HEADER OXIDOREDUCTASE 29-APR-20 6YW3 TITLE HIF PROLYL HYDROXYLASE 2 (PHD2/ EGLN1) IN COMPLEX WITH N-OXALYL TITLE 2 GLYCINE (NOG), HIF-1ALPHA CODD (556-574) AND A RAPID-DERIVED CYCLIC TITLE 3 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 (RESIDUES 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; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: HYPOXIA-INDUCIBLE FACTOR 1-ALPHA; COMPND 15 CHAIN: S; COMPND 16 SYNONYM: HIF1-ALPHA,ARNT-INTERACTING PROTEIN,BASIC-HELIX-LOOP-HELIX- COMPND 17 PAS PROTEIN MOP1,CLASS E BASIC HELIX-LOOP-HELIX PROTEIN 78,BHLHE78, COMPND 18 MEMBER OF PAS PROTEIN 1,PAS DOMAIN-CONTAINING PROTEIN 8; COMPND 19 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; SOURCE 14 MOL_ID: 3; SOURCE 15 SYNTHETIC: YES; SOURCE 16 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 17 ORGANISM_COMMON: HUMAN; SOURCE 18 ORGANISM_TAXID: 9606 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 6YW3 1 REMARK REVDAT 1 30-DEC-20 6YW3 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. 2.28 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) : 2.28 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 55.69 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 12824 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 : 0.208 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.810 REMARK 3 FREE R VALUE TEST SET COUNT : 617 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 55.6860 - 4.9094 1.00 1345 50 0.1863 0.2114 REMARK 3 2 4.9094 - 3.8971 1.00 1255 58 0.1315 0.1395 REMARK 3 3 3.8971 - 3.4045 1.00 1224 62 0.1695 0.1844 REMARK 3 4 3.4045 - 3.0933 1.00 1226 58 0.1910 0.2430 REMARK 3 5 3.0933 - 2.8716 1.00 1202 67 0.2083 0.1944 REMARK 3 6 2.8716 - 2.7023 1.00 1191 64 0.2132 0.2708 REMARK 3 7 2.7023 - 2.5669 1.00 1195 75 0.2217 0.2338 REMARK 3 8 2.5669 - 2.4552 1.00 1213 66 0.2289 0.2901 REMARK 3 9 2.4552 - 2.3607 1.00 1181 65 0.2439 0.2402 REMARK 3 10 2.3607 - 2.2792 0.99 1176 52 0.2526 0.2721 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 : 0.37 REMARK 3 B_SOL : 40.20 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.610 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 30.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.85 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.004 9529 REMARK 3 ANGLE : 0.795 12945 REMARK 3 CHIRALITY : 0.048 1356 REMARK 3 PLANARITY : 0.005 1691 REMARK 3 DIHEDRAL : 16.442 5500 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 188:204) REMARK 3 ORIGIN FOR THE GROUP (A): 79.4642 11.0064 50.0979 REMARK 3 T TENSOR REMARK 3 T11: 0.2960 T22: 0.2611 REMARK 3 T33: 0.3393 T12: -0.0326 REMARK 3 T13: 0.0447 T23: -0.0488 REMARK 3 L TENSOR REMARK 3 L11: 2.9125 L22: 3.9287 REMARK 3 L33: 3.1859 L12: -1.9796 REMARK 3 L13: 0.9361 L23: -0.9787 REMARK 3 S TENSOR REMARK 3 S11: -0.0089 S12: 0.0478 S13: -0.5226 REMARK 3 S21: -0.3510 S22: 0.1683 S23: 0.5470 REMARK 3 S31: 0.5638 S32: -0.0204 S33: -0.0426 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESID 205:215) REMARK 3 ORIGIN FOR THE GROUP (A): 79.9660 17.5862 56.9509 REMARK 3 T TENSOR REMARK 3 T11: 0.2291 T22: 0.1525 REMARK 3 T33: 0.2410 T12: -0.0568 REMARK 3 T13: -0.0463 T23: -0.0001 REMARK 3 L TENSOR REMARK 3 L11: 2.8592 L22: 2.7204 REMARK 3 L33: 3.8949 L12: -0.1159 REMARK 3 L13: 0.8363 L23: -1.2055 REMARK 3 S TENSOR REMARK 3 S11: 0.1828 S12: -0.3198 S13: -0.2189 REMARK 3 S21: -0.0834 S22: 0.1329 S23: 0.4387 REMARK 3 S31: 0.1858 S32: -0.0285 S33: -0.3326 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN A AND RESID 216:232) REMARK 3 ORIGIN FOR THE GROUP (A): 93.2364 23.3634 70.6847 REMARK 3 T TENSOR REMARK 3 T11: 0.5508 T22: 0.4667 REMARK 3 T33: 0.2396 T12: -0.0410 REMARK 3 T13: -0.1491 T23: 0.0648 REMARK 3 L TENSOR REMARK 3 L11: 4.1067 L22: 9.4482 REMARK 3 L33: 1.1454 L12: 2.7012 REMARK 3 L13: -0.7797 L23: 0.5423 REMARK 3 S TENSOR REMARK 3 S11: 0.0543 S12: -0.0510 S13: 0.2510 REMARK 3 S21: 1.7118 S22: -0.0787 S23: -0.0790 REMARK 3 S31: -0.3485 S32: 0.5192 S33: 0.0950 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN A AND RESID 233:266) REMARK 3 ORIGIN FOR THE GROUP (A): 96.5050 35.3331 57.6966 REMARK 3 T TENSOR REMARK 3 T11: 0.3273 T22: 0.4064 REMARK 3 T33: 0.4026 T12: -0.1522 REMARK 3 T13: -0.0985 T23: 0.0077 REMARK 3 L TENSOR REMARK 3 L11: 5.8639 L22: 2.6634 REMARK 3 L33: 3.8058 L12: -0.8411 REMARK 3 L13: 0.4412 L23: -0.4858 REMARK 3 S TENSOR REMARK 3 S11: -0.0915 S12: -0.1623 S13: 0.6428 REMARK 3 S21: 0.4049 S22: -0.1662 S23: -0.3606 REMARK 3 S31: -0.5689 S32: 0.6585 S33: 0.2575 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN A AND RESID 267:283) REMARK 3 ORIGIN FOR THE GROUP (A): 92.8039 14.2720 56.0993 REMARK 3 T TENSOR REMARK 3 T11: 0.2609 T22: 0.2513 REMARK 3 T33: 0.2441 T12: 0.0442 REMARK 3 T13: -0.0583 T23: 0.0255 REMARK 3 L TENSOR REMARK 3 L11: 5.1542 L22: 4.5856 REMARK 3 L33: 6.3779 L12: 0.9688 REMARK 3 L13: 1.0772 L23: 2.0818 REMARK 3 S TENSOR REMARK 3 S11: 0.2686 S12: 0.0048 S13: -0.4024 REMARK 3 S21: 0.4034 S22: 0.0312 S23: -0.4286 REMARK 3 S31: 0.7359 S32: 0.7526 S33: -0.2773 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: (CHAIN A AND RESID 284:293) REMARK 3 ORIGIN FOR THE GROUP (A): 88.5495 15.5209 41.0071 REMARK 3 T TENSOR REMARK 3 T11: 0.3892 T22: 0.3317 REMARK 3 T33: 0.2787 T12: 0.0601 REMARK 3 T13: 0.0265 T23: -0.0188 REMARK 3 L TENSOR REMARK 3 L11: 5.4849 L22: 3.5233 REMARK 3 L33: 3.7869 L12: 1.3464 REMARK 3 L13: -0.3522 L23: 0.2374 REMARK 3 S TENSOR REMARK 3 S11: 0.0171 S12: 0.5901 S13: -0.0407 REMARK 3 S21: -0.3037 S22: 0.0345 S23: -0.2844 REMARK 3 S31: 0.7344 S32: 0.1276 S33: -0.2038 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: (CHAIN A AND RESID 294:306) REMARK 3 ORIGIN FOR THE GROUP (A): 92.6170 30.3889 59.0865 REMARK 3 T TENSOR REMARK 3 T11: 0.2549 T22: 0.3458 REMARK 3 T33: 0.2458 T12: -0.0443 REMARK 3 T13: -0.0648 T23: 0.0081 REMARK 3 L TENSOR REMARK 3 L11: 2.4379 L22: 1.9559 REMARK 3 L33: 2.7066 L12: 0.6144 REMARK 3 L13: 0.6681 L23: 0.3558 REMARK 3 S TENSOR REMARK 3 S11: -0.0250 S12: -0.5301 S13: 0.4594 REMARK 3 S21: 0.3134 S22: 0.2663 S23: -0.5382 REMARK 3 S31: -0.1922 S32: 0.5578 S33: -0.1279 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: (CHAIN A AND RESID 307:320) REMARK 3 ORIGIN FOR THE GROUP (A): 86.4650 35.6705 48.7129 REMARK 3 T TENSOR REMARK 3 T11: 0.2156 T22: 0.1971 REMARK 3 T33: 0.2586 T12: -0.0818 REMARK 3 T13: -0.0492 T23: 0.0504 REMARK 3 L TENSOR REMARK 3 L11: 3.6848 L22: 5.2202 REMARK 3 L33: 5.5514 L12: -1.1903 REMARK 3 L13: -1.7521 L23: 1.1263 REMARK 3 S TENSOR REMARK 3 S11: -0.0043 S12: 0.1575 S13: 0.3371 REMARK 3 S21: -0.1565 S22: -0.1464 S23: -0.1874 REMARK 3 S31: -0.6883 S32: 0.2408 S33: 0.1862 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: (CHAIN A AND RESID 321:335) REMARK 3 ORIGIN FOR THE GROUP (A): 84.6540 25.5793 59.3780 REMARK 3 T TENSOR REMARK 3 T11: 0.2454 T22: 0.2160 REMARK 3 T33: 0.1981 T12: -0.0182 REMARK 3 T13: -0.0411 T23: 0.0240 REMARK 3 L TENSOR REMARK 3 L11: 2.3243 L22: 3.3471 REMARK 3 L33: 3.1600 L12: -0.5495 REMARK 3 L13: -0.5531 L23: 0.7254 REMARK 3 S TENSOR REMARK 3 S11: -0.2650 S12: 0.0240 S13: -0.3492 REMARK 3 S21: 0.5411 S22: -0.3110 S23: 0.0038 REMARK 3 S31: -0.3367 S32: -0.0136 S33: 0.6041 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: (CHAIN A AND RESID 336:350) REMARK 3 ORIGIN FOR THE GROUP (A): 75.2295 32.4505 55.8347 REMARK 3 T TENSOR REMARK 3 T11: 0.1781 T22: 0.3295 REMARK 3 T33: 0.2688 T12: -0.0740 REMARK 3 T13: -0.0511 T23: -0.0201 REMARK 3 L TENSOR REMARK 3 L11: 2.6392 L22: 2.5041 REMARK 3 L33: 1.9579 L12: -0.5041 REMARK 3 L13: -0.6579 L23: -0.7840 REMARK 3 S TENSOR REMARK 3 S11: -0.0257 S12: 0.2511 S13: -0.1167 REMARK 3 S21: 0.0515 S22: -0.1001 S23: 0.1370 REMARK 3 S31: 0.4472 S32: -1.2018 S33: 0.2325 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: (CHAIN A AND RESID 351:361) REMARK 3 ORIGIN FOR THE GROUP (A): 76.0451 26.6034 59.0726 REMARK 3 T TENSOR REMARK 3 T11: 0.2580 T22: 0.2206 REMARK 3 T33: 0.3229 T12: -0.0371 REMARK 3 T13: 0.0274 T23: -0.0101 REMARK 3 L TENSOR REMARK 3 L11: 6.6308 L22: 6.5416 REMARK 3 L33: 7.0400 L12: -3.1133 REMARK 3 L13: 4.4362 L23: -3.4141 REMARK 3 S TENSOR REMARK 3 S11: 0.1414 S12: -0.8331 S13: -0.2829 REMARK 3 S21: 0.3376 S22: 0.2203 S23: 1.2544 REMARK 3 S31: -0.1020 S32: -0.9968 S33: -0.4171 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: (CHAIN A AND RESID 362:371) REMARK 3 ORIGIN FOR THE GROUP (A): 82.6554 24.8145 48.4456 REMARK 3 T TENSOR REMARK 3 T11: 0.2203 T22: 0.2558 REMARK 3 T33: 0.1940 T12: -0.0443 REMARK 3 T13: -0.0137 T23: 0.0009 REMARK 3 L TENSOR REMARK 3 L11: 2.5467 L22: 2.5971 REMARK 3 L33: 2.2782 L12: -1.1787 REMARK 3 L13: 0.5900 L23: -0.0111 REMARK 3 S TENSOR REMARK 3 S11: 0.0335 S12: 0.2763 S13: -0.0009 REMARK 3 S21: -0.2931 S22: -0.1124 S23: 0.2273 REMARK 3 S31: 0.2250 S32: 0.2184 S33: 0.1032 REMARK 3 TLS GROUP : 13 REMARK 3 SELECTION: (CHAIN A AND RESID 372:381) REMARK 3 ORIGIN FOR THE GROUP (A): 80.1116 35.9491 57.3415 REMARK 3 T TENSOR REMARK 3 T11: 0.2505 T22: 0.1820 REMARK 3 T33: 0.3615 T12: -0.0154 REMARK 3 T13: -0.0081 T23: 0.0177 REMARK 3 L TENSOR REMARK 3 L11: 0.6522 L22: 2.0318 REMARK 3 L33: 7.8046 L12: -0.4565 REMARK 3 L13: -0.1458 L23: 3.4307 REMARK 3 S TENSOR REMARK 3 S11: -0.3318 S12: -0.0162 S13: 0.3932 REMARK 3 S21: 0.0909 S22: -0.2817 S23: 0.5135 REMARK 3 S31: 0.0045 S32: -0.3817 S33: 0.6009 REMARK 3 TLS GROUP : 14 REMARK 3 SELECTION: (CHAIN A AND RESID 382:392) REMARK 3 ORIGIN FOR THE GROUP (A): 90.5071 26.2311 55.3994 REMARK 3 T TENSOR REMARK 3 T11: 0.1998 T22: 0.2486 REMARK 3 T33: 0.2108 T12: -0.0074 REMARK 3 T13: -0.0054 T23: 0.0460 REMARK 3 L TENSOR REMARK 3 L11: 2.3711 L22: 3.6481 REMARK 3 L33: 2.4506 L12: -0.1902 REMARK 3 L13: -0.1055 L23: 0.5763 REMARK 3 S TENSOR REMARK 3 S11: 0.0060 S12: 0.1916 S13: 0.0291 REMARK 3 S21: -0.0133 S22: 0.0404 S23: -0.3837 REMARK 3 S31: -0.3027 S32: 0.1795 S33: 0.0065 REMARK 3 TLS GROUP : 15 REMARK 3 SELECTION: (CHAIN A AND RESID 393:407) REMARK 3 ORIGIN FOR THE GROUP (A): 102.0489 30.0658 35.5906 REMARK 3 T TENSOR REMARK 3 T11: 0.2530 T22: 0.3753 REMARK 3 T33: 0.3599 T12: 0.0951 REMARK 3 T13: 0.0525 T23: -0.0114 REMARK 3 L TENSOR REMARK 3 L11: 6.9056 L22: 3.3592 REMARK 3 L33: 7.0564 L12: -0.7182 REMARK 3 L13: -1.1140 L23: -0.3283 REMARK 3 S TENSOR REMARK 3 S11: 0.3678 S12: 0.3679 S13: 0.2588 REMARK 3 S21: -0.1065 S22: -0.0017 S23: -0.3956 REMARK 3 S31: -0.6102 S32: -0.7759 S33: -0.4143 REMARK 3 TLS GROUP : 16 REMARK 3 SELECTION: (CHAIN S AND RESID 558:574) REMARK 3 ORIGIN FOR THE GROUP (A): 97.0521 30.2100 47.0578 REMARK 3 T TENSOR REMARK 3 T11: 0.2507 T22: 0.4272 REMARK 3 T33: 0.4142 T12: -0.0630 REMARK 3 T13: -0.0440 T23: -0.0324 REMARK 3 L TENSOR REMARK 3 L11: 2.0776 L22: 4.7084 REMARK 3 L33: 2.7652 L12: 0.2423 REMARK 3 L13: -1.0719 L23: 1.1387 REMARK 3 S TENSOR REMARK 3 S11: 0.1109 S12: 0.4875 S13: -0.0239 REMARK 3 S21: -0.1765 S22: -0.2517 S23: -0.5696 REMARK 3 S31: -0.2319 S32: 0.7513 S33: 0.0172 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 6YW3 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_1292108413. 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 : 6.5 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) : 0.9762 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 : DIALS REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.22 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12861 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.279 REMARK 200 RESOLUTION RANGE LOW (A) : 55.686 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 9.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.16400 REMARK 200 FOR THE DATA SET : 9.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.28 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.40 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 9.00 REMARK 200 R MERGE FOR SHELL (I) : 1.04300 REMARK 200 R SYM FOR SHELL (I) : 1.04300 REMARK 200 FOR SHELL : 1.770 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 (%): 48.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.36 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, 2.0 MM CODD; RESERVOIR: 19-23% W/V REMARK 280 POLYETHYLENE GLYCOL 3350, 0.25 M LITHIUM SULFATE, 2 MM MNCL2; REMARK 280 SITTING DROP (2 UL), PROTEIN-TO-WELL RATIO, 1:1, PH 6.5, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 38.22150 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 40.64250 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 38.22150 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 40.64250 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4690 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11570 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -32.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, S 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 ASP S 556 REMARK 465 LEU S 557 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 THR A 185 CB OG1 CG2 REMARK 470 GLU A 217 CD OE1 OE2 REMARK 470 LYS A 234 CD CE NZ REMARK 470 LYS A 244 CG CD CE NZ REMARK 470 SER A 245 OG REMARK 470 ASP A 246 CG OD1 OD2 REMARK 470 LYS A 249 NZ REMARK 470 LYS A 255 CE NZ REMARK 470 LYS A 262 CD CE NZ REMARK 470 ASN A 284 CG OD1 ND2 REMARK 470 LYS A 291 CG CD CE NZ REMARK 470 LYS A 332 CD CE NZ REMARK 470 LYS A 337 CD CE NZ REMARK 470 GLU A 348 CD OE1 OE2 REMARK 470 LYS A 350 CD CE NZ REMARK 470 GLN A 352 CG CD OE1 NE2 REMARK 470 GLU A 407 CG CD OE1 OE2 REMARK 470 GLU S 560 CG CD OE1 OE2 REMARK 470 MET S 561 CG SD CE 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 -62.07 -131.53 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 86.3 REMARK 620 3 HIS A 374 NE2 90.7 89.3 REMARK 620 4 OGA A 502 O1 99.1 98.2 168.0 REMARK 620 5 OGA A 502 O2' 103.0 170.6 89.5 81.6 REMARK 620 6 HOH A 612 O 171.8 85.7 87.1 84.1 84.9 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 GOL 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 DBREF 6YW3 A 181 407 UNP Q9GZT9 EGLN1_HUMAN 181 407 DBREF 6YW3 B 0 13 PDB 6YW3 6YW3 0 13 DBREF 6YW3 S 556 574 UNP Q16665 HIF1A_HUMAN 556 574 SEQADV 6YW3 GLY A 175 UNP Q9GZT9 EXPRESSION TAG SEQADV 6YW3 SER A 176 UNP Q9GZT9 EXPRESSION TAG SEQADV 6YW3 HIS A 177 UNP Q9GZT9 EXPRESSION TAG SEQADV 6YW3 MET A 178 UNP Q9GZT9 EXPRESSION TAG SEQADV 6YW3 ALA A 179 UNP Q9GZT9 EXPRESSION TAG SEQADV 6YW3 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 SEQRES 1 S 19 ASP LEU ASP LEU GLU MET LEU ALA PRO TYR ILE PRO MET SEQRES 2 S 19 ASP ASP ASP PHE GLN LEU HET 48V B 0 17 HET DTY B 1 19 HET MN A 501 1 HET OGA A 502 13 HET GOL A 503 14 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 GOL GLYCEROL HETNAM SO4 SULFATE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 48V C5 H10 N2 O3 S FORMUL 2 DTY C9 H11 N O3 FORMUL 4 MN MN 2+ FORMUL 5 OGA C4 H5 N O5 FORMUL 6 GOL C3 H8 O3 FORMUL 7 SO4 O4 S 2- FORMUL 8 HOH *116(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 SER A 247 ILE A 251 5 5 HELIX 5 AA5 CYS A 266 CYS A 283 1 18 HELIX 6 AA6 ASP A 335 GLY A 340 1 6 HELIX 7 AA7 ALA A 393 LYS A 400 1 8 HELIX 8 AA8 LEU S 559 ALA S 563 5 5 SHEET 1 AA1 8 THR A 236 ASP A 237 0 SHEET 2 AA1 8 LYS A 255 ILE A 259 -1 O ILE A 256 N THR A 236 SHEET 3 AA1 8 ALA A 298 PRO A 304 -1 O VAL A 300 N THR A 257 SHEET 4 AA1 8 THR A 382 ASP A 392 -1 O THR A 387 N MET A 299 SHEET 5 AA1 8 ARG A 322 TYR A 329 -1 N CYS A 326 O VAL A 388 SHEET 6 AA1 8 LEU A 363 TRP A 367 -1 O PHE A 366 N THR A 325 SHEET 7 AA1 8 ILE A 207 ASP A 211 -1 N VAL A 210 O LEU A 363 SHEET 8 AA1 8 VAL B 9 SER B 11 1 O LEU B 10 N ASP A 211 SHEET 1 AA2 6 THR A 236 ASP A 237 0 SHEET 2 AA2 6 LYS A 255 ILE A 259 -1 O ILE A 256 N THR A 236 SHEET 3 AA2 6 ALA A 298 PRO A 304 -1 O VAL A 300 N THR A 257 SHEET 4 AA2 6 THR A 382 ASP A 392 -1 O THR A 387 N MET A 299 SHEET 5 AA2 6 ILE A 292 ARG A 295 -1 N GLY A 294 O PHE A 391 SHEET 6 AA2 6 PHE S 572 GLN S 573 -1 O PHE S 572 N ARG A 295 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 ALA A 354 N ILE A 345 LINK C09 48V B 0 N DTY B 1 1555 1555 1.43 LINK N01 48V B 0 C THR B 13 1555 1555 1.33 LINK C DTY B 1 N VAL B 2 1555 1555 1.32 LINK NE2 HIS A 313 MN MN A 501 1555 1555 2.17 LINK OD1 ASP A 315 MN MN A 501 1555 1555 2.18 LINK NE2 HIS A 374 MN MN A 501 1555 1555 2.12 LINK MN MN A 501 O1 OGA A 502 1555 1555 2.21 LINK MN MN A 501 O2' OGA A 502 1555 1555 2.13 LINK MN MN A 501 O HOH A 612 1555 1555 1.98 SITE 1 AC1 5 HIS A 313 ASP A 315 HIS A 374 OGA A 502 SITE 2 AC1 5 HOH A 612 SITE 1 AC2 13 MET A 299 HIS A 313 ASP A 315 TYR A 329 SITE 2 AC2 13 HIS A 374 VAL A 376 ARG A 383 MN A 501 SITE 3 AC2 13 HOH A 602 HOH A 612 HOH A 614 HOH A 630 SITE 4 AC2 13 PRO S 564 SITE 1 AC3 6 ASP A 250 ILE A 251 THR A 308 GLY A 309 SITE 2 AC3 6 VAL A 311 ARG A 344 SITE 1 AC4 5 GLN A 220 ASP A 224 SER A 289 ASP A 392 SITE 2 AC4 5 ASP A 394 CRYST1 76.443 81.285 43.219 90.00 90.00 90.00 P 21 21 2 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 0.013082 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012302 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023138 0.00000