HEADER CYTOKINE 17-JUL-22 8DPV TITLE THE CRYSTAL STRUCTURE OF INTERLEUKIN-11, W147A MUTANT 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 8DPV 1 JRNL REVDAT 1 29-NOV-23 8DPV 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. 1.48 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) : 1.48 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.01 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 24296 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.184 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1216 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 37.0100 - 3.0800 1.00 2772 140 0.1760 0.2120 REMARK 3 2 3.0800 - 2.4400 1.00 2601 125 0.1855 0.1978 REMARK 3 3 2.4400 - 2.1300 1.00 2580 131 0.1611 0.1966 REMARK 3 4 2.1300 - 1.9400 1.00 2561 113 0.1758 0.2277 REMARK 3 5 1.9400 - 1.8000 1.00 2515 148 0.1984 0.2576 REMARK 3 6 1.8000 - 1.6900 1.00 2524 143 0.2012 0.2437 REMARK 3 7 1.6900 - 1.6100 1.00 2528 129 0.2132 0.2335 REMARK 3 8 1.6100 - 1.5400 1.00 2508 147 0.2298 0.2505 REMARK 3 9 1.5400 - 1.4800 1.00 2491 140 0.2700 0.2742 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) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.209 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.39 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.47 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 1343 REMARK 3 ANGLE : 1.284 1840 REMARK 3 CHIRALITY : 0.080 218 REMARK 3 PLANARITY : 0.009 241 REMARK 3 DIHEDRAL : 20.167 518 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 10 THROUGH 178) REMARK 3 ORIGIN FOR THE GROUP (A): -3.7821 18.3456 -6.1422 REMARK 3 T TENSOR REMARK 3 T11: 0.1965 T22: 0.1895 REMARK 3 T33: 0.1855 T12: -0.0224 REMARK 3 T13: 0.0275 T23: -0.0039 REMARK 3 L TENSOR REMARK 3 L11: 1.4440 L22: 2.1545 REMARK 3 L33: 0.6124 L12: 1.3848 REMARK 3 L13: 0.3231 L23: 0.4569 REMARK 3 S TENSOR REMARK 3 S11: -0.1567 S12: 0.0713 S13: -0.1069 REMARK 3 S21: -0.1576 S22: 0.1174 S23: -0.1496 REMARK 3 S31: 0.0398 S32: 0.0698 S33: -0.0114 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 8DPV 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_1000267146. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-OCT-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 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 : 24354 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.480 REMARK 200 RESOLUTION RANGE LOW (A) : 44.670 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 12.90 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08200 REMARK 200 FOR THE DATA SET : 12.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.48 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.51 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) : 1.85900 REMARK 200 FOR SHELL : 1.300 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: PLATES REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.92 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, 200 MM AMMONIUM SULPHATE, REMARK 280 100 MM TRIS PH 8.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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+1/2,-Z REMARK 290 4555 X+1/2,-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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 19.25250 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 66.99800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.25250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 66.99800 REMARK 290 SMTRY3 4 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 376 LIES ON A SPECIAL POSITION. 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 HE ARG A 85 O HOH A 305 1.57 REMARK 500 O HOH A 316 O HOH A 380 1.86 REMARK 500 O HOH A 390 O HOH A 396 1.96 REMARK 500 NE2 GLN A 38 O HOH A 301 2.08 REMARK 500 OD1 ASP A 19 O HOH A 302 2.11 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OG SER A 97 OG SER A 97 2455 2.00 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ASP A 165 CB - CG - OD2 ANGL. DEV. = -5.7 DEGREES 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 ASP A 46 77.89 -102.22 REMARK 500 PRO A 138 171.65 -58.30 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 CL A 202 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: SASDLQ3 RELATED DB: SASBDB DBREF 8DPV A 11 178 UNP P20809 IL11_HUMAN 32 199 SEQADV 8DPV GLY A 10 UNP P20809 EXPRESSION TAG SEQADV 8DPV 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 ALA MET SER ALA SEQRES 5 A 169 GLY 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 HET CL A 202 1 HETNAM SO4 SULFATE ION HETNAM CL CHLORIDE ION FORMUL 2 SO4 O4 S 2- FORMUL 3 CL CL 1- FORMUL 4 HOH *109(H2 O) HELIX 1 AA1 ASP A 13 PHE A 43 1 31 HELIX 2 AA2 GLY A 65 LEU A 67 5 3 HELIX 3 AA3 GLN A 68 GLY A 94 1 27 HELIX 4 AA4 GLY A 95 GLU A 102 5 8 HELIX 5 AA5 PRO A 103 LEU A 126 1 24 HELIX 6 AA6 SER A 145 THR A 176 1 32 CISPEP 1 GLU A 102 PRO A 103 0 5.11 SITE 1 AC1 9 GLY A 10 SER A 11 LEU A 29 ARG A 33 SITE 2 AC1 9 ARG A 91 HIS A 161 HOH A 322 HOH A 325 SITE 3 AC1 9 HOH A 328 SITE 1 AC2 4 ARG A 114 ARG A 118 HOH A 343 HOH A 393 CRYST1 38.505 133.996 27.087 90.00 90.00 90.00 P 21 21 2 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 0.025971 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007463 0.000000 0.00000 SCALE3 0.000000 0.000000 0.036918 0.00000