HEADER OXIDOREDUCTASE 28-APR-20 6YVW TITLE HIF PROLYL HYDROXYLASE 2 (PHD2/ EGLN1) IN COMPLEX WITH MONOCYCLIC BB- TITLE 2 328 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,B.BANERJI,C.J.SCHOFIELD REVDAT 2 24-JAN-24 6YVW 1 REMARK REVDAT 1 30-DEC-20 6YVW 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. 1.97 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) : 1.97 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 18.45 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 19658 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.188 REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.208 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.090 REMARK 3 FREE R VALUE TEST SET COUNT : 1001 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 18.4480 - 3.7594 1.00 2766 141 0.1431 0.1532 REMARK 3 2 3.7594 - 2.9881 1.00 2658 159 0.1632 0.1935 REMARK 3 3 2.9881 - 2.6115 1.00 2674 139 0.2052 0.2477 REMARK 3 4 2.6115 - 2.3733 0.98 2631 129 0.2697 0.3062 REMARK 3 5 2.3733 - 2.2035 1.00 2640 141 0.2557 0.2700 REMARK 3 6 2.2035 - 2.0738 1.00 2644 154 0.2777 0.3191 REMARK 3 7 2.0738 - 1.9700 1.00 2644 138 0.3063 0.3073 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 : 50.80 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.680 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 36.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 59.11 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 : 0.017 1865 REMARK 3 ANGLE : 1.439 2534 REMARK 3 CHIRALITY : 0.074 266 REMARK 3 PLANARITY : 0.011 337 REMARK 3 DIHEDRAL : 16.605 1103 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): -37.3860 -2.5785 1.2381 REMARK 3 T TENSOR REMARK 3 T11: 0.4995 T22: 0.3660 REMARK 3 T33: 0.7961 T12: 0.0403 REMARK 3 T13: 0.0525 T23: -0.1597 REMARK 3 L TENSOR REMARK 3 L11: 0.2909 L22: 0.7694 REMARK 3 L33: 0.3020 L12: 0.3309 REMARK 3 L13: -0.1818 L23: -0.5015 REMARK 3 S TENSOR REMARK 3 S11: -0.0796 S12: -0.2506 S13: 0.9236 REMARK 3 S21: 0.2544 S22: 0.2378 S23: 0.3443 REMARK 3 S31: -0.1658 S32: 0.0186 S33: 0.1302 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESID 205:215) REMARK 3 ORIGIN FOR THE GROUP (A): -31.6048 -9.6675 0.0899 REMARK 3 T TENSOR REMARK 3 T11: 0.4217 T22: 0.4361 REMARK 3 T33: 0.6666 T12: -0.1918 REMARK 3 T13: 0.0621 T23: -0.2442 REMARK 3 L TENSOR REMARK 3 L11: 0.5991 L22: 0.4548 REMARK 3 L33: 0.8399 L12: -0.0987 REMARK 3 L13: -0.7889 L23: 0.0343 REMARK 3 S TENSOR REMARK 3 S11: 0.5442 S12: -0.2842 S13: 1.4922 REMARK 3 S21: -0.0467 S22: 0.2948 S23: -0.2335 REMARK 3 S31: -1.1349 S32: 0.2293 S33: 0.1446 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN A AND RESID 216:232) REMARK 3 ORIGIN FOR THE GROUP (A): -25.0419 -24.5049 11.6828 REMARK 3 T TENSOR REMARK 3 T11: 0.4087 T22: 0.8284 REMARK 3 T33: 0.4176 T12: 0.0205 REMARK 3 T13: -0.1053 T23: -0.1559 REMARK 3 L TENSOR REMARK 3 L11: 0.6352 L22: 0.0691 REMARK 3 L33: 0.4311 L12: 0.2250 REMARK 3 L13: 0.0861 L23: -0.1128 REMARK 3 S TENSOR REMARK 3 S11: 0.1291 S12: -1.5118 S13: -0.3443 REMARK 3 S21: 0.4141 S22: -0.2981 S23: -0.6207 REMARK 3 S31: 0.0775 S32: 0.4828 S33: -0.0423 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN A AND RESID 233:266) REMARK 3 ORIGIN FOR THE GROUP (A): -34.0174 -36.2656 1.8562 REMARK 3 T TENSOR REMARK 3 T11: 0.4245 T22: 0.4938 REMARK 3 T33: 0.4819 T12: -0.0200 REMARK 3 T13: 0.0185 T23: 0.0238 REMARK 3 L TENSOR REMARK 3 L11: 1.9515 L22: 0.7387 REMARK 3 L33: 1.4350 L12: 0.2162 REMARK 3 L13: -0.3330 L23: -0.7612 REMARK 3 S TENSOR REMARK 3 S11: -0.0966 S12: -0.3194 S13: -0.6893 REMARK 3 S21: -0.1078 S22: 0.0813 S23: -0.2610 REMARK 3 S31: 0.2512 S32: -0.0418 S33: 0.1165 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN A AND RESID 267:283) REMARK 3 ORIGIN FOR THE GROUP (A): -38.1911 -13.7669 11.7279 REMARK 3 T TENSOR REMARK 3 T11: 0.4558 T22: 0.5905 REMARK 3 T33: 0.4128 T12: 0.0064 REMARK 3 T13: 0.0237 T23: -0.2676 REMARK 3 L TENSOR REMARK 3 L11: 0.6413 L22: 0.3106 REMARK 3 L33: 0.3508 L12: 0.4669 REMARK 3 L13: -0.3740 L23: -0.2282 REMARK 3 S TENSOR REMARK 3 S11: -0.0868 S12: -1.3446 S13: 0.9521 REMARK 3 S21: 0.3310 S22: 0.1773 S23: 0.0348 REMARK 3 S31: -0.2797 S32: 0.0811 S33: 0.0925 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: (CHAIN A AND RESID 284:293) REMARK 3 ORIGIN FOR THE GROUP (A): -49.8771 -8.1231 1.8610 REMARK 3 T TENSOR REMARK 3 T11: 0.2081 T22: 0.3743 REMARK 3 T33: 0.8675 T12: 0.0304 REMARK 3 T13: 0.0471 T23: -0.0495 REMARK 3 L TENSOR REMARK 3 L11: 0.2544 L22: 2.3288 REMARK 3 L33: 4.9159 L12: 0.7517 REMARK 3 L13: -0.8555 L23: -2.7158 REMARK 3 S TENSOR REMARK 3 S11: -0.4302 S12: -0.1440 S13: 1.4729 REMARK 3 S21: -0.2194 S22: 0.8464 S23: 0.3033 REMARK 3 S31: 0.5226 S32: -0.9942 S33: 0.1046 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: (CHAIN A AND RESID 294:306) REMARK 3 ORIGIN FOR THE GROUP (A): -35.4580 -26.9546 2.4820 REMARK 3 T TENSOR REMARK 3 T11: 0.2909 T22: 0.4078 REMARK 3 T33: 0.3181 T12: 0.0296 REMARK 3 T13: -0.0076 T23: -0.0323 REMARK 3 L TENSOR REMARK 3 L11: 0.3533 L22: 0.7211 REMARK 3 L33: 0.2565 L12: 0.4693 REMARK 3 L13: -0.3678 L23: -0.5937 REMARK 3 S TENSOR REMARK 3 S11: 0.2896 S12: -0.1204 S13: -0.1561 REMARK 3 S21: -0.0801 S22: -0.1393 S23: -0.1066 REMARK 3 S31: -0.1466 S32: -0.0144 S33: -0.0005 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: (CHAIN A AND RESID 307:320) REMARK 3 ORIGIN FOR THE GROUP (A): -41.7501 -25.5337 -8.8594 REMARK 3 T TENSOR REMARK 3 T11: 0.3412 T22: 0.4570 REMARK 3 T33: 0.3608 T12: 0.0101 REMARK 3 T13: -0.0551 T23: -0.0960 REMARK 3 L TENSOR REMARK 3 L11: 0.3257 L22: 0.8559 REMARK 3 L33: 0.2479 L12: 0.5660 REMARK 3 L13: 0.1802 L23: 0.4442 REMARK 3 S TENSOR REMARK 3 S11: -0.1377 S12: 0.4644 S13: -0.9162 REMARK 3 S21: -0.2548 S22: -0.0751 S23: 0.6850 REMARK 3 S31: 0.0326 S32: 0.0251 S33: -0.0065 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: (CHAIN A AND RESID 321:335) REMARK 3 ORIGIN FOR THE GROUP (A): -31.4278 -18.9526 -0.0463 REMARK 3 T TENSOR REMARK 3 T11: 0.2690 T22: 0.4007 REMARK 3 T33: 0.3759 T12: -0.0413 REMARK 3 T13: 0.0209 T23: -0.1741 REMARK 3 L TENSOR REMARK 3 L11: 0.1812 L22: 1.3099 REMARK 3 L33: 1.0209 L12: 0.3533 REMARK 3 L13: -0.4330 L23: -0.3609 REMARK 3 S TENSOR REMARK 3 S11: -0.0083 S12: 0.1307 S13: 0.3925 REMARK 3 S21: -0.0453 S22: 0.1387 S23: -0.1760 REMARK 3 S31: -0.1596 S32: 0.3064 S33: 0.2359 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: (CHAIN A AND RESID 336:350) REMARK 3 ORIGIN FOR THE GROUP (A): -31.1646 -18.6787 -12.7249 REMARK 3 T TENSOR REMARK 3 T11: 0.3374 T22: 0.5763 REMARK 3 T33: 0.3403 T12: 0.0681 REMARK 3 T13: 0.0736 T23: 0.0638 REMARK 3 L TENSOR REMARK 3 L11: 0.3534 L22: 0.8256 REMARK 3 L33: 0.3826 L12: 0.5322 REMARK 3 L13: -0.4736 L23: -0.5694 REMARK 3 S TENSOR REMARK 3 S11: 0.4219 S12: 1.3397 S13: 0.7698 REMARK 3 S21: -0.6038 S22: -0.2705 S23: -0.3878 REMARK 3 S31: -0.1616 S32: 0.2989 S33: 0.2076 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: (CHAIN A AND RESID 351:361) REMARK 3 ORIGIN FOR THE GROUP (A): -27.8310 -15.6188 -7.9524 REMARK 3 T TENSOR REMARK 3 T11: 0.4043 T22: 0.5214 REMARK 3 T33: 0.4230 T12: -0.0102 REMARK 3 T13: 0.0732 T23: 0.0204 REMARK 3 L TENSOR REMARK 3 L11: 0.5613 L22: 0.2290 REMARK 3 L33: 0.3820 L12: -0.4267 REMARK 3 L13: -0.4876 L23: 0.3967 REMARK 3 S TENSOR REMARK 3 S11: 0.1804 S12: 0.3421 S13: 0.6808 REMARK 3 S21: -0.2207 S22: -0.2601 S23: -0.6505 REMARK 3 S31: -0.3190 S32: 0.2647 S33: -0.0023 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: (CHAIN A AND RESID 362:371) REMARK 3 ORIGIN FOR THE GROUP (A): -40.3882 -14.5869 -5.3252 REMARK 3 T TENSOR REMARK 3 T11: 0.2992 T22: 0.3192 REMARK 3 T33: 0.3940 T12: -0.0182 REMARK 3 T13: 0.0054 T23: 0.0052 REMARK 3 L TENSOR REMARK 3 L11: 0.6164 L22: 0.2538 REMARK 3 L33: 0.6729 L12: -0.4052 REMARK 3 L13: -0.6863 L23: 0.2844 REMARK 3 S TENSOR REMARK 3 S11: 0.0001 S12: -0.1563 S13: 0.4593 REMARK 3 S21: -0.1553 S22: 0.1067 S23: 0.1003 REMARK 3 S31: -0.2681 S32: 0.0720 S33: 0.0000 REMARK 3 TLS GROUP : 13 REMARK 3 SELECTION: (CHAIN A AND RESID 372:381) REMARK 3 ORIGIN FOR THE GROUP (A): -30.9799 -24.4251 -10.4195 REMARK 3 T TENSOR REMARK 3 T11: 0.2983 T22: 0.4428 REMARK 3 T33: 0.3371 T12: 0.0116 REMARK 3 T13: 0.0769 T23: -0.0846 REMARK 3 L TENSOR REMARK 3 L11: 0.2970 L22: 0.4238 REMARK 3 L33: 0.1325 L12: 0.3485 REMARK 3 L13: -0.2310 L23: -0.1869 REMARK 3 S TENSOR REMARK 3 S11: -0.0352 S12: 0.0280 S13: 0.4965 REMARK 3 S21: -0.7489 S22: 0.3817 S23: -0.4958 REMARK 3 S31: 0.0487 S32: 0.0943 S33: 0.0213 REMARK 3 TLS GROUP : 14 REMARK 3 SELECTION: (CHAIN A AND RESID 382:392) REMARK 3 ORIGIN FOR THE GROUP (A): -37.9854 -21.3895 2.2183 REMARK 3 T TENSOR REMARK 3 T11: 0.2970 T22: 0.3738 REMARK 3 T33: 0.2992 T12: 0.0002 REMARK 3 T13: 0.0054 T23: -0.0831 REMARK 3 L TENSOR REMARK 3 L11: 0.3868 L22: 1.3955 REMARK 3 L33: 0.3580 L12: 0.6403 REMARK 3 L13: -0.4336 L23: -0.3776 REMARK 3 S TENSOR REMARK 3 S11: 0.1582 S12: -0.3166 S13: 0.5151 REMARK 3 S21: -0.1066 S22: -0.0531 S23: 0.0429 REMARK 3 S31: -0.1268 S32: 0.2076 S33: -0.0007 REMARK 3 TLS GROUP : 15 REMARK 3 SELECTION: (CHAIN A AND RESID 393:403) REMARK 3 ORIGIN FOR THE GROUP (A): -58.4260 -20.7693 -0.4763 REMARK 3 T TENSOR REMARK 3 T11: 0.3872 T22: 0.3929 REMARK 3 T33: 0.5689 T12: 0.0240 REMARK 3 T13: 0.0261 T23: -0.0038 REMARK 3 L TENSOR REMARK 3 L11: 0.1415 L22: 0.3018 REMARK 3 L33: 0.2018 L12: 0.1743 REMARK 3 L13: -0.1105 L23: -0.2844 REMARK 3 S TENSOR REMARK 3 S11: 0.2611 S12: 0.3178 S13: -0.5990 REMARK 3 S21: -0.2605 S22: -0.1567 S23: -0.1789 REMARK 3 S31: 0.6097 S32: -0.0208 S33: -0.0003 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 6YVW 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_1292108403. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-JAN-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU FR-E SUPERBRIGHT REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : CONFOCAL REMARK 200 OPTICS : VARIMAX HF REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19800 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.970 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 (%) : 99.8 REMARK 200 DATA REDUNDANCY : 7.800 REMARK 200 R MERGE (I) : 0.09200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.7700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.97 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : 7.20 REMARK 200 R MERGE FOR SHELL (I) : 0.91500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.380 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 (%): 56.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.79 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SAMPLE: (20 MG/ML PHD2 + 1 MM FESO4 + 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 FESO4; HANGING DROP (2 UL), REMARK 280 PROTEIN-TO-WELL RATIO, 1:1, 293K, VAPOR DIFFUSION, HANGING 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 19.89550 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 19.89550 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 19.89550 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: 300 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11490 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -15.0 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 PRO A 187 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 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 SER A 248 OG REMARK 470 LYS A 249 CG CD CE NZ REMARK 470 ASN A 284 CG OD1 ND2 REMARK 470 LYS A 291 CD CE NZ REMARK 470 LYS A 332 NZ REMARK 470 LYS A 337 CG CD CE NZ REMARK 470 LYS A 350 CE NZ REMARK 470 TYR A 403 OH REMARK 470 GLU A 413 CG CD OE1 OE2 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 H ALA A 336 O HOH A 601 1.60 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 -60.24 -127.96 REMARK 500 LYS A 297 -178.02 -65.58 REMARK 500 PHE A 346 76.39 -116.81 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 FE A 501 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 313 NE2 REMARK 620 2 ASP A 315 OD1 93.5 REMARK 620 3 HIS A 374 NE2 87.4 83.4 REMARK 620 4 PW5 A 502 OAD 91.1 174.2 93.2 REMARK 620 5 PW5 A 502 NAJ 86.9 100.9 173.1 82.9 REMARK 620 6 HOH A 636 O 174.8 87.1 97.7 88.7 87.9 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 FE A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PW5 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 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: 5A3U RELATED DB: PDB DBREF 6YVW A 181 426 UNP Q9GZT9 EGLN1_HUMAN 181 426 SEQADV 6YVW GLY A 175 UNP Q9GZT9 EXPRESSION TAG SEQADV 6YVW SER A 176 UNP Q9GZT9 EXPRESSION TAG SEQADV 6YVW HIS A 177 UNP Q9GZT9 EXPRESSION TAG SEQADV 6YVW MET A 178 UNP Q9GZT9 EXPRESSION TAG SEQADV 6YVW ALA A 179 UNP Q9GZT9 EXPRESSION TAG SEQADV 6YVW 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 FE A 501 1 HET PW5 A 502 29 HET GOL A 503 14 HETNAM FE FE (III) ION HETNAM PW5 4-[(5-BROMANYL-4,6-DIMETHYL-PYRIDIN-2-YL)AMINO]-4- HETNAM 2 PW5 OXIDANYLIDENE-BUTANOIC ACID HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 FE FE 3+ FORMUL 3 PW5 C11 H13 BR N2 O3 FORMUL 4 GOL C3 H8 O3 FORMUL 5 HOH *122(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 HIS A 282 1 17 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 LYS A 255 O CYS A 302 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 TYR A 310 HIS A 313 0 SHEET 2 AA4 4 HIS A 374 VAL A 376 -1 O VAL A 376 N TYR A 310 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 LINK NE2 HIS A 313 FE FE A 501 1555 1555 2.19 LINK OD1 ASP A 315 FE FE A 501 1555 1555 2.19 LINK NE2 HIS A 374 FE FE A 501 1555 1555 2.18 LINK FE FE A 501 OAD PW5 A 502 1555 1555 2.03 LINK FE FE A 501 NAJ PW5 A 502 1555 1555 2.34 LINK FE FE A 501 O HOH A 636 1555 1555 2.13 SITE 1 AC1 5 HIS A 313 ASP A 315 HIS A 374 PW5 A 502 SITE 2 AC1 5 HOH A 636 SITE 1 AC2 18 MET A 299 TYR A 310 HIS A 313 ASP A 315 SITE 2 AC2 18 ILE A 327 TYR A 329 LEU A 343 HIS A 374 SITE 3 AC2 18 VAL A 376 ARG A 383 ARG A 398 VAL A 401 SITE 4 AC2 18 LYS A 402 FE A 501 HOH A 621 HOH A 636 SITE 5 AC2 18 HOH A 653 HOH A 669 SITE 1 AC3 3 LYS A 216 GLU A 217 HOH A 612 CRYST1 110.175 110.175 39.791 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 0.009076 0.005240 0.000000 0.00000 SCALE2 0.000000 0.010481 0.000000 0.00000 SCALE3 0.000000 0.000000 0.025131 0.00000