HEADER IMMUNE SYSTEM 20-AUG-25 9WEN TITLE CRYSTAL STRUCTURE OF THE HOMODIMERIC PORCINE INTERLEUKIN-10 (IL-10) COMPND MOL_ID: 1; COMPND 2 MOLECULE: INTERLEUKIN-10; COMPND 3 CHAIN: B, A; COMPND 4 SYNONYM: IL-10,CYTOKINE SYNTHESIS INHIBITORY FACTOR,CSIF; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SUS SCROFA; SOURCE 3 ORGANISM_COMMON: PIG; SOURCE 4 ORGANISM_TAXID: 9823; SOURCE 5 GENE: IL10; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PORCINE, INTERLEUKIN-10, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR X.WEI REVDAT 1 26-AUG-26 9WEN 0 JRNL AUTH X.WEI JRNL TITL CRYSTAL STRUCTURE OF THE HOMODIMERIC PORCINE INTERLEUKIN-10 JRNL TITL 2 (IL-10) JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.24 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 15500 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.213 REMARK 3 R VALUE (WORKING SET) : 0.212 REMARK 3 FREE R VALUE : 0.232 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 774 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 29.2400 - 4.1800 1.00 2584 146 0.1786 0.1756 REMARK 3 2 4.1700 - 3.3200 1.00 2480 117 0.2002 0.2468 REMARK 3 3 3.3200 - 2.9000 1.00 2414 156 0.2612 0.2898 REMARK 3 4 2.9000 - 2.6300 1.00 2430 118 0.2456 0.2647 REMARK 3 5 2.6300 - 2.4400 1.00 2415 116 0.2648 0.3290 REMARK 3 6 2.4400 - 2.3000 1.00 2403 121 0.2659 0.3332 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.275 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.412 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 62.26 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 : 0.009 2314 REMARK 3 ANGLE : 0.968 3090 REMARK 3 CHIRALITY : 0.067 330 REMARK 3 PLANARITY : 0.006 396 REMARK 3 DIHEDRAL : 18.269 900 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 9WEN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 21-AUG-25. REMARK 100 THE DEPOSITION ID IS D_1300062635. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-MAY-21 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 : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97915 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16740 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.240 REMARK 200 RESOLUTION RANGE LOW (A) : 81.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 11.40 REMARK 200 R MERGE (I) : 0.08500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.24 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.37 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.73500 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: PHENIX PHENIX1.20.1-4487 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.19 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.52 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM FLUORIDE, 20% W/V REMARK 280 POLYETHYLENE GLYCOL (PEG) 3,350, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 21 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,Y+1/2,-Z+1/2 REMARK 290 4555 -X,-Y+1/2,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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 40.60000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 52.86000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 40.60000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 52.86000 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 8800 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14240 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -80.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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 ARG B 159 REMARK 465 LYS B 160 REMARK 465 ARG A 159 REMARK 465 LYS A 160 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 VAL B 76 -61.71 -106.32 REMARK 500 GLN B 132 -119.38 50.49 REMARK 500 VAL A 76 -60.90 -105.15 REMARK 500 SER A 82 44.93 -109.52 REMARK 500 GLN A 132 -120.97 49.80 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 220 DISTANCE = 7.28 ANGSTROMS DBREF 9WEN B 18 160 UNP Q29055 IL10_PIG 32 174 DBREF 9WEN A 18 160 UNP Q29055 IL10_PIG 32 174 SEQRES 1 B 143 SER LEU PRO HIS MET LEU ARG GLU LEU ARG ALA ALA PHE SEQRES 2 B 143 GLY PRO VAL LYS SER PHE PHE GLN THR LYS ASP GLN MET SEQRES 3 B 143 GLY ASP LEU LEU LEU THR GLY SER LEU LEU GLU ASP PHE SEQRES 4 B 143 LYS GLY TYR LEU GLY CYS GLN ALA LEU SER GLU MET ILE SEQRES 5 B 143 GLN PHE TYR LEU GLU ASP VAL MET PRO LYS ALA GLU SER SEQRES 6 B 143 ASP GLY GLU ASP ILE LYS GLU HIS VAL ASN SER LEU GLY SEQRES 7 B 143 GLU LYS LEU LYS THR LEU ARG LEU ARG LEU ARG ARG CYS SEQRES 8 B 143 HIS GLN PHE LEU PRO CYS GLU ASN LYS SER LYS ALA VAL SEQRES 9 B 143 GLU GLU VAL LYS SER ALA PHE SER LYS LEU GLN GLU ARG SEQRES 10 B 143 GLY VAL TYR LYS ALA MET GLY GLU PHE ASP ILE PHE ILE SEQRES 11 B 143 ASN TYR ILE GLU ALA TYR MET THR MET LYS MET ARG LYS SEQRES 1 A 143 SER LEU PRO HIS MET LEU ARG GLU LEU ARG ALA ALA PHE SEQRES 2 A 143 GLY PRO VAL LYS SER PHE PHE GLN THR LYS ASP GLN MET SEQRES 3 A 143 GLY ASP LEU LEU LEU THR GLY SER LEU LEU GLU ASP PHE SEQRES 4 A 143 LYS GLY TYR LEU GLY CYS GLN ALA LEU SER GLU MET ILE SEQRES 5 A 143 GLN PHE TYR LEU GLU ASP VAL MET PRO LYS ALA GLU SER SEQRES 6 A 143 ASP GLY GLU ASP ILE LYS GLU HIS VAL ASN SER LEU GLY SEQRES 7 A 143 GLU LYS LEU LYS THR LEU ARG LEU ARG LEU ARG ARG CYS SEQRES 8 A 143 HIS GLN PHE LEU PRO CYS GLU ASN LYS SER LYS ALA VAL SEQRES 9 A 143 GLU GLU VAL LYS SER ALA PHE SER LYS LEU GLN GLU ARG SEQRES 10 A 143 GLY VAL TYR LYS ALA MET GLY GLU PHE ASP ILE PHE ILE SEQRES 11 A 143 ASN TYR ILE GLU ALA TYR MET THR MET LYS MET ARG LYS FORMUL 3 HOH *40(H2 O) HELIX 1 AA1 SER B 18 LYS B 40 1 23 HELIX 2 AA2 THR B 49 GLY B 58 1 10 HELIX 3 AA3 LEU B 60 ASP B 75 1 16 HELIX 4 AA4 VAL B 76 GLU B 81 5 6 HELIX 5 AA5 GLY B 84 ARG B 107 1 24 HELIX 6 AA6 LEU B 112 ASN B 116 5 5 HELIX 7 AA7 SER B 118 LEU B 131 1 14 HELIX 8 AA8 ARG B 134 GLU B 142 1 9 HELIX 9 AA9 GLU B 142 LYS B 157 1 16 HELIX 10 AB1 LEU A 19 LYS A 40 1 22 HELIX 11 AB2 THR A 49 GLY A 58 1 10 HELIX 12 AB3 LEU A 60 ASP A 75 1 16 HELIX 13 AB4 VAL A 76 GLU A 81 5 6 HELIX 14 AB5 GLY A 84 ARG A 107 1 24 HELIX 15 AB6 LEU A 112 ASN A 116 5 5 HELIX 16 AB7 SER A 118 LEU A 131 1 14 HELIX 17 AB8 ARG A 134 GLU A 142 1 9 HELIX 18 AB9 GLU A 142 LYS A 157 1 16 SSBOND 1 CYS B 62 CYS B 114 1555 1555 2.04 SSBOND 2 CYS A 62 CYS A 114 1555 1555 2.04 CRYST1 38.930 81.200 105.720 90.00 90.00 90.00 P 2 21 21 8 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 0.025687 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012315 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009459 0.00000 CONECT 352 778 CONECT 778 352 CONECT 1490 1916 CONECT 1916 1490 MASTER 244 0 0 18 0 0 0 6 2314 2 4 22 END