HEADER CYTOKINE 13-OCT-20 7D9M TITLE GRASS CARP INTERLEUKIN-2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: INTERLEUKIN; COMPND 3 CHAIN: B, D; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CTENOPHARYNGODON IDELLA; SOURCE 3 ORGANISM_COMMON: GRASS CARP; SOURCE 4 ORGANISM_TAXID: 7959; SOURCE 5 GENE: IL-2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS INTERLEUKIN-2, FISH, GRASS CARP, CYTOKINE EXPDTA X-RAY DIFFRACTION AUTHOR W.JUNYA,Z.JUN REVDAT 3 11-NOV-20 7D9M 1 JRNL REVDAT 2 04-NOV-20 7D9M 1 JRNL REVDAT 1 28-OCT-20 7D9M 0 JRNL AUTH J.WANG,W.WANG,J.XU,Z.JIA,Q.LIU,X.ZHU,C.XIA,J.ZOU JRNL TITL STRUCTURAL INSIGHTS INTO THE CO-EVOLUTION OF IL-2 AND ITS JRNL TITL 2 PRIVATE RECEPTOR IN FISH. JRNL REF DEV.COMP.IMMUNOL. V. 115 03895 2020 JRNL REFN ISSN 0145-305X JRNL PMID 33065202 JRNL DOI 10.1016/J.DCI.2020.103895 REMARK 2 REMARK 2 RESOLUTION. 2.66 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 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) : 2.66 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.42 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.4 REMARK 3 NUMBER OF REFLECTIONS : 17766 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.378 REMARK 3 R VALUE (WORKING SET) : 0.377 REMARK 3 FREE R VALUE : 0.412 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.840 REMARK 3 FREE R VALUE TEST SET COUNT : 860 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 38.4200 - 4.8300 1.00 3201 176 0.4277 0.4282 REMARK 3 2 4.8300 - 3.8300 1.00 3005 160 0.3528 0.4115 REMARK 3 3 3.8300 - 3.3500 1.00 2943 143 0.3558 0.4181 REMARK 3 4 3.3500 - 3.0400 1.00 2934 144 0.3743 0.3972 REMARK 3 5 3.0400 - 2.8200 1.00 2893 147 0.3592 0.3953 REMARK 3 6 2.8200 - 2.6600 0.66 1930 90 0.3461 0.3651 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) : 0.472 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 41.551 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 40.62 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.86 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 : 0.010 1878 REMARK 3 ANGLE : 1.175 2526 REMARK 3 CHIRALITY : 0.048 284 REMARK 3 PLANARITY : 0.007 324 REMARK 3 DIHEDRAL : 20.754 246 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 7D9M COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 14-OCT-20. REMARK 100 THE DEPOSITION ID IS D_1300018992. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-OCT-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54178 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17766 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.660 REMARK 200 RESOLUTION RANGE LOW (A) : 45.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.1 REMARK 200 DATA REDUNDANCY : 5.200 REMARK 200 R MERGE (I) : 0.09700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.66 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 10.00 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) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD 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 (%): 77.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 5.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.4 M SODIUM PHOSPHATE MONOBASIC REMARK 280 MONOHYDRATE, POTASSIUM PHOSPHATE DIBASIC (PH 8.2), VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 291.15K 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 201.95400 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 100.97700 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 151.46550 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 50.48850 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 252.44250 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 201.95400 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 100.97700 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 50.48850 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 151.46550 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 252.44250 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: 1170 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12680 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 APPLY THE FOLLOWING TO CHAINS: D REMARK 350 BIOMT1 2 0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 -50.48850 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 GLN B 1 REMARK 465 PRO B 2 REMARK 465 VAL B 3 REMARK 465 LYS B 4 REMARK 465 THR B 120 REMARK 465 GLN B 121 REMARK 465 GLN D 1 REMARK 465 PRO D 2 REMARK 465 VAL D 3 REMARK 465 LYS D 4 REMARK 465 THR D 120 REMARK 465 GLN D 121 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 ASN D 63 N THR D 65 2.19 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 SER B 25 -77.32 71.56 REMARK 500 THR B 84 53.92 -112.62 REMARK 500 SER B 88 57.03 -146.99 REMARK 500 PHE D 20 -52.89 -140.69 REMARK 500 SER D 25 -60.02 76.17 REMARK 500 ASP D 38 -156.99 -111.85 REMARK 500 CYS D 62 -169.95 -118.57 REMARK 500 ASN D 63 -90.83 -62.62 REMARK 500 VAL D 64 -0.53 36.00 REMARK 500 GLU D 66 -122.68 -100.85 REMARK 500 ASN D 67 109.75 67.77 REMARK 500 REMARK 500 REMARK: NULL DBREF1 7D9M B 1 121 UNP A0A4D6NYT7_CTEID DBREF2 7D9M B A0A4D6NYT7 21 141 DBREF1 7D9M D 1 121 UNP A0A4D6NYT7_CTEID DBREF2 7D9M D A0A4D6NYT7 21 141 SEQRES 1 B 121 GLN PRO VAL LYS ARG SER ILE ILE ALA GLN ASP MET PHE SEQRES 2 B 121 LYS THR ALA PHE LYS GLY PHE LYS ASP GLY ILE SER ALA SEQRES 3 B 121 LYS CYS PRO LYS ASP THR ARG LEU TYR SER PRO ASP ILE SEQRES 4 B 121 GLN GLU ASP CYS LEU SER SER ALA LEU LYS CYS THR ILE SEQRES 5 B 121 ALA GLU LEU LYS VAL LEU GLU VAL GLU CYS ASN VAL THR SEQRES 6 B 121 GLU ASN ASP ASP PHE MET MET ILE TYR GLU GLY LEU ASN SEQRES 7 B 121 LYS GLU LYS TRP ASN THR SER SER SER SER PRO ARG ASN SEQRES 8 B 121 CYS THR CYS GLU LEU TYR ASN GLN THR HIS VAL LYS GLU SEQRES 9 B 121 PHE VAL GLU ASN MET GLU ARG LEU VAL GLN LEU LEU TYR SEQRES 10 B 121 THR ARG THR GLN SEQRES 1 D 121 GLN PRO VAL LYS ARG SER ILE ILE ALA GLN ASP MET PHE SEQRES 2 D 121 LYS THR ALA PHE LYS GLY PHE LYS ASP GLY ILE SER ALA SEQRES 3 D 121 LYS CYS PRO LYS ASP THR ARG LEU TYR SER PRO ASP ILE SEQRES 4 D 121 GLN GLU ASP CYS LEU SER SER ALA LEU LYS CYS THR ILE SEQRES 5 D 121 ALA GLU LEU LYS VAL LEU GLU VAL GLU CYS ASN VAL THR SEQRES 6 D 121 GLU ASN ASP ASP PHE MET MET ILE TYR GLU GLY LEU ASN SEQRES 7 D 121 LYS GLU LYS TRP ASN THR SER SER SER SER PRO ARG ASN SEQRES 8 D 121 CYS THR CYS GLU LEU TYR ASN GLN THR HIS VAL LYS GLU SEQRES 9 D 121 PHE VAL GLU ASN MET GLU ARG LEU VAL GLN LEU LEU TYR SEQRES 10 D 121 THR ARG THR GLN HELIX 1 AA1 SER B 6 ILE B 24 1 19 HELIX 2 AA2 CYS B 43 CYS B 62 1 20 HELIX 3 AA3 ASN B 67 GLU B 80 1 14 HELIX 4 AA4 THR B 93 TYR B 97 5 5 HELIX 5 AA5 HIS B 101 ARG B 119 1 19 HELIX 6 AA6 SER D 6 ASP D 22 1 17 HELIX 7 AA7 CYS D 43 CYS D 62 1 20 HELIX 8 AA8 ASN D 67 GLU D 80 1 14 HELIX 9 AA9 THR D 93 TYR D 97 5 5 HELIX 10 AB1 HIS D 101 ARG D 119 1 19 SHEET 1 AA1 2 LEU B 34 SER B 36 0 SHEET 2 AA1 2 ASN B 98 THR B 100 -1 O ASN B 98 N SER B 36 SHEET 1 AA2 2 LEU D 34 TYR D 35 0 SHEET 2 AA2 2 GLN D 99 THR D 100 -1 O THR D 100 N LEU D 34 SSBOND 1 CYS B 28 CYS B 62 1555 1555 2.07 SSBOND 2 CYS B 43 CYS B 92 1555 1555 2.05 SSBOND 3 CYS B 50 CYS B 94 1555 1555 2.07 SSBOND 4 CYS D 28 CYS D 62 1555 1555 2.08 SSBOND 5 CYS D 43 CYS D 92 1555 1555 2.03 SSBOND 6 CYS D 50 CYS D 94 1555 1555 2.06 CISPEP 1 THR B 65 GLU B 66 0 -13.35 CRYST1 83.090 83.090 302.931 90.00 90.00 120.00 P 65 2 2 24 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 0.012035 0.006948 0.000000 0.00000 SCALE2 0.000000 0.013897 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003301 0.00000