HEADER OXIDOREDUCTASE 29-APR-20 6YW1 TITLE HIF PROLYL HYDROXYLASE 2 (PHD2/ EGLN1) IN COMPLEX WITH 2OG AND RAPID- TITLE 2 DERIVED SILENT ALLOSTERIC CYCLIC PEPTIDE 3C (14-MER) COMPND MOL_ID: 1; COMPND 2 MOLECULE: EGL NINE HOMOLOG 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: HYPOXIA-INDUCIBLE FACTOR PROLYL HYDROXYLASE 2,HPH-2,PROLYL COMPND 5 HYDROXYLASE DOMAIN-CONTAINING PROTEIN 2,PHD2,SM-20; COMPND 6 EC: 1.14.11.29; COMPND 7 ENGINEERED: YES; COMPND 8 OTHER_DETAILS: CATALYTIC DOMAIN (AA 181-407); COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: PHD2-SPECIFIC RAPID CYCLIC PEPTIDE 3C (14-MER); COMPND 11 CHAIN: B; COMPND 12 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: EGLN1, C1ORF12, PNAS-118, PNAS-137; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28A(+); SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 13 ORGANISM_TAXID: 32630 KEYWDS OXIDOREDUCTASE, NON-HEME DIOXYGENASE, IRON, 2-OXOGLUTARATE, HYPOXIA- KEYWDS 2 INDUCIBLE FACTOR, HIF, HIF PROLYL HYDROXYLASE DOMAIN 2, PHD2, EGLN1, KEYWDS 3 OXYGENASE, HYPOXIA, DNA-BINDING, METAL-BINDING, TRANSCRIPTION, KEYWDS 4 HELIX-LOOP-HELIX-BETA, DSBH, FACIAL TRIAD, CYTOPLASM, KEYWDS 5 TRANSCRIPTION/EPIGENETIC REGULATION, SIGNALING, DEVELOPMENT, CELL KEYWDS 6 STRUCTURE, BETA-HYDROXYLATION, TRANSCRIPTION ACTIVATOR/INHIBITOR, KEYWDS 7 UBL CONJUGATION, POLYMORPHISM, VITAMIN C, ZINC-FINGER, FAMILIAL KEYWDS 8 ERYTHROCYTOSIS, BREAST CANCER, TRANSCRIPTION COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR R.CHOWDHURY,C.J.SCHOFIELD REVDAT 2 24-JAN-24 6YW1 1 REMARK REVDAT 1 30-DEC-20 6YW1 0 JRNL AUTH R.CHOWDHURY,M.I.ABBOUD,T.E.MCALLISTER,B.BANERJI,B.BHUSHAN, JRNL AUTH 2 J.L.SORENSEN,A.KAWAMURA,C.J.SCHOFIELD JRNL TITL USE OF CYCLIC PEPTIDES TO INDUCE CRYSTALLIZATION: CASE STUDY JRNL TITL 2 WITH PROLYL HYDROXYLASE DOMAIN 2. JRNL REF SCI REP V. 10 21964 2020 JRNL REFN ESSN 2045-2322 JRNL PMID 33319810 JRNL DOI 10.1038/S41598-020-76307-8 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH R.CHOWDHURY,I.K.LEUNG,Y.M.TIAN,M.I.ABBOUD,W.GE,C.DOMENE, REMARK 1 AUTH 2 F.X.CANTRELLE,I.LANDRIEU,A.P.HARDY,C.W.PUGH,P.J.RATCLIFFE, REMARK 1 AUTH 3 T.D.CLARIDGE,C.J.SCHOFIELD REMARK 1 TITL STRUCTURAL BASIS FOR OXYGEN DEGRADATION DOMAIN SELECTIVITY REMARK 1 TITL 2 OF THE HIF PROLYL HYDROXYLASES. REMARK 1 REF NAT COMMUN V. 7 12673 2016 REMARK 1 REFN ESSN 2041-1723 REMARK 1 DOI 10.1038/NCOMMS12673 REMARK 2 REMARK 2 RESOLUTION. 1.46 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14_3260 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) : 1.46 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.30 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 42753 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.165 REMARK 3 R VALUE (WORKING SET) : 0.164 REMARK 3 FREE R VALUE : 0.175 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.030 REMARK 3 FREE R VALUE TEST SET COUNT : 2152 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 40.2970 - 3.5999 1.00 2714 153 0.1423 0.1464 REMARK 3 2 3.5999 - 2.8576 1.00 2671 186 0.1467 0.1614 REMARK 3 3 2.8576 - 2.4964 1.00 2768 119 0.1555 0.1580 REMARK 3 4 2.4964 - 2.2682 1.00 2707 127 0.1545 0.1677 REMARK 3 5 2.2682 - 2.1056 1.00 2678 164 0.1565 0.1701 REMARK 3 6 2.1056 - 1.9815 1.00 2745 133 0.1633 0.1993 REMARK 3 7 1.9815 - 1.8823 1.00 2713 124 0.1677 0.1738 REMARK 3 8 1.8823 - 1.8003 1.00 2690 150 0.1824 0.1755 REMARK 3 9 1.8003 - 1.7310 1.00 2706 119 0.1941 0.2278 REMARK 3 10 1.7310 - 1.6713 1.00 2741 136 0.2048 0.2374 REMARK 3 11 1.6713 - 1.6190 1.00 2675 164 0.2271 0.2289 REMARK 3 12 1.6190 - 1.5728 1.00 2711 149 0.2384 0.2709 REMARK 3 13 1.5728 - 1.5313 1.00 2740 133 0.2650 0.2766 REMARK 3 14 1.5313 - 1.4940 1.00 2659 138 0.3034 0.3233 REMARK 3 15 1.4940 - 1.4600 1.00 2683 157 0.3416 0.3560 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.38 REMARK 3 B_SOL : 45.30 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.780 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.18 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 : 0.009 1928 REMARK 3 ANGLE : 0.990 2623 REMARK 3 CHIRALITY : 0.081 273 REMARK 3 PLANARITY : 0.008 347 REMARK 3 DIHEDRAL : 7.233 1065 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 15 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN A AND RESID 188:204) REMARK 3 ORIGIN FOR THE GROUP (A): -31.4506 11.1908 -3.5059 REMARK 3 T TENSOR REMARK 3 T11: 0.0859 T22: 0.3542 REMARK 3 T33: 0.2656 T12: 0.0041 REMARK 3 T13: 0.0290 T23: 0.0120 REMARK 3 L TENSOR REMARK 3 L11: 0.1750 L22: 0.1676 REMARK 3 L33: 0.8424 L12: -0.1338 REMARK 3 L13: 0.1869 L23: -0.0078 REMARK 3 S TENSOR REMARK 3 S11: -0.0209 S12: -0.0988 S13: -0.1107 REMARK 3 S21: -0.0690 S22: -0.0891 S23: -0.0300 REMARK 3 S31: -0.1858 S32: -0.4411 S33: -0.0502 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESID 205:215) REMARK 3 ORIGIN FOR THE GROUP (A): -22.9570 10.5628 0.7296 REMARK 3 T TENSOR REMARK 3 T11: 0.2002 T22: 0.2355 REMARK 3 T33: 0.2060 T12: 0.0516 REMARK 3 T13: 0.0093 T23: 0.0173 REMARK 3 L TENSOR REMARK 3 L11: 0.2476 L22: 0.0500 REMARK 3 L33: 0.1005 L12: -0.0816 REMARK 3 L13: -0.1808 L23: 0.0499 REMARK 3 S TENSOR REMARK 3 S11: -0.0823 S12: -0.1379 S13: -0.0622 REMARK 3 S21: 0.2435 S22: 0.2031 S23: 0.2072 REMARK 3 S31: -0.0575 S32: -0.1169 S33: 0.0000 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN A AND RESID 216:232) REMARK 3 ORIGIN FOR THE GROUP (A): -8.6382 -2.7025 1.3918 REMARK 3 T TENSOR REMARK 3 T11: 0.3905 T22: 0.0557 REMARK 3 T33: 0.4631 T12: 0.3019 REMARK 3 T13: -0.1731 T23: 0.0333 REMARK 3 L TENSOR REMARK 3 L11: 0.0661 L22: 0.5371 REMARK 3 L33: 0.8514 L12: 0.0080 REMARK 3 L13: 0.0826 L23: 0.6440 REMARK 3 S TENSOR REMARK 3 S11: -0.0143 S12: -0.1392 S13: -0.2687 REMARK 3 S21: 0.5670 S22: 0.4974 S23: -0.2244 REMARK 3 S31: 0.3821 S32: 0.3828 S33: 0.9343 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN A AND RESID 233:266) REMARK 3 ORIGIN FOR THE GROUP (A): -3.3918 5.3374 -9.8877 REMARK 3 T TENSOR REMARK 3 T11: 0.2212 T22: 0.3951 REMARK 3 T33: 0.3350 T12: 0.0958 REMARK 3 T13: -0.0169 T23: -0.1545 REMARK 3 L TENSOR REMARK 3 L11: 0.3697 L22: 0.7009 REMARK 3 L33: 0.7896 L12: -0.2407 REMARK 3 L13: 0.2475 L23: 0.3197 REMARK 3 S TENSOR REMARK 3 S11: -0.0922 S12: 0.4644 S13: -0.1588 REMARK 3 S21: -0.1588 S22: 0.3933 S23: -0.3110 REMARK 3 S31: 0.1709 S32: 0.6077 S33: -0.0376 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN A AND RESID 267:283) REMARK 3 ORIGIN FOR THE GROUP (A): -21.7448 1.0465 -8.6182 REMARK 3 T TENSOR REMARK 3 T11: 0.2469 T22: 0.2512 REMARK 3 T33: 0.3350 T12: -0.0145 REMARK 3 T13: -0.0123 T23: -0.0426 REMARK 3 L TENSOR REMARK 3 L11: 0.2341 L22: 0.1482 REMARK 3 L33: 0.3037 L12: 0.1682 REMARK 3 L13: -0.1761 L23: 0.0213 REMARK 3 S TENSOR REMARK 3 S11: 0.0445 S12: 0.1672 S13: -0.4036 REMARK 3 S21: -0.0509 S22: -0.0417 S23: 0.0778 REMARK 3 S31: 0.3302 S32: -0.2274 S33: -0.0000 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: (CHAIN A AND RESID 284:293) REMARK 3 ORIGIN FOR THE GROUP (A): -29.0668 12.8533 -16.7132 REMARK 3 T TENSOR REMARK 3 T11: 0.2387 T22: 0.5145 REMARK 3 T33: 0.2464 T12: 0.0282 REMARK 3 T13: -0.0371 T23: -0.0285 REMARK 3 L TENSOR REMARK 3 L11: 0.1460 L22: 0.0678 REMARK 3 L33: 0.0357 L12: 0.0189 REMARK 3 L13: 0.0086 L23: 0.0378 REMARK 3 S TENSOR REMARK 3 S11: 0.0025 S12: 0.7680 S13: 0.0954 REMARK 3 S21: -0.3600 S22: -0.0450 S23: 0.1140 REMARK 3 S31: -0.0521 S32: -0.3184 S33: 0.0028 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: (CHAIN A AND RESID 294:306) REMARK 3 ORIGIN FOR THE GROUP (A): -7.1637 8.4867 -7.5189 REMARK 3 T TENSOR REMARK 3 T11: 0.1372 T22: 0.2972 REMARK 3 T33: 0.2448 T12: 0.0781 REMARK 3 T13: -0.0358 T23: -0.1178 REMARK 3 L TENSOR REMARK 3 L11: 0.2924 L22: 0.1622 REMARK 3 L33: 0.2019 L12: 0.1975 REMARK 3 L13: -0.2430 L23: -0.1749 REMARK 3 S TENSOR REMARK 3 S11: 0.1125 S12: 0.1261 S13: -0.2534 REMARK 3 S21: -0.0211 S22: 0.0982 S23: -0.1757 REMARK 3 S31: 0.2498 S32: 0.3043 S33: 0.0294 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: (CHAIN A AND RESID 307:320) REMARK 3 ORIGIN FOR THE GROUP (A): -8.9862 21.1660 -10.6329 REMARK 3 T TENSOR REMARK 3 T11: 0.2057 T22: 0.2962 REMARK 3 T33: 0.2122 T12: -0.0054 REMARK 3 T13: 0.0055 T23: -0.0155 REMARK 3 L TENSOR REMARK 3 L11: 0.2081 L22: 0.2024 REMARK 3 L33: 0.1291 L12: 0.2027 REMARK 3 L13: -0.1811 L23: -0.0861 REMARK 3 S TENSOR REMARK 3 S11: -0.0254 S12: 0.3552 S13: 0.1223 REMARK 3 S21: -0.0508 S22: 0.1462 S23: -0.1046 REMARK 3 S31: -0.0709 S32: 0.5054 S33: 0.0003 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: (CHAIN A AND RESID 321:335) REMARK 3 ORIGIN FOR THE GROUP (A): -13.8117 10.2799 -1.4429 REMARK 3 T TENSOR REMARK 3 T11: 0.1654 T22: 0.2088 REMARK 3 T33: 0.1813 T12: 0.0332 REMARK 3 T13: -0.0189 T23: -0.0182 REMARK 3 L TENSOR REMARK 3 L11: 0.8751 L22: 0.5566 REMARK 3 L33: 0.1880 L12: 0.7224 REMARK 3 L13: -0.1668 L23: 0.0245 REMARK 3 S TENSOR REMARK 3 S11: 0.0884 S12: 0.0604 S13: -0.1860 REMARK 3 S21: 0.1400 S22: 0.0318 S23: -0.0819 REMARK 3 S31: 0.0710 S32: 0.0165 S33: 0.0001 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: (CHAIN A AND RESID 336:350) REMARK 3 ORIGIN FOR THE GROUP (A): -13.6350 22.9117 1.2641 REMARK 3 T TENSOR REMARK 3 T11: 0.2524 T22: 0.2167 REMARK 3 T33: 0.2216 T12: 0.0521 REMARK 3 T13: -0.0177 T23: -0.0288 REMARK 3 L TENSOR REMARK 3 L11: 0.2579 L22: 0.3065 REMARK 3 L33: 0.2471 L12: 0.1102 REMARK 3 L13: -0.0956 L23: 0.2612 REMARK 3 S TENSOR REMARK 3 S11: -0.0285 S12: -0.1652 S13: 0.0387 REMARK 3 S21: 0.2197 S22: 0.1704 S23: 0.0915 REMARK 3 S31: -0.3770 S32: 0.0237 S33: 0.0002 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: (CHAIN A AND RESID 351:361) REMARK 3 ORIGIN FOR THE GROUP (A): -15.8844 16.5847 4.3771 REMARK 3 T TENSOR REMARK 3 T11: 0.2357 T22: 0.2277 REMARK 3 T33: 0.2298 T12: 0.0893 REMARK 3 T13: -0.0166 T23: -0.0399 REMARK 3 L TENSOR REMARK 3 L11: 0.1249 L22: 0.0379 REMARK 3 L33: 0.2509 L12: -0.0466 REMARK 3 L13: -0.0700 L23: 0.0981 REMARK 3 S TENSOR REMARK 3 S11: -0.1109 S12: -0.4829 S13: 0.0447 REMARK 3 S21: 0.3053 S22: 0.2229 S23: 0.2141 REMARK 3 S31: -0.0986 S32: -0.1685 S33: -0.0404 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: (CHAIN A AND RESID 362:371) REMARK 3 ORIGIN FOR THE GROUP (A): -19.5496 18.6536 -8.2858 REMARK 3 T TENSOR REMARK 3 T11: 0.1776 T22: 0.2359 REMARK 3 T33: 0.1847 T12: 0.0647 REMARK 3 T13: 0.0047 T23: 0.0091 REMARK 3 L TENSOR REMARK 3 L11: 0.0810 L22: 0.1908 REMARK 3 L33: -0.0066 L12: 0.0916 REMARK 3 L13: -0.0479 L23: 0.0219 REMARK 3 S TENSOR REMARK 3 S11: -0.0326 S12: 0.0213 S13: 0.0209 REMARK 3 S21: 0.1603 S22: 0.1595 S23: 0.0738 REMARK 3 S31: -0.1081 S32: -0.2341 S33: 0.0002 REMARK 3 TLS GROUP : 13 REMARK 3 SELECTION: (CHAIN A AND RESID 372:381) REMARK 3 ORIGIN FOR THE GROUP (A): -7.6822 20.1774 -0.2490 REMARK 3 T TENSOR REMARK 3 T11: 0.1647 T22: 0.2503 REMARK 3 T33: 0.2065 T12: 0.0161 REMARK 3 T13: -0.0218 T23: -0.0443 REMARK 3 L TENSOR REMARK 3 L11: 0.2106 L22: 0.1236 REMARK 3 L33: 0.0966 L12: 0.1619 REMARK 3 L13: -0.1000 L23: -0.0205 REMARK 3 S TENSOR REMARK 3 S11: 0.1642 S12: 0.1046 S13: -0.0636 REMARK 3 S21: -0.0280 S22: 0.0731 S23: -0.0420 REMARK 3 S31: -0.0222 S32: 0.1682 S33: 0.0049 REMARK 3 TLS GROUP : 14 REMARK 3 SELECTION: (CHAIN A AND RESID 382:392) REMARK 3 ORIGIN FOR THE GROUP (A): -13.0527 9.8549 -8.6528 REMARK 3 T TENSOR REMARK 3 T11: 0.1464 T22: 0.2398 REMARK 3 T33: 0.2165 T12: 0.0588 REMARK 3 T13: -0.0271 T23: -0.0773 REMARK 3 L TENSOR REMARK 3 L11: 0.6581 L22: 0.5847 REMARK 3 L33: 0.6290 L12: 0.4877 REMARK 3 L13: -0.1446 L23: -0.2012 REMARK 3 S TENSOR REMARK 3 S11: 0.0218 S12: 0.2749 S13: -0.1353 REMARK 3 S21: 0.0417 S22: 0.1948 S23: -0.1879 REMARK 3 S31: 0.0810 S32: 0.0802 S33: 0.0923 REMARK 3 TLS GROUP : 15 REMARK 3 SELECTION: (CHAIN A AND RESID 393:403) REMARK 3 ORIGIN FOR THE GROUP (A): -16.7836 15.9433 -26.2119 REMARK 3 T TENSOR REMARK 3 T11: 0.3535 T22: 0.4675 REMARK 3 T33: 0.2055 T12: -0.1305 REMARK 3 T13: 0.0024 T23: 0.0114 REMARK 3 L TENSOR REMARK 3 L11: 0.0041 L22: 0.3601 REMARK 3 L33: 0.0005 L12: -0.0244 REMARK 3 L13: -0.0034 L23: -0.0208 REMARK 3 S TENSOR REMARK 3 S11: -0.1269 S12: 0.2575 S13: -0.0144 REMARK 3 S21: -0.2999 S22: 0.2683 S23: -0.1690 REMARK 3 S31: 0.1029 S32: -0.3580 S33: 0.0024 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 6YW1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 29-APR-20. REMARK 100 THE DEPOSITION ID IS D_1292108411. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-MAY-17 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 : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : SI 111 REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 42887 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.460 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 7.600 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 28.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.46 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.51 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.20 REMARK 200 R MERGE FOR SHELL (I) : 1.10800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.450 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: 5L9R REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.41 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.53 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SAMPLE: 1.0 MM PHD2, 1.5 MM MNCL2, 2.0 REMARK 280 MM COMPOUND, 1.0 MM 3C; RESERVOIR: 0.1 M BIS-TRIS PH 6.5, 15.0 % REMARK 280 PEG 3350, 0.002 M MNCL2; SITTING DROP (300 NL), PROTEIN-TO-WELL REMARK 280 RATIO, 1:2, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 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+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 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 134.89667 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 67.44833 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 101.17250 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 33.72417 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 168.62083 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2140 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10710 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -18.0 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 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 GLY A 175 REMARK 465 SER A 176 REMARK 465 HIS A 177 REMARK 465 MET A 178 REMARK 465 ALA A 179 REMARK 465 SER A 180 REMARK 465 PRO A 181 REMARK 465 ASN A 182 REMARK 465 GLY A 183 REMARK 465 GLN A 184 REMARK 465 THR A 185 REMARK 465 LEU A 240 REMARK 465 VAL A 241 REMARK 465 SER A 242 REMARK 465 GLN A 243 REMARK 465 LYS A 244 REMARK 465 SER A 245 REMARK 465 ASP A 246 REMARK 465 SER A 247 REMARK 465 SER A 248 REMARK 465 LYS A 249 REMARK 465 THR A 405 REMARK 465 GLY A 406 REMARK 465 GLU A 407 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 186 CG CD CE NZ REMARK 470 LYS A 192 CD CE NZ REMARK 470 LYS A 216 CD CE NZ REMARK 470 ASP A 250 CG OD1 OD2 REMARK 470 LYS A 332 NZ REMARK 470 LYS A 350 CE NZ REMARK 470 GLN A 352 OE1 NE2 REMARK 470 LYS A 359 NZ 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 HZ2 LYS A 402 O HOH A 605 1.44 REMARK 500 REMARK 500 REMARK: NULL 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 TYR A 197 -61.16 -130.99 REMARK 500 ASP A 369 -167.53 -79.43 REMARK 500 ASP A 369 -167.56 -79.43 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 501 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 313 NE2 REMARK 620 2 ASP A 315 OD1 94.1 REMARK 620 3 HIS A 374 NE2 86.0 90.6 REMARK 620 4 AKG A 502 O1 95.0 102.8 166.5 REMARK 620 5 AKG A 502 O5 90.7 175.0 90.7 75.8 REMARK 620 6 HOH A 652 O 177.8 87.5 92.4 86.2 87.6 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue AKG A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue BCT A 503 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5L9B RELATED DB: PDB REMARK 900 RELATED ID: 5L9R RELATED DB: PDB REMARK 900 RELATED ID: 5L9V RELATED DB: PDB DBREF 6YW1 A 181 407 UNP Q9GZT9 EGLN1_HUMAN 181 407 DBREF 6YW1 B 0 13 PDB 6YW1 6YW1 0 13 SEQADV 6YW1 GLY A 175 UNP Q9GZT9 EXPRESSION TAG SEQADV 6YW1 SER A 176 UNP Q9GZT9 EXPRESSION TAG SEQADV 6YW1 HIS A 177 UNP Q9GZT9 EXPRESSION TAG SEQADV 6YW1 MET A 178 UNP Q9GZT9 EXPRESSION TAG SEQADV 6YW1 ALA A 179 UNP Q9GZT9 EXPRESSION TAG SEQADV 6YW1 SER A 180 UNP Q9GZT9 EXPRESSION TAG SEQRES 1 A 233 GLY SER HIS MET ALA SER PRO ASN GLY GLN THR LYS PRO SEQRES 2 A 233 LEU PRO ALA LEU LYS LEU ALA LEU GLU TYR ILE VAL PRO SEQRES 3 A 233 CYS MET ASN LYS HIS GLY ILE CYS VAL VAL ASP ASP PHE SEQRES 4 A 233 LEU GLY LYS GLU THR GLY GLN GLN ILE GLY ASP GLU VAL SEQRES 5 A 233 ARG ALA LEU HIS ASP THR GLY LYS PHE THR ASP GLY GLN SEQRES 6 A 233 LEU VAL SER GLN LYS SER ASP SER SER LYS ASP ILE ARG SEQRES 7 A 233 GLY ASP LYS ILE THR TRP ILE GLU GLY LYS GLU PRO GLY SEQRES 8 A 233 CYS GLU THR ILE GLY LEU LEU MET SER SER MET ASP ASP SEQRES 9 A 233 LEU ILE ARG HIS CYS ASN GLY LYS LEU GLY SER TYR LYS SEQRES 10 A 233 ILE ASN GLY ARG THR LYS ALA MET VAL ALA CYS TYR PRO SEQRES 11 A 233 GLY ASN GLY THR GLY TYR VAL ARG HIS VAL ASP ASN PRO SEQRES 12 A 233 ASN GLY ASP GLY ARG CYS VAL THR CYS ILE TYR TYR LEU SEQRES 13 A 233 ASN LYS ASP TRP ASP ALA LYS VAL SER GLY GLY ILE LEU SEQRES 14 A 233 ARG ILE PHE PRO GLU GLY LYS ALA GLN PHE ALA ASP ILE SEQRES 15 A 233 GLU PRO LYS PHE ASP ARG LEU LEU PHE PHE TRP SER ASP SEQRES 16 A 233 ARG ARG ASN PRO HIS GLU VAL GLN PRO ALA TYR ALA THR SEQRES 17 A 233 ARG TYR ALA ILE THR VAL TRP TYR PHE ASP ALA ASP GLU SEQRES 18 A 233 ARG ALA ARG ALA LYS VAL LYS TYR LEU THR GLY GLU SEQRES 1 B 14 48V DTY VAL TRP LEU THR ASP THR TRP VAL LEU SER ARG SEQRES 2 B 14 THR HET 48V B 0 17 HET DTY B 1 19 HET MN A 501 1 HET AKG A 502 14 HET BCT A 503 5 HETNAM 48V {[(2R)-2,3-DIAMINO-3-OXOPROPYL]SULFANYL}ACETIC ACID HETNAM DTY D-TYROSINE HETNAM MN MANGANESE (II) ION HETNAM AKG 2-OXOGLUTARIC ACID HETNAM BCT BICARBONATE ION FORMUL 2 48V C5 H10 N2 O3 S FORMUL 2 DTY C9 H11 N O3 FORMUL 3 MN MN 2+ FORMUL 4 AKG C5 H6 O5 FORMUL 5 BCT C H O3 1- FORMUL 6 HOH *244(H2 O) HELIX 1 AA1 PRO A 189 TYR A 197 1 9 HELIX 2 AA2 TYR A 197 GLY A 206 1 10 HELIX 3 AA3 GLY A 215 THR A 232 1 18 HELIX 4 AA4 CYS A 266 CYS A 283 1 18 HELIX 5 AA5 ASP A 335 GLY A 340 1 6 HELIX 6 AA6 ALA A 393 ARG A 398 1 6 SHEET 1 AA1 5 THR A 236 ASP A 237 0 SHEET 2 AA1 5 LYS A 255 ILE A 259 -1 O ILE A 256 N THR A 236 SHEET 3 AA1 5 ALA A 298 PRO A 304 -1 O VAL A 300 N THR A 257 SHEET 4 AA1 5 THR A 382 ASP A 392 -1 O THR A 387 N MET A 299 SHEET 5 AA1 5 ILE A 292 ARG A 295 -1 N GLY A 294 O PHE A 391 SHEET 1 AA2 8 THR A 236 ASP A 237 0 SHEET 2 AA2 8 LYS A 255 ILE A 259 -1 O ILE A 256 N THR A 236 SHEET 3 AA2 8 ALA A 298 PRO A 304 -1 O VAL A 300 N THR A 257 SHEET 4 AA2 8 THR A 382 ASP A 392 -1 O THR A 387 N MET A 299 SHEET 5 AA2 8 ARG A 322 TYR A 329 -1 N CYS A 323 O TYR A 390 SHEET 6 AA2 8 ARG A 362 TRP A 367 -1 O PHE A 366 N THR A 325 SHEET 7 AA2 8 ILE A 207 ASP A 211 -1 N VAL A 210 O LEU A 363 SHEET 8 AA2 8 VAL B 9 SER B 11 1 O LEU B 10 N ASP A 211 SHEET 1 AA3 4 THR A 308 HIS A 313 0 SHEET 2 AA3 4 HIS A 374 ALA A 379 -1 O ALA A 379 N THR A 308 SHEET 3 AA3 4 LEU A 343 ILE A 345 -1 N ARG A 344 O GLU A 375 SHEET 4 AA3 4 ALA A 354 ILE A 356 -1 O ILE A 356 N LEU A 343 LINK C09 48V B 0 N DTY B 1 1555 1555 1.36 LINK N01 48V B 0 C THR B 13 1555 1555 1.32 LINK C DTY B 1 N VAL B 2 1555 1555 1.33 LINK NE2 HIS A 313 MN MN A 501 1555 1555 2.19 LINK OD1 ASP A 315 MN MN A 501 1555 1555 2.13 LINK NE2 HIS A 374 MN MN A 501 1555 1555 2.18 LINK MN MN A 501 O1 AKG A 502 1555 1555 2.13 LINK MN MN A 501 O5 AKG A 502 1555 1555 2.11 LINK MN MN A 501 O HOH A 652 1555 1555 2.17 SITE 1 AC1 5 HIS A 313 ASP A 315 HIS A 374 AKG A 502 SITE 2 AC1 5 HOH A 652 SITE 1 AC2 15 MET A 299 TYR A 310 HIS A 313 ASP A 315 SITE 2 AC2 15 TYR A 329 LEU A 343 HIS A 374 VAL A 376 SITE 3 AC2 15 ARG A 383 MN A 501 HOH A 624 HOH A 634 SITE 4 AC2 15 HOH A 637 HOH A 652 HOH A 655 SITE 1 AC3 3 ARG A 312 PRO A 373 HOH A 756 CRYST1 46.531 46.531 202.345 90.00 90.00 120.00 P 65 6 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 0.021491 0.012408 0.000000 0.00000 SCALE2 0.000000 0.024816 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004942 0.00000