HEADER OXIDOREDUCTASE 29-APR-20 6YVZ TITLE HIF PROLYL HYDROXYLASE 2 (PHD2/ EGLN1) IN COMPLEX WITH BICYCLIC JLS- TITLE 2 367 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 181-426) 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(+) 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,J.L.SORENSEN,C.J.SCHOFIELD REVDAT 2 24-JAN-24 6YVZ 1 REMARK REVDAT 1 30-DEC-20 6YVZ 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,J.I.CANDELA-LENA,M.C.CHAN,D.J.GREENALD,K.K.YEOH, REMARK 1 AUTH 2 Y.M.TIAN,M.A.MCDONOUGH,A.TUMBER,N.R.ROSE,A.CONEJO-GARCIA, REMARK 1 AUTH 3 M.DEMETRIADES,S.MATHAVAN,A.KAWAMURA,M.K.LEE,F.VAN EEDEN, REMARK 1 AUTH 4 C.W.PUGH,P.J.RATCLIFFE,C.J.SCHOFIELD REMARK 1 TITL SELECTIVE SMALL MOLECULE PROBES FOR THE HYPOXIA INDUCIBLE REMARK 1 TITL 2 FACTOR (HIF) PROLYL HYDROXYLASES. REMARK 1 REF ACS CHEM. BIOL. V. 8 1488 2013 REMARK 1 REFN ESSN 1554-8937 REMARK 1 DOI 10.1021/CB400088Q REMARK 2 REMARK 2 RESOLUTION. 1.91 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) : 1.91 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.15 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 21221 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.168 REMARK 3 R VALUE (WORKING SET) : 0.167 REMARK 3 FREE R VALUE : 0.204 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 1064 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 36.1500 - 3.8189 1.00 2610 135 0.1492 0.2023 REMARK 3 2 3.8189 - 3.0316 1.00 2531 132 0.1541 0.1897 REMARK 3 3 3.0316 - 2.6486 1.00 2535 113 0.1764 0.1938 REMARK 3 4 2.6486 - 2.4064 1.00 2530 123 0.1860 0.2018 REMARK 3 5 2.4064 - 2.2340 1.00 2498 129 0.1711 0.1890 REMARK 3 6 2.2340 - 2.1023 1.00 2491 141 0.1865 0.2114 REMARK 3 7 2.1023 - 1.9970 1.00 2490 141 0.2186 0.2537 REMARK 3 8 1.9970 - 1.9101 1.00 2472 150 0.2659 0.3122 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 : 0.46 REMARK 3 B_SOL : 65.40 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.170 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 37.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 57.76 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 : 0.014 1809 REMARK 3 ANGLE : 1.173 2453 REMARK 3 CHIRALITY : 0.075 260 REMARK 3 PLANARITY : 0.009 320 REMARK 3 DIHEDRAL : 15.513 1062 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): 37.3907 2.6151 3.8243 REMARK 3 T TENSOR REMARK 3 T11: 0.5392 T22: 0.3799 REMARK 3 T33: 0.4458 T12: 0.0470 REMARK 3 T13: 0.0051 T23: 0.1088 REMARK 3 L TENSOR REMARK 3 L11: 0.5287 L22: 0.4846 REMARK 3 L33: 0.0798 L12: 0.5430 REMARK 3 L13: 0.0143 L23: 0.0715 REMARK 3 S TENSOR REMARK 3 S11: -0.1293 S12: 0.1772 S13: -0.8306 REMARK 3 S21: -0.0423 S22: -0.0336 S23: -0.0560 REMARK 3 S31: 0.6870 S32: -0.2161 S33: 0.0256 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESID 205:215) REMARK 3 ORIGIN FOR THE GROUP (A): 31.9991 9.4452 2.3098 REMARK 3 T TENSOR REMARK 3 T11: 0.4294 T22: 0.3451 REMARK 3 T33: 0.3521 T12: -0.1199 REMARK 3 T13: 0.0152 T23: 0.0769 REMARK 3 L TENSOR REMARK 3 L11: 0.4306 L22: 0.1830 REMARK 3 L33: 0.3184 L12: -0.1140 REMARK 3 L13: -0.0962 L23: -0.1655 REMARK 3 S TENSOR REMARK 3 S11: -0.2508 S12: 0.2104 S13: -0.8901 REMARK 3 S21: 0.2982 S22: -0.1236 S23: 0.1896 REMARK 3 S31: 1.0740 S32: -0.2422 S33: 0.0095 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN A AND RESID 216:232) REMARK 3 ORIGIN FOR THE GROUP (A): 25.0584 24.7127 13.9236 REMARK 3 T TENSOR REMARK 3 T11: 0.4662 T22: 0.6251 REMARK 3 T33: 0.4572 T12: -0.0133 REMARK 3 T13: 0.1082 T23: 0.0675 REMARK 3 L TENSOR REMARK 3 L11: 0.6163 L22: 0.1713 REMARK 3 L33: 0.1975 L12: 0.3150 REMARK 3 L13: 0.1830 L23: 0.0190 REMARK 3 S TENSOR REMARK 3 S11: 0.0506 S12: -0.6790 S13: 0.5200 REMARK 3 S21: 0.4996 S22: -0.2338 S23: 0.9318 REMARK 3 S31: -0.0592 S32: -0.6968 S33: -0.0278 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN A AND RESID 233:266) REMARK 3 ORIGIN FOR THE GROUP (A): 33.9997 35.9212 4.4317 REMARK 3 T TENSOR REMARK 3 T11: 0.5328 T22: 0.4006 REMARK 3 T33: 0.4841 T12: 0.0027 REMARK 3 T13: -0.0594 T23: 0.0147 REMARK 3 L TENSOR REMARK 3 L11: 0.4341 L22: 0.7691 REMARK 3 L33: 0.4409 L12: 0.5656 REMARK 3 L13: 0.1586 L23: 0.6459 REMARK 3 S TENSOR REMARK 3 S11: -0.3060 S12: -0.1440 S13: 0.4187 REMARK 3 S21: 0.3115 S22: 0.0177 S23: 0.1986 REMARK 3 S31: -0.7347 S32: 0.0017 S33: -0.0001 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN A AND RESID 267:283) REMARK 3 ORIGIN FOR THE GROUP (A): 38.1837 13.6429 13.7211 REMARK 3 T TENSOR REMARK 3 T11: 0.5395 T22: 0.3855 REMARK 3 T33: 0.4099 T12: -0.0088 REMARK 3 T13: -0.0444 T23: 0.0920 REMARK 3 L TENSOR REMARK 3 L11: 0.2183 L22: 0.1311 REMARK 3 L33: 0.1634 L12: 0.0598 REMARK 3 L13: 0.3028 L23: 0.1767 REMARK 3 S TENSOR REMARK 3 S11: 0.0997 S12: -0.1199 S13: -0.1756 REMARK 3 S21: 0.7234 S22: -0.1887 S23: -0.5732 REMARK 3 S31: 0.2175 S32: -0.2870 S33: 0.0001 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: (CHAIN A AND RESID 284:293) REMARK 3 ORIGIN FOR THE GROUP (A): 49.8038 7.9080 4.3711 REMARK 3 T TENSOR REMARK 3 T11: 0.5497 T22: 0.6231 REMARK 3 T33: 0.7074 T12: -0.0413 REMARK 3 T13: -0.0912 T23: 0.0286 REMARK 3 L TENSOR REMARK 3 L11: 0.1167 L22: 0.1066 REMARK 3 L33: -0.0044 L12: 0.0101 REMARK 3 L13: 0.0698 L23: -0.0168 REMARK 3 S TENSOR REMARK 3 S11: -0.6169 S12: 0.9852 S13: -0.9078 REMARK 3 S21: -0.1261 S22: 1.1959 S23: 0.1759 REMARK 3 S31: 0.5310 S32: 0.6790 S33: -0.0004 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: (CHAIN A AND RESID 294:306) REMARK 3 ORIGIN FOR THE GROUP (A): 35.3911 26.8552 4.9917 REMARK 3 T TENSOR REMARK 3 T11: 0.3480 T22: 0.3667 REMARK 3 T33: 0.4029 T12: 0.0199 REMARK 3 T13: -0.0421 T23: 0.0617 REMARK 3 L TENSOR REMARK 3 L11: 0.1461 L22: 0.3436 REMARK 3 L33: 0.1696 L12: -0.0033 REMARK 3 L13: 0.0160 L23: 0.3795 REMARK 3 S TENSOR REMARK 3 S11: 0.2922 S12: -0.0117 S13: -0.0753 REMARK 3 S21: 0.0811 S22: -0.0511 S23: 0.2462 REMARK 3 S31: -0.0724 S32: -0.0555 S33: -0.0003 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: (CHAIN A AND RESID 307:320) REMARK 3 ORIGIN FOR THE GROUP (A): 41.6527 25.3398 -6.4170 REMARK 3 T TENSOR REMARK 3 T11: 0.2745 T22: 0.4061 REMARK 3 T33: 0.4180 T12: 0.0066 REMARK 3 T13: -0.0265 T23: 0.1335 REMARK 3 L TENSOR REMARK 3 L11: 0.4152 L22: 0.4603 REMARK 3 L33: 0.1318 L12: 0.1830 REMARK 3 L13: 0.1615 L23: -0.0541 REMARK 3 S TENSOR REMARK 3 S11: -0.1895 S12: 0.1609 S13: 0.8280 REMARK 3 S21: -0.0680 S22: -0.1200 S23: -0.6512 REMARK 3 S31: -0.2664 S32: 0.1550 S33: -0.0049 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: (CHAIN A AND RESID 321:335) REMARK 3 ORIGIN FOR THE GROUP (A): 31.8514 18.7421 2.5202 REMARK 3 T TENSOR REMARK 3 T11: 0.2611 T22: 0.3126 REMARK 3 T33: 0.3312 T12: -0.0216 REMARK 3 T13: 0.0148 T23: 0.0997 REMARK 3 L TENSOR REMARK 3 L11: 0.1479 L22: 1.0117 REMARK 3 L33: 0.7488 L12: 0.4029 REMARK 3 L13: -0.0695 L23: 0.0530 REMARK 3 S TENSOR REMARK 3 S11: -0.0537 S12: 0.0604 S13: -0.2245 REMARK 3 S21: 0.1336 S22: 0.0042 S23: 0.0715 REMARK 3 S31: 0.2778 S32: -0.0713 S33: -0.0001 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: (CHAIN A AND RESID 336:350) REMARK 3 ORIGIN FOR THE GROUP (A): 30.9301 18.4433 -10.1978 REMARK 3 T TENSOR REMARK 3 T11: 0.3156 T22: 0.4433 REMARK 3 T33: 0.3825 T12: 0.0004 REMARK 3 T13: -0.0213 T23: 0.0120 REMARK 3 L TENSOR REMARK 3 L11: 0.3042 L22: 0.5841 REMARK 3 L33: 0.3304 L12: 0.5012 REMARK 3 L13: 0.3388 L23: 0.5137 REMARK 3 S TENSOR REMARK 3 S11: -0.1535 S12: 0.4727 S13: -0.6226 REMARK 3 S21: -0.2133 S22: -0.0671 S23: 0.2916 REMARK 3 S31: 0.0875 S32: -0.0311 S33: -0.0003 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: (CHAIN A AND RESID 351:361) REMARK 3 ORIGIN FOR THE GROUP (A): 28.2702 15.2467 -5.4419 REMARK 3 T TENSOR REMARK 3 T11: 0.4148 T22: 0.4721 REMARK 3 T33: 0.3472 T12: -0.0393 REMARK 3 T13: 0.0027 T23: 0.0502 REMARK 3 L TENSOR REMARK 3 L11: 0.3488 L22: 0.2324 REMARK 3 L33: 0.1869 L12: 0.0511 REMARK 3 L13: 0.2876 L23: -0.0847 REMARK 3 S TENSOR REMARK 3 S11: -0.3648 S12: 0.2505 S13: -0.4865 REMARK 3 S21: -0.1025 S22: -0.1548 S23: 0.2003 REMARK 3 S31: 0.7594 S32: -0.1411 S33: 0.0008 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: (CHAIN A AND RESID 362:371) REMARK 3 ORIGIN FOR THE GROUP (A): 40.2569 14.5060 -2.7820 REMARK 3 T TENSOR REMARK 3 T11: 0.3215 T22: 0.3245 REMARK 3 T33: 0.3495 T12: -0.0259 REMARK 3 T13: 0.0195 T23: 0.0653 REMARK 3 L TENSOR REMARK 3 L11: 0.2284 L22: -0.0342 REMARK 3 L33: 0.2244 L12: 0.0060 REMARK 3 L13: 0.2325 L23: 0.0793 REMARK 3 S TENSOR REMARK 3 S11: -0.1255 S12: -0.2162 S13: -0.0105 REMARK 3 S21: -0.1359 S22: 0.0503 S23: -0.0693 REMARK 3 S31: 0.3025 S32: 0.2174 S33: 0.0003 REMARK 3 TLS GROUP : 13 REMARK 3 SELECTION: (CHAIN A AND RESID 372:381) REMARK 3 ORIGIN FOR THE GROUP (A): 30.8314 24.1817 -7.8881 REMARK 3 T TENSOR REMARK 3 T11: 0.3205 T22: 0.3753 REMARK 3 T33: 0.3518 T12: 0.0335 REMARK 3 T13: -0.0453 T23: 0.0807 REMARK 3 L TENSOR REMARK 3 L11: 0.2144 L22: 0.1801 REMARK 3 L33: 0.1230 L12: 0.2496 REMARK 3 L13: 0.1745 L23: 0.1896 REMARK 3 S TENSOR REMARK 3 S11: 0.2109 S12: -0.0283 S13: -0.2112 REMARK 3 S21: -0.5633 S22: -0.1264 S23: 0.3126 REMARK 3 S31: -0.0365 S32: -0.1211 S33: 0.0001 REMARK 3 TLS GROUP : 14 REMARK 3 SELECTION: (CHAIN A AND RESID 382:392) REMARK 3 ORIGIN FOR THE GROUP (A): 37.7167 21.4605 4.5771 REMARK 3 T TENSOR REMARK 3 T11: 0.2693 T22: 0.3468 REMARK 3 T33: 0.3200 T12: 0.0083 REMARK 3 T13: -0.0401 T23: 0.0675 REMARK 3 L TENSOR REMARK 3 L11: 0.4157 L22: 1.4283 REMARK 3 L33: 0.3916 L12: 0.9005 REMARK 3 L13: 0.3668 L23: 0.3673 REMARK 3 S TENSOR REMARK 3 S11: -0.1371 S12: -0.3706 S13: -0.3931 REMARK 3 S21: 0.1773 S22: 0.2001 S23: 0.0803 REMARK 3 S31: 0.0683 S32: -0.0878 S33: 0.0002 REMARK 3 TLS GROUP : 15 REMARK 3 SELECTION: (CHAIN A AND RESID 393:403) REMARK 3 ORIGIN FOR THE GROUP (A): 58.1253 20.8263 1.9652 REMARK 3 T TENSOR REMARK 3 T11: 0.3248 T22: 0.4606 REMARK 3 T33: 0.5925 T12: 0.0519 REMARK 3 T13: -0.0831 T23: 0.0753 REMARK 3 L TENSOR REMARK 3 L11: 0.0826 L22: 0.1155 REMARK 3 L33: 0.1091 L12: 0.1004 REMARK 3 L13: 0.0737 L23: 0.0750 REMARK 3 S TENSOR REMARK 3 S11: -0.1130 S12: 1.0656 S13: 0.4798 REMARK 3 S21: -0.0245 S22: 0.0412 S23: 0.0913 REMARK 3 S31: -0.0545 S32: -0.1899 S33: 0.0008 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 6YVZ 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_1292108407. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-MAY-15 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 : I02 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9800 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 : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.1 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21231 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.910 REMARK 200 RESOLUTION RANGE LOW (A) : 36.150 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 11.40 REMARK 200 R MERGE (I) : 0.09800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.91 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.96 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 12.00 REMARK 200 R MERGE FOR SHELL (I) : 1.33600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.100 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: 2G19 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.94 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.73 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SAMPLE: (~20 MG/ML-1 PHD2 + 1 MM MNCL2 REMARK 280 + 2 MM COMPOUND); RESERVOIR: 1.6-2.0 M (NH4)2SO4, 2-8% DIOXANE, REMARK 280 0.1 M MES-NA PH 6.5, AND 1 MM MNCL2; SITTING DROP (2 UL), REMARK 280 PROTEIN-TO-WELL RATIO, 1:1, 293K, VAPOR DIFFUSION, SITTING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/2 REMARK 290 6555 X-Y,X,Z+1/2 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 0.00000 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 0.00000 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 19.54000 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 19.54000 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 19.54000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 290 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11220 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -6.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 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 LYS A 186 REMARK 465 THR A 405 REMARK 465 GLY A 406 REMARK 465 GLU A 407 REMARK 465 LYS A 408 REMARK 465 GLY A 409 REMARK 465 VAL A 410 REMARK 465 ASN A 415 REMARK 465 LYS A 416 REMARK 465 PRO A 417 REMARK 465 SER A 418 REMARK 465 ASP A 419 REMARK 465 SER A 420 REMARK 465 VAL A 421 REMARK 465 GLY A 422 REMARK 465 LYS A 423 REMARK 465 ASP A 424 REMARK 465 VAL A 425 REMARK 465 PHE A 426 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 216 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 SER A 248 OG REMARK 470 LYS A 249 CG CD CE NZ REMARK 470 LYS A 332 CE NZ REMARK 470 LYS A 337 CD CE NZ REMARK 470 LYS A 350 CE NZ REMARK 470 LYS A 359 CE NZ REMARK 470 LYS A 400 CD CE NZ REMARK 470 LYS A 402 CE NZ REMARK 470 ARG A 411 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 413 CD OE1 OE2 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 GLN A 221 CD REMARK 480 GLU A 267 CD REMARK 480 ARG A 281 CD CZ REMARK 480 GLU A 348 CD 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 -58.15 -126.51 REMARK 500 PHE A 346 73.54 -118.77 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 91.0 REMARK 620 3 HIS A 374 NE2 90.7 91.8 REMARK 620 4 PW8 A 502 O18 92.4 174.6 92.3 REMARK 620 5 PW8 A 502 N17 85.3 94.4 172.7 81.8 REMARK 620 6 HOH A 617 O 174.3 87.8 94.9 88.4 89.2 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 PW8 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: 4BQW RELATED DB: PDB REMARK 900 RELATED ID: 4BQX RELATED DB: PDB REMARK 900 RELATED ID: 4BQY RELATED DB: PDB REMARK 900 RELATED ID: 6YVW RELATED DB: PDB REMARK 900 RELATED ID: 6YVX RELATED DB: PDB DBREF 6YVZ A 181 426 UNP Q9GZT9 EGLN1_HUMAN 181 426 SEQADV 6YVZ GLY A 175 UNP Q9GZT9 EXPRESSION TAG SEQADV 6YVZ SER A 176 UNP Q9GZT9 EXPRESSION TAG SEQADV 6YVZ HIS A 177 UNP Q9GZT9 EXPRESSION TAG SEQADV 6YVZ MET A 178 UNP Q9GZT9 EXPRESSION TAG SEQADV 6YVZ ALA A 179 UNP Q9GZT9 EXPRESSION TAG SEQADV 6YVZ SER A 180 UNP Q9GZT9 EXPRESSION TAG SEQRES 1 A 252 GLY SER HIS MET ALA SER PRO ASN GLY GLN THR LYS PRO SEQRES 2 A 252 LEU PRO ALA LEU LYS LEU ALA LEU GLU TYR ILE VAL PRO SEQRES 3 A 252 CYS MET ASN LYS HIS GLY ILE CYS VAL VAL ASP ASP PHE SEQRES 4 A 252 LEU GLY LYS GLU THR GLY GLN GLN ILE GLY ASP GLU VAL SEQRES 5 A 252 ARG ALA LEU HIS ASP THR GLY LYS PHE THR ASP GLY GLN SEQRES 6 A 252 LEU VAL SER GLN LYS SER ASP SER SER LYS ASP ILE ARG SEQRES 7 A 252 GLY ASP LYS ILE THR TRP ILE GLU GLY LYS GLU PRO GLY SEQRES 8 A 252 CYS GLU THR ILE GLY LEU LEU MET SER SER MET ASP ASP SEQRES 9 A 252 LEU ILE ARG HIS CYS ASN GLY LYS LEU GLY SER TYR LYS SEQRES 10 A 252 ILE ASN GLY ARG THR LYS ALA MET VAL ALA CYS TYR PRO SEQRES 11 A 252 GLY ASN GLY THR GLY TYR VAL ARG HIS VAL ASP ASN PRO SEQRES 12 A 252 ASN GLY ASP GLY ARG CYS VAL THR CYS ILE TYR TYR LEU SEQRES 13 A 252 ASN LYS ASP TRP ASP ALA LYS VAL SER GLY GLY ILE LEU SEQRES 14 A 252 ARG ILE PHE PRO GLU GLY LYS ALA GLN PHE ALA ASP ILE SEQRES 15 A 252 GLU PRO LYS PHE ASP ARG LEU LEU PHE PHE TRP SER ASP SEQRES 16 A 252 ARG ARG ASN PRO HIS GLU VAL GLN PRO ALA TYR ALA THR SEQRES 17 A 252 ARG TYR ALA ILE THR VAL TRP TYR PHE ASP ALA ASP GLU SEQRES 18 A 252 ARG ALA ARG ALA LYS VAL LYS TYR LEU THR GLY GLU LYS SEQRES 19 A 252 GLY VAL ARG VAL GLU LEU ASN LYS PRO SER ASP SER VAL SEQRES 20 A 252 GLY LYS ASP VAL PHE HET MN A 501 1 HET PW8 A 502 29 HET BCT A 503 5 HETNAM MN MANGANESE (II) ION HETNAM PW8 4-[(5-BROMANYLISOQUINOLIN-3-YL)AMINO]-4-OXIDANYLIDENE- HETNAM 2 PW8 BUTANOIC ACID HETNAM BCT BICARBONATE ION FORMUL 2 MN MN 2+ FORMUL 3 PW8 C13 H11 BR N2 O3 FORMUL 4 BCT C H O3 1- FORMUL 5 HOH *89(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 LEU A 404 1 12 SHEET 1 AA1 6 ILE A 207 VAL A 210 0 SHEET 2 AA1 6 ARG A 362 TRP A 367 -1 O LEU A 363 N VAL A 210 SHEET 3 AA1 6 ARG A 322 TYR A 329 -1 N THR A 325 O PHE A 366 SHEET 4 AA1 6 ARG A 383 ASP A 392 -1 O ILE A 386 N TYR A 328 SHEET 5 AA1 6 ALA A 298 TYR A 303 -1 N MET A 299 O THR A 387 SHEET 6 AA1 6 LYS A 255 ILE A 259 -1 N THR A 257 O VAL A 300 SHEET 1 AA2 5 ILE A 207 VAL A 210 0 SHEET 2 AA2 5 ARG A 362 TRP A 367 -1 O LEU A 363 N VAL A 210 SHEET 3 AA2 5 ARG A 322 TYR A 329 -1 N THR A 325 O PHE A 366 SHEET 4 AA2 5 ARG A 383 ASP A 392 -1 O ILE A 386 N TYR A 328 SHEET 5 AA2 5 ILE A 292 ARG A 295 -1 N GLY A 294 O PHE A 391 SHEET 1 AA3 2 LEU A 240 SER A 242 0 SHEET 2 AA3 2 ILE A 251 ARG A 252 -1 O ILE A 251 N VAL A 241 SHEET 1 AA4 4 THR A 308 HIS A 313 0 SHEET 2 AA4 4 HIS A 374 ALA A 379 -1 O HIS A 374 N HIS A 313 SHEET 3 AA4 4 LEU A 343 ILE A 345 -1 N ARG A 344 O GLU A 375 SHEET 4 AA4 4 ALA A 354 ILE A 356 -1 O ILE A 356 N LEU A 343 SSBOND 1 CYS A 201 CYS A 208 1555 1555 2.05 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 2.02 LINK MN MN A 501 O18 PW8 A 502 1555 1555 2.15 LINK MN MN A 501 N17 PW8 A 502 1555 1555 2.00 LINK MN MN A 501 O HOH A 617 1555 1555 2.25 SITE 1 AC1 5 HIS A 313 ASP A 315 HIS A 374 PW8 A 502 SITE 2 AC1 5 HOH A 617 SITE 1 AC2 16 TYR A 310 HIS A 313 ASP A 315 ILE A 327 SITE 2 AC2 16 TYR A 329 LEU A 343 HIS A 374 VAL A 376 SITE 3 AC2 16 ARG A 383 ARG A 398 VAL A 401 MN A 501 SITE 4 AC2 16 HOH A 617 HOH A 633 HOH A 641 HOH A 643 SITE 1 AC3 2 ARG A 312 PRO A 373 CRYST1 109.880 109.880 39.080 90.00 90.00 120.00 P 63 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 0.009101 0.005254 0.000000 0.00000 SCALE2 0.000000 0.010509 0.000000 0.00000 SCALE3 0.000000 0.000000 0.025589 0.00000