HEADER CYTOKINE 30-JUN-21 7RA9 TITLE DESIGNED STABIL-2 SEQ1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: INTERLEUKIN-2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: IL-2,T-CELL GROWTH FACTOR,TCGF; 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: IL2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SYNTHETIC PROTEIN, CYTOKINE EXPDTA X-RAY DIFFRACTION AUTHOR K.M.JUDE,A.E.CHU,P.-S.HUANG,K.C.GARCIA REVDAT 4 25-OCT-23 7RA9 1 REMARK REVDAT 3 29-MAR-23 7RA9 1 JRNL REVDAT 2 23-MAR-22 7RA9 1 REMARK REVDAT 1 16-MAR-22 7RA9 0 JRNL AUTH J.REN,A.E.CHU,K.M.JUDE,L.K.PICTON,A.J.KARE,L.SU, JRNL AUTH 2 A.MONTANO ROMERO,P.S.HUANG,K.C.GARCIA JRNL TITL INTERLEUKIN-2 SUPERKINES BY COMPUTATIONAL DESIGN. JRNL REF PROC.NATL.ACAD.SCI.USA V. 119 01119 2022 JRNL REFN ESSN 1091-6490 JRNL PMID 35294290 JRNL DOI 10.1073/PNAS.2117401119 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.1_4122+SVN 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.35 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 3 NUMBER OF REFLECTIONS : 8094 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.257 REMARK 3 R VALUE (WORKING SET) : 0.253 REMARK 3 FREE R VALUE : 0.293 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 809 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 40.3500 - 4.0000 0.98 1385 153 0.2262 0.2708 REMARK 3 2 3.9900 - 3.1700 0.99 1268 143 0.2384 0.2582 REMARK 3 3 3.1700 - 2.7700 1.00 1247 138 0.2820 0.3352 REMARK 3 4 2.7700 - 2.5200 0.91 1119 124 0.3018 0.3111 REMARK 3 5 2.5200 - 2.3400 1.00 1211 134 0.3044 0.3756 REMARK 3 6 2.3400 - 2.2000 0.87 1055 117 0.3721 0.4129 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) : 0.343 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 33.577 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 47.25 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 56.60 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 : 0.001 1073 REMARK 3 ANGLE : 0.407 1456 REMARK 3 CHIRALITY : 0.032 172 REMARK 3 PLANARITY : 0.004 177 REMARK 3 DIHEDRAL : 11.222 411 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 135) REMARK 3 ORIGIN FOR THE GROUP (A): 16.0716 26.7229 118.8870 REMARK 3 T TENSOR REMARK 3 T11: 0.2711 T22: 0.2055 REMARK 3 T33: 0.4476 T12: -0.0043 REMARK 3 T13: 0.0466 T23: 0.0075 REMARK 3 L TENSOR REMARK 3 L11: 3.4859 L22: 2.3964 REMARK 3 L33: 6.5312 L12: -1.0741 REMARK 3 L13: 1.7263 L23: -0.6362 REMARK 3 S TENSOR REMARK 3 S11: 0.1325 S12: 0.2105 S13: 0.2225 REMARK 3 S21: -0.0905 S22: 0.0091 S23: -0.0060 REMARK 3 S31: -0.0545 S32: 0.0575 S33: -0.0630 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 7RA9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-JUL-21. REMARK 100 THE DEPOSITION ID IS D_1000257551. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-NOV-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 10.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 23-ID-B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.033167 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 : XDS JAN 31, 2020 REMARK 200 DATA SCALING SOFTWARE : XDS JAN 31, 2020 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8217 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 40.350 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 200 DATA REDUNDANCY : 16.90 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.29970 REMARK 200 FOR THE DATA SET : 5.7800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 78.8 REMARK 200 DATA REDUNDANCY IN SHELL : 9.60 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 3.41100 REMARK 200 FOR SHELL : 0.570 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: 4NEJ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.27 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.42 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M LI2SO4, 0.1 M CAPS PH 10.5, 1.2 REMARK 280 M NAH2PO4, AND 0.8 M K2HPO4, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+1/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+5/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 156.17000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 78.08500 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 117.12750 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 39.04250 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 195.21250 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 156.17000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 78.08500 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 39.04250 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 117.12750 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 195.21250 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 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 4 REMARK 465 ALA A 5 REMARK 465 PRO A 6 REMARK 465 THR A 7 REMARK 465 SER A 8 REMARK 465 SER A 9 DBREF 7RA9 A 5 135 UNP P60568 IL2_HUMAN 21 153 SEQADV 7RA9 MET A 4 UNP P60568 INITIATING METHIONINE SEQADV 7RA9 MET A 31 UNP P60568 GLY 47 ENGINEERED MUTATION SEQADV 7RA9 LEU A 32 UNP P60568 ILE 48 ENGINEERED MUTATION SEQADV 7RA9 ASP A 36 UNP P60568 LYS 52 ENGINEERED MUTATION SEQADV 7RA9 LEU A 43 UNP P60568 MET 59 ENGINEERED MUTATION SEQADV 7RA9 SER A 56 UNP P60568 GLU 72 ENGINEERED MUTATION SEQADV 7RA9 ALA A 73 UNP P60568 VAL 89 ENGINEERED MUTATION SEQADV 7RA9 ALA A 76 UNP P60568 LEU 92 ENGINEERED MUTATION SEQADV 7RA9 GLY A 78 UNP P60568 GLN 94 ENGINEERED MUTATION SEQADV 7RA9 ASP A 79 UNP P60568 SER 95 ENGINEERED MUTATION SEQADV 7RA9 ASP A 80 UNP P60568 LYS 96 ENGINEERED MUTATION SEQADV 7RA9 PRO A 81 UNP P60568 ASN 97 ENGINEERED MUTATION SEQADV 7RA9 LYS A 82 UNP P60568 PHE 98 ENGINEERED MUTATION SEQADV 7RA9 THR A 83 UNP P60568 HIS 99 ENGINEERED MUTATION SEQADV 7RA9 ILE A 84 UNP P60568 LEU 100 ENGINEERED MUTATION SEQADV 7RA9 A UNP P60568 ARG 101 DELETION SEQADV 7RA9 A UNP P60568 PRO 102 DELETION SEQADV 7RA9 VAL A 87 UNP P60568 LEU 105 ENGINEERED MUTATION SEQADV 7RA9 VAL A 88 UNP P60568 ILE 106 ENGINEERED MUTATION SEQADV 7RA9 PHE A 94 UNP P60568 ILE 112 ENGINEERED MUTATION SEQADV 7RA9 ILE A 117 UNP P60568 VAL 135 ENGINEERED MUTATION SEQRES 1 A 132 MET ALA PRO THR SER SER SER THR LYS LYS THR GLN LEU SEQRES 2 A 132 GLN LEU GLU HIS LEU LEU LEU ASP LEU GLN MET ILE LEU SEQRES 3 A 132 ASN MET LEU ASN ASN TYR ASP ASN PRO LYS LEU THR ARG SEQRES 4 A 132 LEU LEU THR PHE LYS PHE TYR MET PRO LYS LYS ALA THR SEQRES 5 A 132 SER LEU LYS HIS LEU GLN CYS LEU GLU GLU GLU LEU LYS SEQRES 6 A 132 PRO LEU GLU GLU ALA LEU ASN ALA ALA GLY ASP ASP PRO SEQRES 7 A 132 LYS THR ILE ARG ASP VAL VAL SER ASN ILE ASN VAL PHE SEQRES 8 A 132 VAL LEU GLU LEU LYS GLY SER GLU THR THR PHE MET CYS SEQRES 9 A 132 GLU TYR ALA ASP GLU THR ALA THR ILE ILE GLU PHE LEU SEQRES 10 A 132 ASN ARG TRP ILE THR PHE CYS GLN SER ILE ILE SER THR SEQRES 11 A 132 LEU THR HET PO4 A 201 5 HET PO4 A 202 5 HET PO4 A 203 5 HET EPE A 204 15 HETNAM PO4 PHOSPHATE ION HETNAM EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HETSYN EPE HEPES FORMUL 2 PO4 3(O4 P 3-) FORMUL 5 EPE C8 H18 N2 O4 S FORMUL 6 HOH *34(H2 O) HELIX 1 AA1 SER A 10 ASN A 34 1 25 HELIX 2 AA2 ASP A 36 THR A 45 1 10 HELIX 3 AA3 SER A 56 HIS A 59 5 4 HELIX 4 AA4 LEU A 60 GLU A 65 1 6 HELIX 5 AA5 GLU A 66 ALA A 76 1 11 HELIX 6 AA6 ASP A 80 GLY A 100 1 21 HELIX 7 AA7 THR A 115 THR A 135 1 21 SHEET 1 AA1 2 PHE A 48 PRO A 51 0 SHEET 2 AA1 2 TYR A 109 ALA A 114 -1 O ALA A 110 N MET A 50 SSBOND 1 CYS A 62 CYS A 107 1555 1555 2.03 CRYST1 46.588 46.588 234.255 90.00 90.00 120.00 P 65 2 2 12 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 0.021465 0.012393 0.000000 0.00000 SCALE2 0.000000 0.024785 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004269 0.00000