HEADER PROTEIN BINDING 19-NOV-24 9HGD TITLE CRYSTAL STRUCTURE OF HUMAN GABARAP IN COMPLEX WITH CYCLIC PEPTIDE TITLE 2 GAB_D23 COMPND MOL_ID: 1; COMPND 2 MOLECULE: GAMMA-AMINOBUTYRIC ACID RECEPTOR-ASSOCIATED PROTEIN; COMPND 3 CHAIN: A, C; COMPND 4 SYNONYM: GABA(A) RECEPTOR-ASSOCIATED PROTEIN,MM46; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: GAB_D23; COMPND 8 CHAIN: B, D; COMPND 9 ENGINEERED: YES; COMPND 10 OTHER_DETAILS: CYCLIC PEPTIDE SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: GABARAP, FLC3B, HT004; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 11 ORGANISM_TAXID: 32630 KEYWDS AUTOPHAGY-RELATED PROTEIN, CYCLIC PEPTIDE, GABARAP, INHIBITOR, KEYWDS 2 PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR A.UEFFING,J.A.WILMS,D.WILLBOLD,O.H.WEIERGRAEBER REVDAT 2 03-DEC-25 9HGD 1 JRNL REVDAT 1 09-JUL-25 9HGD 0 JRNL AUTH S.A.RETTIE,D.JUERGENS,V.ADEBOMI,Y.F.BUESO,Q.ZHAO, JRNL AUTH 2 A.N.LEVEILLE,A.LIU,A.K.BERA,J.A.WILMS,A.UFFING,A.KANG, JRNL AUTH 3 E.BRACKENBROUGH,M.LAMB,S.R.GERBEN,A.MURRAY,P.M.LEVINE, JRNL AUTH 4 M.SCHNEIDER,V.VASIREDDY,S.OVCHINNIKOV,O.H.WEIERGRABER, JRNL AUTH 5 D.WILLBOLD,J.A.KRITZER,J.D.MOUGOUS,D.BAKER,F.DIMAIO, JRNL AUTH 6 G.BHARDWAJ JRNL TITL ACCURATE DE NOVO DESIGN OF HIGH-AFFINITY PROTEIN-BINDING JRNL TITL 2 MACROCYCLES USING DEEP LEARNING. JRNL REF NAT.CHEM.BIOL. V. 21 1948 2025 JRNL REFN ESSN 1552-4469 JRNL PMID 40542165 JRNL DOI 10.1038/S41589-025-01929-W REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.A.RETTIE,D.JUERGENS,V.ADEBOMI,Y.F.BUESO,Q.ZHAO, REMARK 1 AUTH 2 A.N.LEVEILLE,A.LIU,A.K.BERA,J.A.WILMS,A.UFFING,A.KANG, REMARK 1 AUTH 3 E.BRACKENBROUGH,M.LAMB,S.R.GERBEN,A.MURRAY,P.M.LEVINE, REMARK 1 AUTH 4 M.SCHNEIDER,V.VASIREDDY,S.OVCHINNIKOV,O.H.WEIERGRABER, REMARK 1 AUTH 5 D.WILLBOLD,J.A.KRITZER,J.D.MOUGOUS,D.BAKER,F.DIMAIO, REMARK 1 AUTH 6 G.BHARDWAJ REMARK 1 TITL ACCURATE DE NOVO DESIGN OF HIGH-AFFINITY PROTEIN BINDING REMARK 1 TITL 2 MACROCYCLES USING DEEP LEARNING. REMARK 1 REF BIORXIV 2024 REMARK 1 REFN ISSN 2692-8205 REMARK 1 PMID 39605685 REMARK 1 DOI 10.1101/2024.11.18.622547 REMARK 2 REMARK 2 RESOLUTION. 1.50 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 18.42 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 3 NUMBER OF REFLECTIONS : 38949 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) : 0.188 REMARK 3 FREE R VALUE : 0.222 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1949 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 18.4200 - 3.6100 0.98 2762 145 0.1562 0.1940 REMARK 3 2 3.6100 - 2.8700 0.98 2701 142 0.1656 0.1906 REMARK 3 3 2.8700 - 2.5100 0.99 2688 142 0.1844 0.2226 REMARK 3 4 2.5000 - 2.2800 0.97 2657 140 0.1846 0.2152 REMARK 3 5 2.2800 - 2.1100 0.99 2669 140 0.1860 0.2224 REMARK 3 6 2.1100 - 1.9900 0.98 2678 142 0.1910 0.2258 REMARK 3 7 1.9900 - 1.8900 0.98 2601 137 0.1994 0.2521 REMARK 3 8 1.8900 - 1.8100 0.96 2622 138 0.2157 0.2880 REMARK 3 9 1.8100 - 1.7400 0.97 2629 138 0.2456 0.2757 REMARK 3 10 1.7400 - 1.6800 0.97 2594 137 0.2684 0.3203 REMARK 3 11 1.6800 - 1.6300 0.98 2633 139 0.3057 0.2941 REMARK 3 12 1.6300 - 1.5800 0.97 2621 138 0.3265 0.3335 REMARK 3 13 1.5800 - 1.5400 0.95 2595 136 0.3676 0.3882 REMARK 3 14 1.5400 - 1.5000 0.94 2550 135 0.4255 0.4350 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) : 0.239 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.911 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.39 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.25 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 : 0.006 2637 REMARK 3 ANGLE : 0.836 3595 REMARK 3 CHIRALITY : 0.080 363 REMARK 3 PLANARITY : 0.009 481 REMARK 3 DIHEDRAL : 13.554 1027 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 16 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID -1 THROUGH 10 ) REMARK 3 ORIGIN FOR THE GROUP (A): 0.9315 -8.9137 24.1861 REMARK 3 T TENSOR REMARK 3 T11: 0.2943 T22: 0.3577 REMARK 3 T33: 0.4366 T12: 0.0383 REMARK 3 T13: 0.0300 T23: 0.0382 REMARK 3 L TENSOR REMARK 3 L11: 9.0579 L22: 5.8449 REMARK 3 L33: 5.9526 L12: -2.0566 REMARK 3 L13: -1.7303 L23: 2.3186 REMARK 3 S TENSOR REMARK 3 S11: -0.6530 S12: -0.5072 S13: -0.4980 REMARK 3 S21: 0.8069 S22: 0.5145 S23: 1.1297 REMARK 3 S31: 0.5269 S32: -0.9268 S33: 0.1020 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 11 THROUGH 35 ) REMARK 3 ORIGIN FOR THE GROUP (A): 8.0237 2.6980 20.3990 REMARK 3 T TENSOR REMARK 3 T11: 0.1449 T22: 0.2614 REMARK 3 T33: 0.2166 T12: 0.0254 REMARK 3 T13: -0.0082 T23: -0.0379 REMARK 3 L TENSOR REMARK 3 L11: 2.0185 L22: 4.0257 REMARK 3 L33: 4.4686 L12: 0.0142 REMARK 3 L13: 0.1627 L23: -2.0059 REMARK 3 S TENSOR REMARK 3 S11: 0.0539 S12: 0.1317 S13: -0.1092 REMARK 3 S21: 0.1765 S22: -0.1616 S23: -0.2178 REMARK 3 S31: -0.1224 S32: 0.6551 S33: 0.1159 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 36 THROUGH 47 ) REMARK 3 ORIGIN FOR THE GROUP (A): -5.3820 -11.0999 13.0624 REMARK 3 T TENSOR REMARK 3 T11: 0.3246 T22: 0.3230 REMARK 3 T33: 0.7864 T12: 0.0691 REMARK 3 T13: -0.0245 T23: -0.1648 REMARK 3 L TENSOR REMARK 3 L11: 7.1416 L22: 4.9017 REMARK 3 L33: 2.4703 L12: 3.7235 REMARK 3 L13: 3.2221 L23: -0.0169 REMARK 3 S TENSOR REMARK 3 S11: 0.2071 S12: 0.3673 S13: -1.5697 REMARK 3 S21: -0.2397 S22: -0.1204 S23: 0.9149 REMARK 3 S31: 0.1172 S32: -0.0896 S33: 0.0780 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 48 THROUGH 98 ) REMARK 3 ORIGIN FOR THE GROUP (A): -7.8470 1.8463 12.3525 REMARK 3 T TENSOR REMARK 3 T11: 0.1822 T22: 0.3368 REMARK 3 T33: 0.1925 T12: -0.0043 REMARK 3 T13: -0.0470 T23: -0.0254 REMARK 3 L TENSOR REMARK 3 L11: 4.5668 L22: 3.2610 REMARK 3 L33: 2.1757 L12: -0.6623 REMARK 3 L13: -0.1006 L23: -1.2205 REMARK 3 S TENSOR REMARK 3 S11: 0.0230 S12: 0.4830 S13: -0.1603 REMARK 3 S21: -0.3021 S22: -0.0001 S23: 0.2851 REMARK 3 S31: 0.1448 S32: -0.2576 S33: -0.0055 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 99 THROUGH 117 ) REMARK 3 ORIGIN FOR THE GROUP (A): -6.2861 -3.0516 20.7153 REMARK 3 T TENSOR REMARK 3 T11: 0.1608 T22: 0.2549 REMARK 3 T33: 0.3321 T12: 0.0029 REMARK 3 T13: -0.0092 T23: 0.0134 REMARK 3 L TENSOR REMARK 3 L11: 6.4952 L22: 2.8477 REMARK 3 L33: 4.4507 L12: 1.4357 REMARK 3 L13: 3.0239 L23: 0.9363 REMARK 3 S TENSOR REMARK 3 S11: 0.2997 S12: -0.3764 S13: -0.6771 REMARK 3 S21: 0.2434 S22: -0.0916 S23: 0.3766 REMARK 3 S31: 0.2750 S32: -0.4400 S33: -0.1750 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1 THROUGH 13 ) REMARK 3 ORIGIN FOR THE GROUP (A): 7.3962 1.7530 8.1516 REMARK 3 T TENSOR REMARK 3 T11: 0.3689 T22: 0.7671 REMARK 3 T33: 0.3247 T12: 0.0676 REMARK 3 T13: 0.0713 T23: -0.0202 REMARK 3 L TENSOR REMARK 3 L11: 3.8643 L22: 3.5449 REMARK 3 L33: 3.3869 L12: 0.0540 REMARK 3 L13: -3.6139 L23: 0.0035 REMARK 3 S TENSOR REMARK 3 S11: 0.4768 S12: 1.2283 S13: 0.3978 REMARK 3 S21: -0.5895 S22: -0.3023 S23: -0.5104 REMARK 3 S31: 0.0251 S32: 2.1822 S33: -0.2100 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'C' AND (RESID -1 THROUGH 3 ) REMARK 3 ORIGIN FOR THE GROUP (A): -33.5745 7.8854 19.3777 REMARK 3 T TENSOR REMARK 3 T11: 0.7089 T22: 0.6062 REMARK 3 T33: 0.4073 T12: 0.0833 REMARK 3 T13: 0.0481 T23: -0.0100 REMARK 3 L TENSOR REMARK 3 L11: 6.4010 L22: 6.1342 REMARK 3 L33: 6.3142 L12: -6.2151 REMARK 3 L13: 6.3322 L23: -6.1340 REMARK 3 S TENSOR REMARK 3 S11: -1.0615 S12: -2.5229 S13: -0.3282 REMARK 3 S21: 2.8291 S22: 1.0274 S23: 0.1681 REMARK 3 S31: -1.0694 S32: -1.5585 S33: 0.2459 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 4 THROUGH 10 ) REMARK 3 ORIGIN FOR THE GROUP (A): -42.8370 10.9189 12.3017 REMARK 3 T TENSOR REMARK 3 T11: 0.3165 T22: 0.3817 REMARK 3 T33: 0.4356 T12: 0.1177 REMARK 3 T13: 0.0777 T23: 0.0210 REMARK 3 L TENSOR REMARK 3 L11: 2.2218 L22: 6.2983 REMARK 3 L33: 5.9178 L12: 2.6158 REMARK 3 L13: -0.7249 L23: -5.0817 REMARK 3 S TENSOR REMARK 3 S11: 0.4941 S12: 0.7413 S13: 1.2752 REMARK 3 S21: -0.1535 S22: -0.3413 S23: -0.7525 REMARK 3 S31: -0.1597 S32: 0.1371 S33: -0.2100 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 11 THROUGH 24 ) REMARK 3 ORIGIN FOR THE GROUP (A): -49.0881 -0.6151 10.6983 REMARK 3 T TENSOR REMARK 3 T11: 0.2186 T22: 0.4422 REMARK 3 T33: 0.2426 T12: 0.0020 REMARK 3 T13: -0.0232 T23: 0.0012 REMARK 3 L TENSOR REMARK 3 L11: 2.9066 L22: 6.8591 REMARK 3 L33: 6.8738 L12: -1.5901 REMARK 3 L13: -1.2410 L23: 5.4709 REMARK 3 S TENSOR REMARK 3 S11: 0.0019 S12: 0.1496 S13: 0.0302 REMARK 3 S21: -0.2388 S22: -0.2242 S23: 0.2178 REMARK 3 S31: -0.1496 S32: -0.8176 S33: 0.3102 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 25 THROUGH 56 ) REMARK 3 ORIGIN FOR THE GROUP (A): -33.5611 0.1122 6.8121 REMARK 3 T TENSOR REMARK 3 T11: 0.1540 T22: 0.3308 REMARK 3 T33: 0.1348 T12: 0.0202 REMARK 3 T13: -0.0073 T23: -0.0019 REMARK 3 L TENSOR REMARK 3 L11: 5.8754 L22: 3.7524 REMARK 3 L33: 3.5200 L12: 2.1395 REMARK 3 L13: 0.4639 L23: 0.3897 REMARK 3 S TENSOR REMARK 3 S11: -0.1585 S12: 0.5918 S13: 0.1159 REMARK 3 S21: -0.1591 S22: -0.0650 S23: 0.1392 REMARK 3 S31: -0.0798 S32: -0.1883 S33: 0.2473 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 57 THROUGH 68 ) REMARK 3 ORIGIN FOR THE GROUP (A): -24.9175 -1.3673 3.9426 REMARK 3 T TENSOR REMARK 3 T11: 0.2640 T22: 0.4574 REMARK 3 T33: 0.2176 T12: 0.0157 REMARK 3 T13: 0.0399 T23: -0.0173 REMARK 3 L TENSOR REMARK 3 L11: 7.8902 L22: 6.8820 REMARK 3 L33: 6.8911 L12: -1.8776 REMARK 3 L13: 3.2084 L23: -6.1846 REMARK 3 S TENSOR REMARK 3 S11: -0.1655 S12: 0.9250 S13: -0.1808 REMARK 3 S21: -0.0794 S22: 0.0722 S23: 0.0861 REMARK 3 S31: -0.0956 S32: -0.2029 S33: 0.1248 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 69 THROUGH 80 ) REMARK 3 ORIGIN FOR THE GROUP (A): -19.8685 4.6437 7.8719 REMARK 3 T TENSOR REMARK 3 T11: 0.2680 T22: 0.7388 REMARK 3 T33: 0.2997 T12: -0.0173 REMARK 3 T13: 0.0082 T23: 0.1623 REMARK 3 L TENSOR REMARK 3 L11: 0.0695 L22: 1.6098 REMARK 3 L33: 0.1476 L12: -0.2436 REMARK 3 L13: 0.0176 L23: 0.4191 REMARK 3 S TENSOR REMARK 3 S11: -0.0938 S12: 1.4044 S13: 0.7581 REMARK 3 S21: -0.4123 S22: 0.0741 S23: 0.0143 REMARK 3 S31: 0.0294 S32: -0.0827 S33: -0.0327 REMARK 3 TLS GROUP : 13 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 81 THROUGH 98 ) REMARK 3 ORIGIN FOR THE GROUP (A): -30.3317 -7.0353 16.6636 REMARK 3 T TENSOR REMARK 3 T11: 0.1965 T22: 0.2439 REMARK 3 T33: 0.2585 T12: 0.0039 REMARK 3 T13: 0.0075 T23: 0.0196 REMARK 3 L TENSOR REMARK 3 L11: 9.7417 L22: 3.0412 REMARK 3 L33: 2.6947 L12: 2.2938 REMARK 3 L13: 0.7872 L23: 0.0790 REMARK 3 S TENSOR REMARK 3 S11: -0.1920 S12: -0.1765 S13: -0.8922 REMARK 3 S21: -0.0187 S22: 0.1391 S23: -0.1908 REMARK 3 S31: 0.1344 S32: -0.0403 S33: 0.0443 REMARK 3 TLS GROUP : 14 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 99 THROUGH 104 ) REMARK 3 ORIGIN FOR THE GROUP (A): -42.8415 -1.7462 16.2809 REMARK 3 T TENSOR REMARK 3 T11: 0.2122 T22: 0.3760 REMARK 3 T33: 0.2605 T12: -0.0204 REMARK 3 T13: -0.0091 T23: -0.0667 REMARK 3 L TENSOR REMARK 3 L11: 7.6145 L22: 3.4493 REMARK 3 L33: 9.3698 L12: -4.6050 REMARK 3 L13: 1.9483 L23: -3.4848 REMARK 3 S TENSOR REMARK 3 S11: -0.1657 S12: 0.0067 S13: 0.1400 REMARK 3 S21: 0.2461 S22: 0.0726 S23: -0.1568 REMARK 3 S31: -0.4836 S32: 0.1992 S33: 0.0889 REMARK 3 TLS GROUP : 15 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 105 THROUGH 117 ) REMARK 3 ORIGIN FOR THE GROUP (A): -25.7749 6.2784 15.3089 REMARK 3 T TENSOR REMARK 3 T11: 0.1993 T22: 0.2598 REMARK 3 T33: 0.2529 T12: 0.0058 REMARK 3 T13: -0.0147 T23: 0.0144 REMARK 3 L TENSOR REMARK 3 L11: 4.9534 L22: 3.5230 REMARK 3 L33: 4.2299 L12: 0.0253 REMARK 3 L13: -1.1309 L23: -0.7357 REMARK 3 S TENSOR REMARK 3 S11: -0.0750 S12: -0.2083 S13: 0.7605 REMARK 3 S21: 0.1246 S22: -0.1151 S23: -0.0666 REMARK 3 S31: -0.3516 S32: 0.3250 S33: 0.1911 REMARK 3 TLS GROUP : 16 REMARK 3 SELECTION: CHAIN 'D' AND (RESID 1 THROUGH 13 ) REMARK 3 ORIGIN FOR THE GROUP (A): -39.7896 -1.0998 -1.3235 REMARK 3 T TENSOR REMARK 3 T11: 0.5801 T22: 0.7781 REMARK 3 T33: 0.2781 T12: 0.1090 REMARK 3 T13: -0.0191 T23: -0.0222 REMARK 3 L TENSOR REMARK 3 L11: 3.3959 L22: 2.3795 REMARK 3 L33: 6.6592 L12: 1.3389 REMARK 3 L13: -3.6483 L23: 0.7836 REMARK 3 S TENSOR REMARK 3 S11: 0.2174 S12: 2.1367 S13: -0.2406 REMARK 3 S21: -1.0211 S22: -0.3646 S23: 0.1771 REMARK 3 S31: -0.3815 S32: 0.2453 S33: 0.1539 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 9HGD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 19-NOV-24. REMARK 100 THE DEPOSITION ID IS D_1292143219. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-JUN-24 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM07 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.980 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39046 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 20.020 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 200 DATA REDUNDANCY : 6.850 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.3400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.54 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.5 REMARK 200 DATA REDUNDANCY IN SHELL : 6.62 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.580 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.12 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.02 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MES PH 5, 30% PEG 6000, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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+1/2,Y+1/2,Z 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 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 54.31500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.89500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 54.31500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 21.89500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: 1680 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7650 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -24.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 REMARK 350 BIOMOLECULE: 2 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: 1530 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7500 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -3.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D 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 HOH B 107 LIES ON A SPECIAL POSITION. REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 38 CD CE NZ REMARK 470 LYS C 2 CG CD CE NZ REMARK 470 LYS D 12 CD CE NZ 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 ARG A 40 59.91 -99.14 REMARK 500 ILE A 41 -50.36 -124.33 REMARK 500 LYS C 38 -6.88 70.88 REMARK 500 ASN C 81 50.84 29.44 REMARK 500 ASN C 82 9.71 85.80 REMARK 500 GLU D 2 -153.40 -138.50 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 PGE A 203 REMARK 610 MES C 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 9HGC RELATED DB: PDB DBREF 9HGD A 1 117 UNP O95166 GBRAP_HUMAN 1 117 DBREF 9HGD B 1 13 PDB 9HGD 9HGD 1 13 DBREF 9HGD C 1 117 UNP O95166 GBRAP_HUMAN 1 117 DBREF 9HGD D 1 13 PDB 9HGD 9HGD 1 13 SEQADV 9HGD GLY A -1 UNP O95166 EXPRESSION TAG SEQADV 9HGD SER A 0 UNP O95166 EXPRESSION TAG SEQADV 9HGD GLY C -1 UNP O95166 EXPRESSION TAG SEQADV 9HGD SER C 0 UNP O95166 EXPRESSION TAG SEQRES 1 A 119 GLY SER MET LYS PHE VAL TYR LYS GLU GLU HIS PRO PHE SEQRES 2 A 119 GLU LYS ARG ARG SER GLU GLY GLU LYS ILE ARG LYS LYS SEQRES 3 A 119 TYR PRO ASP ARG VAL PRO VAL ILE VAL GLU LYS ALA PRO SEQRES 4 A 119 LYS ALA ARG ILE GLY ASP LEU ASP LYS LYS LYS TYR LEU SEQRES 5 A 119 VAL PRO SER ASP LEU THR VAL GLY GLN PHE TYR PHE LEU SEQRES 6 A 119 ILE ARG LYS ARG ILE HIS LEU ARG ALA GLU ASP ALA LEU SEQRES 7 A 119 PHE PHE PHE VAL ASN ASN VAL ILE PRO PRO THR SER ALA SEQRES 8 A 119 THR MET GLY GLN LEU TYR GLN GLU HIS HIS GLU GLU ASP SEQRES 9 A 119 PHE PHE LEU TYR ILE ALA TYR SER ASP GLU SER VAL TYR SEQRES 10 A 119 GLY LEU SEQRES 1 B 13 LEU GLU ASP GLY TRP VAL ASP ILE GLU THR GLY LYS GLU SEQRES 1 C 119 GLY SER MET LYS PHE VAL TYR LYS GLU GLU HIS PRO PHE SEQRES 2 C 119 GLU LYS ARG ARG SER GLU GLY GLU LYS ILE ARG LYS LYS SEQRES 3 C 119 TYR PRO ASP ARG VAL PRO VAL ILE VAL GLU LYS ALA PRO SEQRES 4 C 119 LYS ALA ARG ILE GLY ASP LEU ASP LYS LYS LYS TYR LEU SEQRES 5 C 119 VAL PRO SER ASP LEU THR VAL GLY GLN PHE TYR PHE LEU SEQRES 6 C 119 ILE ARG LYS ARG ILE HIS LEU ARG ALA GLU ASP ALA LEU SEQRES 7 C 119 PHE PHE PHE VAL ASN ASN VAL ILE PRO PRO THR SER ALA SEQRES 8 C 119 THR MET GLY GLN LEU TYR GLN GLU HIS HIS GLU GLU ASP SEQRES 9 C 119 PHE PHE LEU TYR ILE ALA TYR SER ASP GLU SER VAL TYR SEQRES 10 C 119 GLY LEU SEQRES 1 D 13 LEU GLU ASP GLY TRP VAL ASP ILE GLU THR GLY LYS GLU HET CL A 201 1 HET CL A 202 1 HET PGE A 203 6 HET MES C 201 7 HET MES C 202 12 HET TRS C 203 8 HETNAM CL CHLORIDE ION HETNAM PGE TRIETHYLENE GLYCOL HETNAM MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETSYN TRS TRIS BUFFER FORMUL 5 CL 2(CL 1-) FORMUL 7 PGE C6 H14 O4 FORMUL 8 MES 2(C6 H13 N O4 S) FORMUL 10 TRS C4 H12 N O3 1+ FORMUL 11 HOH *158(H2 O) HELIX 1 AA1 PHE A 3 HIS A 9 1 7 HELIX 2 AA2 PRO A 10 TYR A 25 1 16 HELIX 3 AA3 THR A 56 HIS A 69 1 14 HELIX 4 AA4 THR A 90 HIS A 99 1 10 HELIX 5 AA5 LEU B 1 TRP B 5 5 5 HELIX 6 AA6 PHE C 3 HIS C 9 1 7 HELIX 7 AA7 PRO C 10 TYR C 25 1 16 HELIX 8 AA8 THR C 56 ILE C 68 1 13 HELIX 9 AA9 THR C 90 HIS C 99 1 10 HELIX 10 AB1 LEU D 1 TRP D 5 5 5 SHEET 1 AA1 5 PHE A 77 PHE A 79 0 SHEET 2 AA1 5 LEU A 105 SER A 110 -1 O SER A 110 N PHE A 77 SHEET 3 AA1 5 ARG A 28 LYS A 35 1 N ILE A 32 O LEU A 105 SHEET 4 AA1 5 LYS A 48 PRO A 52 -1 O TYR A 49 N VAL A 31 SHEET 5 AA1 5 VAL B 6 ASP B 7 1 O VAL B 6 N LEU A 50 SHEET 1 AA2 5 PHE C 77 PHE C 79 0 SHEET 2 AA2 5 LEU C 105 SER C 110 -1 O ALA C 108 N PHE C 79 SHEET 3 AA2 5 ARG C 28 LYS C 35 1 N ILE C 32 O LEU C 105 SHEET 4 AA2 5 LYS C 48 PRO C 52 -1 O VAL C 51 N VAL C 29 SHEET 5 AA2 5 VAL D 6 ASP D 7 1 O VAL D 6 N LEU C 50 LINK N LEU B 1 C GLU B 13 1555 1555 1.33 LINK N ALEU D 1 C AGLU D 13 1555 1555 1.33 LINK N BLEU D 1 C BGLU D 13 1555 1555 1.33 CRYST1 108.630 43.790 67.520 90.00 128.38 90.00 C 1 2 1 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 0.009206 0.000000 0.007290 0.00000 SCALE2 0.000000 0.022836 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018892 0.00000 CONECT 1084 1189 CONECT 1189 1084 CONECT 2362 2509 CONECT 2363 2510 CONECT 2509 2362 CONECT 2510 2363 CONECT 2526 2527 2528 CONECT 2527 2526 CONECT 2528 2526 2529 CONECT 2529 2528 2530 CONECT 2530 2529 2531 CONECT 2531 2530 CONECT 2532 2533 CONECT 2533 2532 2534 CONECT 2534 2533 2535 CONECT 2535 2534 2536 2537 2538 CONECT 2536 2535 CONECT 2537 2535 CONECT 2538 2535 CONECT 2539 2540 2544 CONECT 2540 2539 2541 CONECT 2541 2540 2542 CONECT 2542 2541 2543 2545 CONECT 2543 2542 2544 CONECT 2544 2539 2543 CONECT 2545 2542 2546 CONECT 2546 2545 2547 CONECT 2547 2546 2548 2549 2550 CONECT 2548 2547 CONECT 2549 2547 CONECT 2550 2547 CONECT 2551 2552 2553 2554 2555 CONECT 2552 2551 2556 CONECT 2553 2551 2557 CONECT 2554 2551 2558 CONECT 2555 2551 CONECT 2556 2552 CONECT 2557 2553 CONECT 2558 2554 MASTER 522 0 6 10 10 0 0 6 2385 4 39 22 END