HEADER LIPID BINDING PROTEIN 03-SEP-25 9WM8 TITLE THE CRYSTAL STRUCTURE OF ASTAP-PINK1 FROM A MICROALGA COMPND MOL_ID: 1; COMPND 2 MOLECULE: ASTAP-PINK1; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: GENBANK:BBN91623.1 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SCENEDESMACEAE SP.; SOURCE 3 ORGANISM_TAXID: 2589027; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS FAS1 DOMAIN SUPERFAMILY, CAROTENOPROTEIN, ASTAXANTHIN, COLORATION, KEYWDS 2 BATHOCHROMIC SHIFT, LIPID BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Y.SHOMURA,S.KAWASAKI REVDAT 1 22-APR-26 9WM8 0 JRNL AUTH T.MITSUI,Y.SHOMURA,M.FURUBAYASHI,R.KATO,S.TAKAICHI, JRNL AUTH 2 S.KAWASAKI JRNL TITL STRUCTURAL BASIS FOR SPECTRAL RED SHIFT AND UVA ABSORPTION JRNL TITL 2 IN THE MICROALGAL WATER-SOLUBLE ASTAXANTHIN-BINDING PROTEIN JRNL TITL 3 ASTAP-PINK1. JRNL REF J.STRUCT.BIOL. V. 218 08288 2026 JRNL REFN ESSN 1095-8657 JRNL PMID 41500483 JRNL DOI 10.1016/J.JSB.2026.108288 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.21.2_5419 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.36 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 17926 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.182 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.220 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.150 REMARK 3 FREE R VALUE TEST SET COUNT : 923 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 42.3600 - 3.2500 1.00 2560 149 0.1879 0.2366 REMARK 3 2 3.2500 - 2.5800 1.00 2465 119 0.1845 0.2091 REMARK 3 3 2.5800 - 2.2500 1.00 2437 125 0.1645 0.1691 REMARK 3 4 2.2500 - 2.0500 1.00 2403 139 0.1565 0.2150 REMARK 3 5 2.0500 - 1.9000 1.00 2373 123 0.1589 0.2207 REMARK 3 6 1.9000 - 1.7900 1.00 2403 128 0.1858 0.2127 REMARK 3 7 1.7900 - 1.7000 1.00 2362 140 0.2266 0.3039 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.664 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.04 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.49 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 : 0.016 1365 REMARK 3 ANGLE : 1.375 1869 REMARK 3 CHIRALITY : 0.100 225 REMARK 3 PLANARITY : 0.012 252 REMARK 3 DIHEDRAL : 14.640 518 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -7.7487 -8.2754 13.5789 REMARK 3 T TENSOR REMARK 3 T11: 0.1522 T22: 0.1584 REMARK 3 T33: 0.1462 T12: 0.0017 REMARK 3 T13: -0.0180 T23: -0.0127 REMARK 3 L TENSOR REMARK 3 L11: 1.1761 L22: 1.6213 REMARK 3 L33: 1.1051 L12: -0.0930 REMARK 3 L13: 0.1938 L23: -0.0578 REMARK 3 S TENSOR REMARK 3 S11: 0.0300 S12: 0.0097 S13: 0.0292 REMARK 3 S21: 0.0311 S22: -0.0720 S23: 0.0124 REMARK 3 S31: -0.0206 S32: -0.1507 S33: -0.0003 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 9WM8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-SEP-25. REMARK 100 THE DEPOSITION ID IS D_1300063333. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-JUN-24 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 : PHOTON FACTORY REMARK 200 BEAMLINE : BL-1A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.018 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 4M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17985 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 71.370 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : 0.06700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.2000 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) : 1.73 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : 5.20 REMARK 200 R MERGE FOR SHELL (I) : 0.58400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: ALPHAFOLD REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.53 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.97 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS-HCL, 20% (V/V) PEG300, 5% REMARK 280 (W/V) PEG8000, AND 10% (V/V) GLYCEROL, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 20.92250 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 35.68500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.31450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 35.68500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.92250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.31450 REMARK 290 SMTRY3 4 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1250 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8600 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 KCAL/MOL 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 LYS A 2 REMARK 465 SER A 3 REMARK 465 PHE A 4 REMARK 465 ILE A 5 REMARK 465 SER A 6 REMARK 465 LEU A 7 REMARK 465 CYS A 8 REMARK 465 VAL A 9 REMARK 465 LEU A 10 REMARK 465 GLY A 11 REMARK 465 CYS A 12 REMARK 465 LEU A 13 REMARK 465 PHE A 14 REMARK 465 SER A 15 REMARK 465 ALA A 16 REMARK 465 ALA A 17 REMARK 465 LEU A 18 REMARK 465 GLY A 19 REMARK 465 ARG A 20 REMARK 465 GLN A 21 REMARK 465 LEU A 22 REMARK 465 GLN A 23 REMARK 465 GLN A 24 REMARK 465 ALA A 25 REMARK 465 PRO A 26 REMARK 465 ALA A 27 REMARK 465 PRO A 28 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 ALA A 44 74.60 -119.10 REMARK 500 GLN A 46 -7.60 -59.12 REMARK 500 REMARK 500 REMARK: NULL DBREF 9WM8 A 1 191 PDB 9WM8 9WM8 1 191 SEQRES 1 A 191 MET LYS SER PHE ILE SER LEU CYS VAL LEU GLY CYS LEU SEQRES 2 A 191 PHE SER ALA ALA LEU GLY ARG GLN LEU GLN GLN ALA PRO SEQRES 3 A 191 ALA PRO ALA LYS ARG GLY LEU THR ALA ALA LEU GLN GLN SEQRES 4 A 191 ALA ALA ALA SER ALA PRO GLN LEU SER THR LEU VAL ALA SEQRES 5 A 191 ALA ILE GLN ALA SER GLY LEU GLN ILE PRO ASP ASP ALA SEQRES 6 A 191 ALA TRP THR ILE PHE ALA PRO THR ASN GLU ALA PHE ALA SEQRES 7 A 191 ASP ASP ASP VAL ARG GLU LYS THR GLY LEU THR ALA GLN SEQRES 8 A 191 GLN LEU LEU LYS PRO ALA ASN LYS ASP ALA LEU VAL LYS SEQRES 9 A 191 LEU LEU SER TYR HIS VAL VAL PRO ALA GLY ALA VAL ARG SEQRES 10 A 191 SER THR LYS LEU THR ASP GLY GLN VAL LEU GLN THR LEU SEQRES 11 A 191 LEU LYS GLY ALA THR LEU LYS VAL ASP LEU ASP GLU ASP SEQRES 12 A 191 ASP GLY ARG ARG LYS ILE GLU ILE GLU SER SER ALA GLY SEQRES 13 A 191 ASP ASP ASP GLY ALA ASP VAL VAL ARG ALA ASP ILE VAL SEQRES 14 A 191 ALA GLY ASN SER ILE ILE HIS VAL VAL ASP ASP VAL LEU SEQRES 15 A 191 ILE PRO ALA ALA LEU ARG LYS SER GLY HET AXT A 201 44 HETNAM AXT ASTAXANTHIN HETSYN AXT 3,3'-DIHYDROXY-BETA,BETA-CAROTENE-4,4'-DIONE FORMUL 2 AXT C40 H52 O4 FORMUL 3 HOH *101(H2 O) HELIX 1 AA1 ARG A 31 ALA A 44 1 14 HELIX 2 AA2 LEU A 47 GLY A 58 1 12 HELIX 3 AA3 THR A 73 ASP A 79 1 7 HELIX 4 AA4 ASP A 79 GLY A 87 1 9 HELIX 5 AA5 THR A 89 LEU A 94 1 6 HELIX 6 AA6 LYS A 95 ALA A 97 5 3 HELIX 7 AA7 ASN A 98 TYR A 108 1 11 HELIX 8 AA8 ARG A 117 LEU A 121 5 5 HELIX 9 AA9 PRO A 184 ARG A 188 5 5 SHEET 1 AA1 7 VAL A 110 VAL A 111 0 SHEET 2 AA1 7 THR A 68 PRO A 72 -1 N THR A 68 O VAL A 111 SHEET 3 AA1 7 SER A 173 VAL A 178 1 O ILE A 174 N ILE A 69 SHEET 4 AA1 7 GLY A 160 ALA A 170 -1 N ARG A 165 O VAL A 177 SHEET 5 AA1 7 ARG A 146 SER A 153 -1 N ILE A 151 O ALA A 161 SHEET 6 AA1 7 THR A 135 ASP A 143 -1 N LYS A 137 O GLU A 152 SHEET 7 AA1 7 VAL A 126 GLN A 128 -1 N LEU A 127 O LEU A 136 CRYST1 41.845 52.629 71.370 90.00 90.00 90.00 P 21 21 21 4 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 0.023898 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019001 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014011 0.00000 CONECT 1304 1305 1309 1319 1320 CONECT 1305 1304 1306 CONECT 1306 1305 1307 1324 CONECT 1307 1306 1308 1325 CONECT 1308 1307 1309 1321 CONECT 1309 1304 1308 1310 CONECT 1310 1309 1311 CONECT 1311 1310 1312 CONECT 1312 1311 1313 1322 CONECT 1313 1312 1314 CONECT 1314 1313 1315 CONECT 1315 1314 1316 CONECT 1316 1315 1317 1323 CONECT 1317 1316 1318 CONECT 1318 1317 1340 CONECT 1319 1304 CONECT 1320 1304 CONECT 1321 1308 CONECT 1322 1312 CONECT 1323 1316 CONECT 1324 1306 CONECT 1325 1307 CONECT 1326 1327 1331 1341 1342 CONECT 1327 1326 1328 CONECT 1328 1327 1329 1347 CONECT 1329 1328 1330 1346 CONECT 1330 1329 1331 1343 CONECT 1331 1326 1330 1332 CONECT 1332 1331 1333 CONECT 1333 1332 1334 CONECT 1334 1333 1335 1344 CONECT 1335 1334 1336 CONECT 1336 1335 1337 CONECT 1337 1336 1338 CONECT 1338 1337 1339 1345 CONECT 1339 1338 1340 CONECT 1340 1318 1339 CONECT 1341 1326 CONECT 1342 1326 CONECT 1343 1330 CONECT 1344 1334 CONECT 1345 1338 CONECT 1346 1329 CONECT 1347 1328 MASTER 268 0 1 9 7 0 0 6 1342 1 44 15 END