HEADER IMMUNE SYSTEM 13-MAY-16 5JXD TITLE CRYSTAL STRUCTURE OF MURINE TNFAIP8 C165S MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: TUMOR NECROSIS FACTOR ALPHA-INDUCED PROTEIN 8; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: TNF ALPHA-INDUCED PROTEIN 8; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 4 ORGANISM_COMMON: MOUSE; SOURCE 5 ORGANISM_TAXID: 10090 KEYWDS TNFAIP8, OXI-A, PHOSPHATIDYLETHANOLAMINE, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR J.PARK,M.S.KIM,D.LEE,D.H.SHIN REVDAT 3 08-NOV-23 5JXD 1 REMARK REVDAT 2 01-NOV-17 5JXD 1 JRNL REVDAT 1 28-JUN-17 5JXD 0 JRNL AUTH J.S.KIM,J.PARK,M.S.KIM,J.Y.HA,Y.W.JANG,D.H.SHIN,J.H.SON JRNL TITL THE TNFAIP8-PE COMPLEX IS A NOVEL UPSTREAM EFFECTOR IN THE JRNL TITL 2 ANTI-AUTOPHAGIC ACTION OF INSULIN JRNL REF SCI REP V. 7 6248 2017 JRNL REFN ESSN 2045-2322 JRNL PMID 28740220 JRNL DOI 10.1038/S41598-017-06576-3 REMARK 2 REMARK 2 RESOLUTION. 2.03 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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) : 2.03 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.14 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.910 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 3 NUMBER OF REFLECTIONS : 13973 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.240 REMARK 3 R VALUE (WORKING SET) : 0.237 REMARK 3 FREE R VALUE : 0.287 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 699 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 33.1424 - 3.4687 1.00 2853 123 0.2222 0.2825 REMARK 3 2 3.4687 - 2.7537 1.00 2691 156 0.2502 0.2983 REMARK 3 3 2.7537 - 2.4057 1.00 2687 151 0.2418 0.2897 REMARK 3 4 2.4057 - 2.1858 0.99 2667 122 0.2475 0.2569 REMARK 3 5 2.1858 - 2.0291 0.90 2376 147 0.2896 0.3047 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 33.180 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.008 1590 REMARK 3 ANGLE : 1.702 2125 REMARK 3 CHIRALITY : 0.096 240 REMARK 3 PLANARITY : 0.005 267 REMARK 3 DIHEDRAL : 19.600 624 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 5JXD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 23-MAY-16. REMARK 100 THE DEPOSITION ID IS D_1000221249. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-APR-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 7A (6B, 6C1) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97933 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13998 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.029 REMARK 200 RESOLUTION RANGE LOW (A) : 33.140 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : 0.07800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.1500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.03 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 74.8 REMARK 200 DATA REDUNDANCY IN SHELL : 4.80 REMARK 200 R MERGE FOR SHELL (I) : 0.86900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.580 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 3F4M REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.03 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.41 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M BIS-TRIS PROPANE, PH 7.7, 1.2M REMARK 280 SODIUM CITRATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 296K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 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,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-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 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 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 1.000000 0.000000 0.000000 33.13800 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 35.78500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 45.29800 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 33.13800 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 35.78500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 45.29800 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 33.13800 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 35.78500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 45.29800 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 33.13800 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 35.78500 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 45.29800 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 1 REMARK 465 LEU A 2 REMARK 465 SER A 3 REMARK 465 GLU A 4 REMARK 465 ALA A 5 REMARK 465 GLU A 6 REMARK 465 GLU A 7 REMARK 465 PRO A 8 REMARK 465 ARG A 9 REMARK 465 GLU A 10 REMARK 465 VAL A 11 REMARK 465 ALA A 12 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 OD2 ASP A 44 OG1 THR A 46 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 NE2 GLN A 26 CG2 VAL A 34 2565 1.89 REMARK 500 CG GLN A 26 CD2 LEU A 30 4565 2.12 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 6OU A 201 DBREF 5JXD A 1 198 UNP Q921Z5 TFIP8_MOUSE 1 198 SEQADV 5JXD SER A 165 UNP Q921Z5 CYS 165 ENGINEERED MUTATION SEQRES 1 A 198 MET LEU SER GLU ALA GLU GLU PRO ARG GLU VAL ALA THR SEQRES 2 A 198 ASP VAL PHE ASN SER LYS ASN LEU ALA VAL GLN ALA GLN SEQRES 3 A 198 LYS LYS ILE LEU GLY LYS MET VAL SER LYS SER ILE ALA SEQRES 4 A 198 THR THR LEU ILE ASP ASP THR SER SER GLU VAL LEU ASP SEQRES 5 A 198 GLU LEU TYR ARG VAL THR LYS GLU TYR THR GLN ASN LYS SEQRES 6 A 198 LYS GLU ALA GLU ARG VAL ILE LYS ASN LEU ILE LYS THR SEQRES 7 A 198 VAL ILE LYS LEU ALA VAL LEU HIS ARG ASN ASN GLN PHE SEQRES 8 A 198 ASN GLN ASP GLU LEU ALA LEU MET GLU LYS PHE LYS LYS SEQRES 9 A 198 LYS VAL HIS GLN LEU ALA MET THR VAL VAL SER PHE HIS SEQRES 10 A 198 GLN VAL GLU TYR THR PHE ASP ARG ASN VAL LEU SER ARG SEQRES 11 A 198 LEU LEU ASN GLU CYS ARG GLU LEU LEU HIS GLU ILE ILE SEQRES 12 A 198 GLN ARG HIS LEU THR ALA LYS SER HIS GLY ARG VAL ASN SEQRES 13 A 198 ASN VAL PHE ASP HIS PHE SER ASP SER ASP PHE LEU ALA SEQRES 14 A 198 ALA LEU TYR ASN PRO PHE GLY LYS PHE LYS PRO HIS LEU SEQRES 15 A 198 GLN LYS LEU CYS ASP GLY ILE ASN LYS MET LEU ASP GLU SEQRES 16 A 198 GLU ASN ILE HET 6OU A 201 49 HETNAM 6OU [(2~{R})-1-[2-AZANYLETHOXY(OXIDANYL)PHOSPHORYL]OXY-3- HETNAM 2 6OU HEXADECANOYLOXY-PROPAN-2-YL] (~{Z})-OCTADEC-9-ENOATE FORMUL 2 6OU C39 H76 N O8 P FORMUL 3 HOH *21(H2 O) HELIX 1 AA1 SER A 18 VAL A 34 1 17 HELIX 2 AA2 VAL A 34 THR A 40 1 7 HELIX 3 AA3 ASP A 44 GLN A 63 1 20 HELIX 4 AA4 ASN A 64 ASN A 88 1 25 HELIX 5 AA5 ASN A 92 VAL A 119 1 28 HELIX 6 AA6 ASP A 124 GLN A 144 1 21 HELIX 7 AA7 THR A 148 SER A 163 1 16 HELIX 8 AA8 ASP A 164 TYR A 172 1 9 HELIX 9 AA9 PHE A 178 GLU A 195 1 18 SITE 1 AC1 12 THR A 40 THR A 41 SER A 47 LEU A 51 SITE 2 AC1 12 VAL A 79 HIS A 86 ARG A 87 LYS A 103 SITE 3 AC1 12 PHE A 162 LEU A 171 ASN A 197 ILE A 198 CRYST1 66.276 71.570 90.596 90.00 90.00 90.00 I 2 2 2 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 0.015088 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013972 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011038 0.00000