T11: 0.2061 T22: 0.2494 REMARK 3 T33: 0.2589 T12: -0.0029 REMARK 3 T13: -0.0057 T23: 0.0097 REMARK 3 L TENSOR REMARK 3 L11: 0.3669 L22: 0.5495 REMARK 3 L33: 2.5433 L12: -0.0494 REMARK 3 L13: 0.2687 L23: 0.6439 REMARK 3 S TENSOR REMARK 3 S11: 0.0383 S12: 0.1147 S13: 0.0682 REMARK 3 S21: 0.0204 S22: -0.0893 S23: 0.0928 REMARK 3 S31: -0.0570 S32: 0.0333 S33: 0.0000 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 8DPW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-JUL-22. REMARK 100 THE DEPOSITION ID IS D_1000267147. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-AUG-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9537 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : AIMLESS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12637 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 37.101 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07000 REMARK 200 FOR THE DATA SET : 11.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.84 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.90 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 1.16700 REMARK 200 FOR SHELL : 1.400 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: 4MHL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 33.68 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.85 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 27% PEG 3350, 0.1 M BIS-TRIS PROPANE REMARK 280 PH 9, 0.2 M AMMONIUM SULFATE, 5 MM PRASEODYMIUM CHLORIDE, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z 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 18.54850 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 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: 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 LEU A 67 O HOH A 302 1.95 REMARK 500 O ASP A 134 O HOH A 303 2.06 REMARK 500 O GLY A 94 O HOH A 304 2.13 REMARK 500 NE ARG A 75 O HOH A 305 2.13 REMARK 500 NH2 ARG A 75 O HOH A 305 2.17 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 ALA A 45 -128.83 56.66 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 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: SASDLR3 RELATED DB: SASBDB DBREF 8DPW A 11 178 UNP P20809 IL11_HUMAN 32 199 SEQADV 8DPW GLY A 10 UNP P20809 EXPRESSION TAG SEQADV 8DPW PRO A 58 UNP P20809 ALA 79 ENGINEERED MUTATION SEQADV 8DPW ALA A 59 UNP P20809 MET 80 ENGINEERED MUTATION SEQADV 8DPW ILE A 60 UNP P20809 SER 81 ENGINEERED MUTATION SEQADV 8DPW ASP A 61 UNP P20809 ALA 82 ENGINEERED MUTATION SEQADV 8DPW TYR A 62 UNP P20809 GLY 83 ENGINEERED MUTATION SEQADV 8DPW ALA A 147 UNP P20809 TRP 168 ENGINEERED MUTATION SEQRES 1 A 169 GLY SER PRO ASP PRO ARG ALA GLU LEU ASP SER THR VAL SEQRES 2 A 169 LEU LEU THR ARG SER LEU LEU ALA ASP THR ARG GLN LEU SEQRES 3 A 169 ALA ALA GLN LEU ARG ASP LYS PHE PRO ALA ASP GLY ASP SEQRES 4 A 169 HIS ASN LEU ASP SER LEU PRO THR LEU PRO ALA ILE ASP SEQRES 5 A 169 TYR ALA LEU GLY ALA LEU GLN LEU PRO GLY VAL LEU THR SEQRES 6 A 169 ARG LEU ARG ALA ASP LEU LEU SER TYR LEU ARG HIS VAL SEQRES 7 A 169 GLN TRP LEU ARG ARG ALA GLY GLY SER SER LEU LYS THR SEQRES 8 A 169 LEU GLU PRO GLU LEU GLY THR LEU GLN ALA ARG LEU ASP SEQRES 9 A 169 ARG LEU LEU ARG ARG LEU GLN LEU LEU MET SER ARG LEU SEQRES 10 A 169 ALA LEU PRO GLN PRO PRO PRO ASP PRO PRO ALA PRO PRO SEQRES 11 A 169 LEU ALA PRO PRO SER SER ALA ALA GLY GLY ILE ARG ALA SEQRES 12 A 169 ALA HIS ALA ILE LEU GLY GLY LEU HIS LEU THR LEU ASP SEQRES 13 A 169 TRP ALA VAL ARG GLY LEU LEU LEU LEU LYS THR ARG LEU HET SO4 A 201 5 HETNAM SO4 SULFATE ION FORMUL 2 SO4 O4 S 2- FORMUL 3 HOH *71(H2 O) HELIX 1 AA1 ASP A 13 PHE A 43 1 31 HELIX 2 AA2 ASN A 50 LEU A 54 5 5 HELIX 3 AA3 GLN A 68 GLY A 94 1 27 HELIX 4 AA4 GLY A 95 THR A 100 5 6 HELIX 5 AA5 LEU A 101 LEU A 126 1 26 HELIX 6 AA6 SER A 145 THR A 176 1 32 SITE 1 AC1 2 SER A 11 HOH A 338 CRYST1 27.230 37.097 68.532 90.00 101.31 90.00 P 1 21 1 2 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 0.036724 0.000000 0.007342 0.00000 SCALE2 0.000000 0.026956 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014880 0.00000