HEADER LIPID BINDING PROTEIN 23-SEP-22 8GYN TITLE ZEBRAFISH TIPE1 STRUCUTRE IN COMPLEX WITH PE COMPND MOL_ID: 1; COMPND 2 MOLECULE: TUMOR NECROSIS FACTOR ALPHA-INDUCED PROTEIN 8-LIKE PROTEIN COMPND 3 1; COMPND 4 CHAIN: A; COMPND 5 SYNONYM: TIPE1,TNF ALPHA-INDUCED PROTEIN 8-LIKE PROTEIN 1,TNFAIP8- COMPND 6 LIKE PROTEIN 1; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DANIO RERIO; SOURCE 3 ORGANISM_COMMON: ZEBRAFISH; SOURCE 4 ORGANISM_TAXID: 7955; SOURCE 5 GENE: TNFAIP8L1, TNFAIP8, SI:DKEY-49M19.6, ZGC:55331; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS LIPID TRANSFER PROTEIN, TIPE FAMILY, LIPID BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR W.WANG,S.J.CAO REVDAT 3 20-DEC-23 8GYN 1 JRNL REVDAT 2 08-NOV-23 8GYN 1 REMARK REVDAT 1 19-APR-23 8GYN 0 JRNL AUTH S.CAO,Y.ZHANG,H.JIANG,X.HOU,W.WANG JRNL TITL STRUCTURAL INSIGHT INTO TIPE1 FUNCTIONING AS A LIPID JRNL TITL 2 TRANSFER PROTEIN. JRNL REF J.BIOMOL.STRUCT.DYN. V. 41 14049 2023 JRNL REFN ESSN 1538-0254 JRNL PMID 36898854 JRNL DOI 10.1080/07391102.2023.2187641 REMARK 2 REMARK 2 RESOLUTION. 1.38 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) : 1.38 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.66 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.390 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 30268 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.149 REMARK 3 R VALUE (WORKING SET) : 0.146 REMARK 3 FREE R VALUE : 0.184 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.610 REMARK 3 FREE R VALUE TEST SET COUNT : 2000 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 25.6600 - 3.3300 0.98 2053 150 0.1437 0.1708 REMARK 3 2 3.3300 - 2.6500 0.99 2023 142 0.1559 0.1946 REMARK 3 3 2.6500 - 2.3100 1.00 2032 145 0.1516 0.1961 REMARK 3 4 2.3100 - 2.1000 0.99 2037 144 0.1406 0.1858 REMARK 3 5 2.1000 - 1.9500 0.99 2049 148 0.1501 0.1603 REMARK 3 6 1.9500 - 1.8400 1.00 2034 149 0.1479 0.1898 REMARK 3 7 1.8400 - 1.7400 1.00 2015 139 0.1391 0.1840 REMARK 3 8 1.7400 - 1.6700 1.00 2062 145 0.1313 0.1754 REMARK 3 9 1.6700 - 1.6000 1.00 2008 137 0.1244 0.1905 REMARK 3 10 1.6000 - 1.5500 1.00 2007 154 0.1320 0.1881 REMARK 3 11 1.5500 - 1.5000 0.99 2026 146 0.1341 0.1862 REMARK 3 12 1.5000 - 1.4600 0.97 2015 125 0.1445 0.2312 REMARK 3 13 1.4600 - 1.4200 0.98 1953 145 0.1655 0.2016 REMARK 3 14 1.4200 - 1.3800 0.95 1954 131 0.1795 0.2542 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) : 0.116 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.393 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.82 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.77 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 : 0.004 1438 REMARK 3 ANGLE : 0.617 1933 REMARK 3 CHIRALITY : 0.061 212 REMARK 3 PLANARITY : 0.006 245 REMARK 3 DIHEDRAL : 14.934 589 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 8GYN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 04-OCT-22. REMARK 100 THE DEPOSITION ID IS D_1300032445. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-MAY-20 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 : BL17U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97918 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 : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30289 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.380 REMARK 200 RESOLUTION RANGE LOW (A) : 34.020 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 6.100 REMARK 200 R MERGE (I) : 0.05700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.38 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.42 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.50 REMARK 200 R MERGE FOR SHELL (I) : 0.39400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.700 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: 3F4M REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.85 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SUCCINIC ACID, PH 7.0, 12% (W/V) REMARK 280 PEG 3350, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z 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 32.96000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 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 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 502 DISTANCE = 6.42 ANGSTROMS REMARK 525 HOH A 503 DISTANCE = 7.14 ANGSTROMS DBREF 8GYN A 31 186 UNP Q7SZE8 TP8L1_DANRE 31 186 SEQADV 8GYN GLY A 27 UNP Q7SZE8 EXPRESSION TAG SEQADV 8GYN PRO A 28 UNP Q7SZE8 EXPRESSION TAG SEQADV 8GYN LYS A 29 UNP Q7SZE8 EXPRESSION TAG SEQADV 8GYN LEU A 30 UNP Q7SZE8 EXPRESSION TAG SEQRES 1 A 160 GLY PRO LYS LEU ILE ASP ASP THR SER SER GLU VAL LEU SEQRES 2 A 160 ASP GLU LEU TYR ARG VAL THR LYS GLU TYR THR ARG ASN SEQRES 3 A 160 ARG LYS GLU ALA GLN LYS ILE ILE LYS ASN LEU ILE LYS SEQRES 4 A 160 MET VAL VAL LYS LEU GLY VAL LEU TYR ARG ASN GLY GLN SEQRES 5 A 160 PHE ASN ASN GLU GLU LEU ALA LEU VAL GLU ARG PHE ARG SEQRES 6 A 160 LYS LYS VAL HIS THR LEU ALA MET THR ALA VAL SER PHE SEQRES 7 A 160 TYR GLN ILE ASP PHE THR PHE ASP ARG ARG VAL MET SER SEQRES 8 A 160 ASN LEU LEU ASN ASP CYS ARG GLU LEU LEU HIS GLN ALA SEQRES 9 A 160 ILE ASN ARG HIS LEU THR ALA LYS SER HIS ALA ARG ILE SEQRES 10 A 160 ASN HIS VAL PHE ASN HIS PHE ALA ASP CYS ASP PHE LEU SEQRES 11 A 160 ALA THR LEU TYR GLY PRO SER GLU VAL TYR ARG GLY HIS SEQRES 12 A 160 LEU GLN LYS ILE CYS GLU GLY VAL ASN LYS MET LEU ASP SEQRES 13 A 160 GLU GLY ASN LEU 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 *203(H2 O) HELIX 1 AA1 ASP A 32 ARG A 51 1 20 HELIX 2 AA2 ASN A 52 ASN A 76 1 25 HELIX 3 AA3 ASN A 80 ILE A 107 1 28 HELIX 4 AA4 ASP A 112 ASN A 132 1 21 HELIX 5 AA5 THR A 136 ALA A 151 1 16 HELIX 6 AA6 ASP A 152 TYR A 160 1 9 HELIX 7 AA7 SER A 163 GLY A 184 1 22 CRYST1 34.080 65.920 35.490 90.00 106.55 90.00 P 1 21 1 2 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 0.029343 0.000000 0.008720 0.00000 SCALE2 0.000000 0.015170 0.000000 0.00000 SCALE3 0.000000 0.000000 0.029395 0.00000