HEADER IMMUNE SYSTEM 01-NOV-08 3F4M TITLE CRYSTAL STRUCTURE OF TIPE2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: TUMOR NECROSIS FACTOR, ALPHA-INDUCED PROTEIN 8-LIKE PROTEIN COMPND 3 2; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: RESIDUES 24-184; COMPND 6 SYNONYM: TIPE2, INFLAMMATION FACTOR 20; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: TNFAIP8L2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX2T KEYWDS TIPE2, IMMUNE HOMEOSTASIS, TNFAIP8, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR X.ZHANG,J.WANG,Y.SHI REVDAT 2 27-DEC-23 3F4M 1 REMARK REVDAT 1 17-MAR-09 3F4M 0 JRNL AUTH X.ZHANG,J.WANG,C.FAN,H.LI,H.SUN,S.GONG,Y.H.CHEN,Y.SHI JRNL TITL CRYSTAL STRUCTURE OF TIPE2 PROVIDES INSIGHTS INTO IMMUNE JRNL TITL 2 HOMEOSTASIS JRNL REF NAT.STRUCT.MOL.BIOL. V. 16 89 2009 JRNL REFN ISSN 1545-9993 JRNL PMID 19079267 JRNL DOI 10.1038/NSMB.1522 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.83 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 18952 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.190 REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.243 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.130 REMARK 3 FREE R VALUE TEST SET COUNT : 972 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 25.8320 - 3.2424 0.94 2631 125 0.2167 0.2473 REMARK 3 2 3.2424 - 2.5743 1.00 2614 147 0.1834 0.2219 REMARK 3 3 2.5743 - 2.2491 0.99 2559 145 0.1535 0.2503 REMARK 3 4 2.2491 - 2.0436 1.00 2563 148 0.1462 0.2335 REMARK 3 5 2.0436 - 1.8971 0.99 2559 124 0.1544 0.2266 REMARK 3 6 1.8971 - 1.7853 1.00 2524 143 0.1503 0.2812 REMARK 3 7 1.7853 - 1.6959 0.99 2530 140 0.1515 0.2649 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 : 0.43 REMARK 3 B_SOL : 80.29 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.210 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.02 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.15 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.20200 REMARK 3 B22 (A**2) : -0.20200 REMARK 3 B33 (A**2) : 0.40300 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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 : 0.004 1253 REMARK 3 ANGLE : 0.726 1694 REMARK 3 CHIRALITY : 0.047 194 REMARK 3 PLANARITY : 0.003 219 REMARK 3 DIHEDRAL : 12.949 468 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 3F4M COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 11-NOV-08. REMARK 100 THE DEPOSITION ID IS D_1000050140. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-MAY-08; 28-MAY-08; 10-FEB-08 REMARK 200 TEMPERATURE (KELVIN) : 100; 100; 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 3 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y; N REMARK 200 RADIATION SOURCE : SPRING-8; SPRING-8; ROTATING REMARK 200 ANODE REMARK 200 BEAMLINE : BL41XU; BL41XU; NULL REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL; BRUKER AXS MICROSTAR REMARK 200 -H REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M; M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5; 1; 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE; GRAPHITE; GRAPHITE REMARK 200 OPTICS : NULL; NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; CCD; CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210; ADSC QUANTUM REMARK 200 210; BRUKER PLATINUM 135 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19032 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.696 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : 0.05600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 6.50 REMARK 200 R MERGE FOR SHELL (I) : 0.66100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; SINGLE WAVELENGTH; SINGLE REMARK 200 WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELXS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.09 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 13% PEGMME2000, 0.23M SODIUM CITRATE, REMARK 280 PH 5.6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 62 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 REMARK 290 5555 Y,-X+Y,Z+2/3 REMARK 290 6555 X-Y,X,Z+1/3 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+2/3 REMARK 290 11555 -X+Y,Y,-Z REMARK 290 12555 X,X-Y,-Z+1/3 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 45.30133 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 22.65067 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 0.00000 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 45.30133 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 22.65067 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 45.30133 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 22.65067 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 45.30133 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 0.00000 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 22.65067 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 CL CL A 201 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 231 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 234 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 249 LIES ON A SPECIAL POSITION. 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 A 24 REMARK 465 SER A 25 REMARK 465 VAL A 26 REMARK 465 ALA A 27 REMARK 465 HIS A 28 REMARK 465 LEU A 29 REMARK 465 PHE A 30 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 201 DBREF 3F4M A 24 184 UNP Q6P589 TP8L2_HUMAN 24 184 SEQRES 1 A 161 ARG SER VAL ALA HIS LEU PHE ILE ASP GLU THR SER SER SEQRES 2 A 161 GLU VAL LEU ASP GLU LEU TYR ARG VAL SER LYS GLU TYR SEQRES 3 A 161 THR HIS SER ARG PRO GLN ALA GLN ARG VAL ILE LYS ASP SEQRES 4 A 161 LEU ILE LYS VAL ALA ILE LYS VAL ALA VAL LEU HIS ARG SEQRES 5 A 161 ASN GLY SER PHE GLY PRO SER GLU LEU ALA LEU ALA THR SEQRES 6 A 161 ARG PHE ARG GLN LYS LEU ARG GLN GLY ALA MET THR ALA SEQRES 7 A 161 LEU SER PHE GLY GLU VAL ASP PHE THR PHE GLU ALA ALA SEQRES 8 A 161 VAL LEU ALA GLY LEU LEU THR GLU CYS ARG ASP VAL LEU SEQRES 9 A 161 LEU GLU LEU VAL GLU HIS HIS LEU THR PRO LYS SER HIS SEQRES 10 A 161 GLY ARG ILE ARG HIS VAL PHE ASP HIS PHE SER ASP PRO SEQRES 11 A 161 GLY LEU LEU THR ALA LEU TYR GLY PRO ASP PHE THR GLN SEQRES 12 A 161 HIS LEU GLY LYS ILE CYS ASP GLY LEU ARG LYS LEU LEU SEQRES 13 A 161 ASP GLU GLY LYS LEU HET CL A 201 1 HETNAM CL CHLORIDE ION FORMUL 2 CL CL 1- FORMUL 3 HOH *99(H2 O) HELIX 1 1 ASP A 32 HIS A 51 1 20 HELIX 2 2 SER A 52 ASN A 76 1 25 HELIX 3 3 GLY A 80 GLY A 105 1 26 HELIX 4 4 GLU A 112 GLU A 132 1 21 HELIX 5 5 THR A 136 SER A 151 1 16 HELIX 6 6 ASP A 152 TYR A 160 1 9 HELIX 7 7 GLY A 161 ASP A 163 5 3 HELIX 8 8 PHE A 164 GLU A 181 1 18 SITE 1 AC1 2 GLY A 80 SER A 82 CRYST1 91.815 91.815 67.952 90.00 90.00 120.00 P 62 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 0.010891 0.006288 0.000000 0.00000 SCALE2 0.000000 0.012576 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014716 0.00000