HEADER OXIDOREDUCTASE 29-APR-20 6YW4 TITLE HIF PROLYL HYDROXYLASE 2 (PHD2/ EGLN1) IN COMPLEX WITH N-OXALYLGLYCINE TITLE 2 (NOG) AND A RAPID-DERIVED SILENT ALLOSTERIC CYCLIC PEPTIDE 3C (14- TITLE 3 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 MUTATION: YES; COMPND 9 OTHER_DETAILS: CATALYTIC DOMAIN (AA 181-407); COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: PHD2-SPECIFIC RAPID CYCLIC PEPTIDE 3C (14-MER); COMPND 12 CHAIN: B; COMPND 13 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 3 24-JAN-24 6YW4 1 REMARK REVDAT 2 20-JAN-21 6YW4 1 DBREF SEQADV REVDAT 1 30-DEC-20 6YW4 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. 1.53 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) : 1.53 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.61 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 37652 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.163 REMARK 3 R VALUE (WORKING SET) : 0.162 REMARK 3 FREE R VALUE : 0.177 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.890 REMARK 3 FREE R VALUE TEST SET COUNT : 1841 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 39.6050 - 3.5917 1.00 2751 156 0.1597 0.1682 REMARK 3 2 3.5917 - 2.8511 1.00 2761 145 0.1577 0.1500 REMARK 3 3 2.8511 - 2.4908 1.00 2764 140 0.1504 0.1675 REMARK 3 4 2.4908 - 2.2630 1.00 2725 166 0.1440 0.1826 REMARK 3 5 2.2630 - 2.1008 1.00 2770 126 0.1443 0.1644 REMARK 3 6 2.1008 - 1.9770 1.00 2775 130 0.1526 0.1825 REMARK 3 7 1.9770 - 1.8780 1.00 2730 162 0.1507 0.1728 REMARK 3 8 1.8780 - 1.7962 1.00 2740 137 0.1613 0.1999 REMARK 3 9 1.7962 - 1.7271 1.00 2774 120 0.1875 0.2201 REMARK 3 10 1.7271 - 1.6675 1.00 2743 157 0.1998 0.2626 REMARK 3 11 1.6675 - 1.6153 1.00 2759 142 0.2305 0.2521 REMARK 3 12 1.6153 - 1.5692 1.00 2814 139 0.2472 0.2828 REMARK 3 13 1.5692 - 1.5280 0.98 2705 121 0.2731 0.2822 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 : 0.41 REMARK 3 B_SOL : 50.20 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.180 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.47 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 1854 REMARK 3 ANGLE : 1.407 2513 REMARK 3 CHIRALITY : 0.087 264 REMARK 3 PLANARITY : 0.012 326 REMARK 3 DIHEDRAL : 11.882 1081 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): -31.0342 11.1408 -3.3499 REMARK 3 T TENSOR REMARK 3 T11: 0.1138 T22: 0.3986 REMARK 3 T33: 0.2799 T12: 0.0076 REMARK 3 T13: -0.0034 T23: -0.0035 REMARK 3 L TENSOR REMARK 3 L11: 0.0143 L22: 0.1349 REMARK 3 L33: 1.2422 L12: 0.0302 REMARK 3 L13: 0.0365 L23: 0.1153 REMARK 3 S TENSOR REMARK 3 S11: -0.0884 S12: -0.0224 S13: -0.2097 REMARK 3 S21: -0.0752 S22: -0.0232 S23: 0.0529 REMARK 3 S31: -0.1132 S32: -0.5336 S33: -0.0276 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESID 205:215) REMARK 3 ORIGIN FOR THE GROUP (A): -22.4627 10.5392 0.8719 REMARK 3 T TENSOR REMARK 3 T11: 0.1393 T22: 0.2716 REMARK 3 T33: 0.1862 T12: 0.0298 REMARK 3 T13: 0.0082 T23: 0.0127 REMARK 3 L TENSOR REMARK 3 L11: 0.0144 L22: 0.4176 REMARK 3 L33: 0.1095 L12: -0.0663 REMARK 3 L13: -0.0109 L23: -0.0615 REMARK 3 S TENSOR REMARK 3 S11: 0.0101 S12: -0.2219 S13: -0.0642 REMARK 3 S21: -0.1441 S22: 0.0904 S23: 0.2960 REMARK 3 S31: 0.0275 S32: -0.3196 S33: 0.0066 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN A AND RESID 216:232) REMARK 3 ORIGIN FOR THE GROUP (A): -6.9375 -2.2192 0.6227 REMARK 3 T TENSOR REMARK 3 T11: 0.3662 T22: 0.2760 REMARK 3 T33: 0.3866 T12: 0.1194 REMARK 3 T13: -0.1151 T23: 0.0065 REMARK 3 L TENSOR REMARK 3 L11: 0.1146 L22: 0.4000 REMARK 3 L33: 0.9353 L12: 0.1057 REMARK 3 L13: 0.1498 L23: 0.6165 REMARK 3 S TENSOR REMARK 3 S11: 0.1693 S12: -0.0558 S13: -0.2147 REMARK 3 S21: 0.2504 S22: 0.2349 S23: -0.2713 REMARK 3 S31: 0.3570 S32: 0.2021 S33: 0.1451 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN A AND RESID 233:266) REMARK 3 ORIGIN FOR THE GROUP (A): -2.8280 6.0257 -9.7309 REMARK 3 T TENSOR REMARK 3 T11: 0.2272 T22: 0.4165 REMARK 3 T33: 0.3883 T12: 0.0708 REMARK 3 T13: 0.0096 T23: -0.1453 REMARK 3 L TENSOR REMARK 3 L11: 0.1115 L22: 0.5172 REMARK 3 L33: 0.5691 L12: 0.1070 REMARK 3 L13: 0.2568 L23: 0.0691 REMARK 3 S TENSOR REMARK 3 S11: -0.0233 S12: 0.0944 S13: -0.4281 REMARK 3 S21: -0.3845 S22: 0.2025 S23: -0.3038 REMARK 3 S31: 0.1663 S32: 0.5373 S33: 0.0465 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN A AND RESID 267:283) REMARK 3 ORIGIN FOR THE GROUP (A): -21.2807 1.1099 -8.5589 REMARK 3 T TENSOR REMARK 3 T11: 0.2403 T22: 0.2732 REMARK 3 T33: 0.3340 T12: -0.0235 REMARK 3 T13: -0.0326 T23: -0.0172 REMARK 3 L TENSOR REMARK 3 L11: 0.0209 L22: 0.0474 REMARK 3 L33: 0.1108 L12: 0.0018 REMARK 3 L13: -0.0017 L23: 0.0621 REMARK 3 S TENSOR REMARK 3 S11: 0.1421 S12: 0.0505 S13: -0.6063 REMARK 3 S21: -0.0251 S22: -0.0636 S23: 0.3213 REMARK 3 S31: 0.2862 S32: -0.2267 S33: 0.0003 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: (CHAIN A AND RESID 284:293) REMARK 3 ORIGIN FOR THE GROUP (A): -28.2866 13.2003 -16.2276 REMARK 3 T TENSOR REMARK 3 T11: 0.3273 T22: 0.3703 REMARK 3 T33: 0.2804 T12: 0.0241 REMARK 3 T13: -0.0665 T23: -0.0101 REMARK 3 L TENSOR REMARK 3 L11: 0.0182 L22: 0.0060 REMARK 3 L33: 0.0304 L12: 0.0140 REMARK 3 L13: 0.0285 L23: 0.0186 REMARK 3 S TENSOR REMARK 3 S11: -0.1095 S12: 0.3391 S13: 0.0871 REMARK 3 S21: -0.0139 S22: -0.0262 S23: -0.0048 REMARK 3 S31: -0.0469 S32: -0.3013 S33: 0.0002 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: (CHAIN A AND RESID 294:306) REMARK 3 ORIGIN FOR THE GROUP (A): -6.6931 8.5494 -7.4260 REMARK 3 T TENSOR REMARK 3 T11: 0.0781 T22: 0.3599 REMARK 3 T33: 0.2647 T12: 0.0412 REMARK 3 T13: -0.0188 T23: -0.1242 REMARK 3 L TENSOR REMARK 3 L11: 1.6989 L22: 1.1661 REMARK 3 L33: 1.5251 L12: 0.8467 REMARK 3 L13: 1.3550 L23: 0.4112 REMARK 3 S TENSOR REMARK 3 S11: 0.0974 S12: -0.0084 S13: -0.2553 REMARK 3 S21: -0.1101 S22: 0.1506 S23: -0.2440 REMARK 3 S31: 0.2148 S32: 0.2424 S33: -0.1315 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: (CHAIN A AND RESID 307:320) REMARK 3 ORIGIN FOR THE GROUP (A): -8.7876 21.1045 -10.7187 REMARK 3 T TENSOR REMARK 3 T11: 0.2124 T22: 0.2934 REMARK 3 T33: 0.1943 T12: -0.0405 REMARK 3 T13: -0.0068 T23: -0.0114 REMARK 3 L TENSOR REMARK 3 L11: 0.0863 L22: 0.0606 REMARK 3 L33: 0.0589 L12: 0.0728 REMARK 3 L13: -0.0742 L23: -0.0578 REMARK 3 S TENSOR REMARK 3 S11: -0.0347 S12: 0.2843 S13: 0.0548 REMARK 3 S21: -0.1498 S22: 0.1145 S23: -0.1735 REMARK 3 S31: -0.1355 S32: 0.4370 S33: 0.0009 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: (CHAIN A AND RESID 321:335) REMARK 3 ORIGIN FOR THE GROUP (A): -13.3009 10.1977 -1.2299 REMARK 3 T TENSOR REMARK 3 T11: 0.1629 T22: 0.2382 REMARK 3 T33: 0.1973 T12: 0.0128 REMARK 3 T13: -0.0370 T23: 0.0001 REMARK 3 L TENSOR REMARK 3 L11: 0.2047 L22: 0.3120 REMARK 3 L33: 0.0263 L12: 0.2579 REMARK 3 L13: 0.0573 L23: 0.0806 REMARK 3 S TENSOR REMARK 3 S11: 0.0697 S12: 0.0080 S13: -0.1481 REMARK 3 S21: 0.1036 S22: 0.1050 S23: -0.0977 REMARK 3 S31: -0.1172 S32: 0.0423 S33: 0.0001 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: (CHAIN A AND RESID 336:350) REMARK 3 ORIGIN FOR THE GROUP (A): -12.5767 22.3385 2.3960 REMARK 3 T TENSOR REMARK 3 T11: 0.2099 T22: 0.2586 REMARK 3 T33: 0.1814 T12: 0.0398 REMARK 3 T13: -0.0247 T23: -0.0499 REMARK 3 L TENSOR REMARK 3 L11: 0.0767 L22: 0.1726 REMARK 3 L33: 0.0879 L12: 0.0801 REMARK 3 L13: -0.0223 L23: 0.0789 REMARK 3 S TENSOR REMARK 3 S11: -0.0488 S12: -0.1421 S13: 0.1479 REMARK 3 S21: 0.0936 S22: -0.0065 S23: -0.0599 REMARK 3 S31: -0.3253 S32: 0.1184 S33: -0.0022 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: (CHAIN A AND RESID 351:361) REMARK 3 ORIGIN FOR THE GROUP (A): -15.3010 16.7878 4.4651 REMARK 3 T TENSOR REMARK 3 T11: 0.2473 T22: 0.3118 REMARK 3 T33: 0.2437 T12: 0.0700 REMARK 3 T13: -0.0154 T23: -0.0458 REMARK 3 L TENSOR REMARK 3 L11: 0.2532 L22: 0.2598 REMARK 3 L33: 0.0955 L12: 0.0430 REMARK 3 L13: -0.0326 L23: 0.0735 REMARK 3 S TENSOR REMARK 3 S11: -0.0475 S12: -0.5716 S13: 0.1116 REMARK 3 S21: 0.2500 S22: 0.1399 S23: 0.0079 REMARK 3 S31: -0.0976 S32: -0.1284 S33: -0.0626 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: (CHAIN A AND RESID 362:371) REMARK 3 ORIGIN FOR THE GROUP (A): -19.0454 18.7072 -8.0929 REMARK 3 T TENSOR REMARK 3 T11: 0.1724 T22: 0.2324 REMARK 3 T33: 0.1767 T12: 0.0358 REMARK 3 T13: -0.0150 T23: -0.0094 REMARK 3 L TENSOR REMARK 3 L11: 0.0420 L22: 0.0785 REMARK 3 L33: 0.0009 L12: 0.0315 REMARK 3 L13: 0.0129 L23: 0.0076 REMARK 3 S TENSOR REMARK 3 S11: -0.0522 S12: -0.1547 S13: 0.0803 REMARK 3 S21: -0.1006 S22: 0.1232 S23: 0.2064 REMARK 3 S31: -0.0714 S32: -0.2156 S33: 0.0010 REMARK 3 TLS GROUP : 13 REMARK 3 SELECTION: (CHAIN A AND RESID 372:381) REMARK 3 ORIGIN FOR THE GROUP (A): -7.2162 20.1802 -0.0134 REMARK 3 T TENSOR REMARK 3 T11: 0.1668 T22: 0.2744 REMARK 3 T33: 0.2218 T12: -0.0118 REMARK 3 T13: -0.0156 T23: -0.0571 REMARK 3 L TENSOR REMARK 3 L11: 0.1482 L22: 0.1212 REMARK 3 L33: 0.2410 L12: 0.0794 REMARK 3 L13: 0.1854 L23: 0.0878 REMARK 3 S TENSOR REMARK 3 S11: 0.1280 S12: -0.0493 S13: -0.1419 REMARK 3 S21: -0.0710 S22: 0.0252 S23: 0.1046 REMARK 3 S31: -0.1183 S32: 0.1134 S33: 0.0396 REMARK 3 TLS GROUP : 14 REMARK 3 SELECTION: (CHAIN A AND RESID 382:392) REMARK 3 ORIGIN FOR THE GROUP (A): -12.4925 9.6643 -8.4581 REMARK 3 T TENSOR REMARK 3 T11: 0.1124 T22: 0.2856 REMARK 3 T33: 0.2274 T12: 0.0371 REMARK 3 T13: -0.0305 T23: -0.0829 REMARK 3 L TENSOR REMARK 3 L11: 0.8475 L22: 1.2551 REMARK 3 L33: 0.5855 L12: 0.1295 REMARK 3 L13: 0.3884 L23: -0.1869 REMARK 3 S TENSOR REMARK 3 S11: 0.0607 S12: -0.0043 S13: -0.0824 REMARK 3 S21: -0.1677 S22: 0.2856 S23: -0.3273 REMARK 3 S31: 0.1472 S32: 0.0367 S33: 0.1255 REMARK 3 TLS GROUP : 15 REMARK 3 SELECTION: (CHAIN A AND RESID 393:403) REMARK 3 ORIGIN FOR THE GROUP (A): -15.2177 16.4338 -26.1929 REMARK 3 T TENSOR REMARK 3 T11: 0.3992 T22: 0.3596 REMARK 3 T33: 0.2440 T12: -0.1044 REMARK 3 T13: 0.0295 T23: -0.0207 REMARK 3 L TENSOR REMARK 3 L11: 0.1871 L22: 0.1433 REMARK 3 L33: 0.1873 L12: -0.1610 REMARK 3 L13: 0.1739 L23: -0.1561 REMARK 3 S TENSOR REMARK 3 S11: -0.1781 S12: -0.1575 S13: 0.1134 REMARK 3 S21: -0.3714 S22: 0.2319 S23: -0.1772 REMARK 3 S31: -0.0339 S32: -0.2864 S33: 0.0052 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 6YW4 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_1292108414. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-SEP-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I02 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 : 37807 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.528 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 : 16.00 REMARK 200 R MERGE (I) : 0.12400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.0700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.53 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.58 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 13.10 REMARK 200 R MERGE FOR SHELL (I) : 0.81400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.730 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 (%): 51.96 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.56 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SAMPLE: 1.0 MM CPHD2, 1.5 MM MNCL2, REMARK 280 2.0 MM COMPOUND, 1.0 MM 3C; RESERVOIR: 0.2 M LITHIUM SULFATE, REMARK 280 0.1 M TRIS-HCL PH 8.5, 1.26 M AMMONIUM SULFATE; SITTING DROP REMARK 280 (300 NL), PROTEIN-TO-WELL RATIO, 1:1, VAPOR DIFFUSION, SITTING REMARK 280 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 135.80733 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 67.90367 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 101.85550 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 33.95183 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 169.75917 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: 2350 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10650 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -43.0 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 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 192 CD CE NZ REMARK 470 LYS A 216 CD CE NZ REMARK 470 GLU A 217 CD OE1 OE2 REMARK 470 LYS A 234 CD CE NZ REMARK 470 ASN A 284 CG OD1 ND2 REMARK 470 LYS A 291 CG CD CE NZ REMARK 470 LYS A 350 CE NZ REMARK 470 GLN A 352 CG CD OE1 NE2 REMARK 470 THR A 405 CB OG1 CG2 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 H1 48V B 0 C THR B 13 1.54 REMARK 500 O LYS A 186 HH DTY B 1 1.54 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 -56.02 -128.53 REMARK 500 LYS A 297 170.51 -58.77 REMARK 500 PRO A 304 48.82 -85.06 REMARK 500 PHE A 346 72.60 -117.96 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 94.2 REMARK 620 3 HIS A 374 NE2 87.7 89.7 REMARK 620 4 OGA A 502 O1 93.7 101.6 168.5 REMARK 620 5 OGA A 502 O2' 91.5 174.3 90.9 77.6 REMARK 620 6 HOH A 621 O 179.7 85.4 92.4 86.3 88.9 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 OGA A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 504 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 REMARK 900 RELATED ID: 6YW1 RELATED DB: PDB REMARK 900 RELATED ID: 6YW2 RELATED DB: PDB REMARK 900 RELATED ID: 6YW3 RELATED DB: PDB DBREF 6YW4 A 181 407 UNP Q9GZT9 EGLN1_HUMAN 181 407 DBREF 6YW4 B 0 13 PDB 6YW4 6YW4 0 13 SEQADV 6YW4 GLY A 175 UNP Q9GZT9 EXPRESSION TAG SEQADV 6YW4 SER A 176 UNP Q9GZT9 EXPRESSION TAG SEQADV 6YW4 HIS A 177 UNP Q9GZT9 EXPRESSION TAG SEQADV 6YW4 MET A 178 UNP Q9GZT9 EXPRESSION TAG SEQADV 6YW4 ALA A 179 UNP Q9GZT9 EXPRESSION TAG SEQADV 6YW4 SER A 180 UNP Q9GZT9 EXPRESSION TAG SEQADV 6YW4 ALA A 201 UNP Q9GZT9 CYS 201 CONFLICT SEQADV 6YW4 ALA A 398 UNP Q9GZT9 ARG 398 CONFLICT 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 ALA 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 ALA 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 19 HET DTY B 1 20 HET MN A 501 1 HET OGA A 502 13 HET SO4 A 503 5 HET SO4 A 504 5 HETNAM 48V {[(2R)-2,3-DIAMINO-3-OXOPROPYL]SULFANYL}ACETIC ACID HETNAM DTY D-TYROSINE HETNAM MN MANGANESE (II) ION HETNAM OGA N-OXALYLGLYCINE HETNAM SO4 SULFATE ION FORMUL 2 48V C5 H10 N2 O3 S FORMUL 2 DTY C9 H11 N O3 FORMUL 3 MN MN 2+ FORMUL 4 OGA C4 H5 N O5 FORMUL 5 SO4 2(O4 S 2-) FORMUL 7 HOH *193(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 ASN A 284 1 19 HELIX 5 AA5 ASP A 335 GLY A 340 1 6 HELIX 6 AA6 ALA A 393 ALA 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 HIS A 374 N HIS A 313 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 1.44 LINK N01 48V B 0 C THR B 13 1555 1555 1.32 LINK C DTY B 1 N VAL B 2 1555 1555 1.32 LINK NE2 HIS A 313 MN MN A 501 1555 1555 2.14 LINK OD1 ASP A 315 MN MN A 501 1555 1555 2.14 LINK NE2 HIS A 374 MN MN A 501 1555 1555 2.16 LINK MN MN A 501 O1 OGA A 502 1555 1555 2.11 LINK MN MN A 501 O2' OGA A 502 1555 1555 2.13 LINK MN MN A 501 O HOH A 621 1555 1555 2.18 SITE 1 AC1 5 HIS A 313 ASP A 315 HIS A 374 OGA A 502 SITE 2 AC1 5 HOH A 621 SITE 1 AC2 14 MET A 299 TYR A 310 HIS A 313 ASP A 315 SITE 2 AC2 14 TYR A 329 HIS A 374 VAL A 376 ARG A 383 SITE 3 AC2 14 MN A 501 HOH A 614 HOH A 620 HOH A 621 SITE 4 AC2 14 HOH A 635 HOH A 666 SITE 1 AC3 4 ILE A 292 GLY A 294 LYS A 337 TYR A 390 SITE 1 AC4 5 PRO A 189 ALA A 190 HOH A 602 HOH A 604 SITE 2 AC4 5 ARG B 12 CRYST1 46.622 46.622 203.711 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 0.021449 0.012384 0.000000 0.00000 SCALE2 0.000000 0.024767 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004909 0.00000