HEADER SIGNALING PROTEIN/ANTAGONIST 15-JUN-15 5C1M TITLE CRYSTAL STRUCTURE OF ACTIVE MU-OPIOID RECEPTOR BOUND TO THE AGONIST TITLE 2 BU72 COMPND MOL_ID: 1; COMPND 2 MOLECULE: MU-TYPE OPIOID RECEPTOR; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: MOR-1; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: NANOBODY 39; COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: OPRM1, MOR, OPRM; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: LAMA GLAMA; SOURCE 10 ORGANISM_TAXID: 9844; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS LIGANDS, MICE, AGONISTS, MORPHINANS, ACTIVATION, RECEPTORS, OPIOID, KEYWDS 2 MU, NANOBODY, SIGNALING PROTEIN-ANTAGONIST COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR W.J.HUANG,A.MANGLIK,A.J.VENKATAKRISHNAN,T.LAEREMANS,E.N.FEINBERG, AUTHOR 2 A.L.SANBORN,H.E.KATO,K.E.LIVINGSTON,T.S.THORSEN,R.KLING,S.GRANIER, AUTHOR 3 P.GMEINER,S.M.HUSBANDS,J.R.TRAYNOR,W.I.WEIS,J.STEYAERT,R.O.DROR, AUTHOR 4 B.K.KOBILKA REVDAT 8 27-SEP-23 5C1M 1 REMARK REVDAT 7 10-FEB-21 5C1M 1 COMPND REMARK HET HETNAM REVDAT 7 2 1 HETSYN FORMUL HELIX SHEET REVDAT 7 3 1 SSBOND LINK SITE CRYST1 REVDAT 7 4 1 ATOM REVDAT 6 11-DEC-19 5C1M 1 REMARK REVDAT 5 06-SEP-17 5C1M 1 JRNL REMARK REVDAT 4 02-SEP-15 5C1M 1 JRNL REVDAT 3 26-AUG-15 5C1M 1 REMARK REVDAT 2 19-AUG-15 5C1M 1 JRNL REVDAT 1 05-AUG-15 5C1M 0 JRNL AUTH W.HUANG,A.MANGLIK,A.J.VENKATAKRISHNAN,T.LAEREMANS, JRNL AUTH 2 E.N.FEINBERG,A.L.SANBORN,H.E.KATO,K.E.LIVINGSTON, JRNL AUTH 3 T.S.THORSEN,R.C.KLING,S.GRANIER,P.GMEINER,S.M.HUSBANDS, JRNL AUTH 4 J.R.TRAYNOR,W.I.WEIS,J.STEYAERT,R.O.DROR,B.K.KOBILKA JRNL TITL STRUCTURAL INSIGHTS INTO MU-OPIOID RECEPTOR ACTIVATION. JRNL REF NATURE V. 524 315 2015 JRNL REFN ESSN 1476-4687 JRNL PMID 26245379 JRNL DOI 10.1038/NATURE14886 REMARK 2 REMARK 2 RESOLUTION. 2.07 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.07 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.47 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 41704 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.200 REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2086 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 43.4700 - 5.1000 0.99 2808 148 0.2027 0.2347 REMARK 3 2 5.1000 - 4.0500 0.99 2680 141 0.1858 0.2210 REMARK 3 3 4.0500 - 3.5400 1.00 2688 142 0.1911 0.1991 REMARK 3 4 3.5400 - 3.2200 1.00 2641 139 0.1999 0.2371 REMARK 3 5 3.2200 - 2.9900 1.00 2645 139 0.1945 0.2277 REMARK 3 6 2.9900 - 2.8100 1.00 2623 138 0.1883 0.2252 REMARK 3 7 2.8100 - 2.6700 1.00 2650 140 0.1776 0.2023 REMARK 3 8 2.6700 - 2.5500 1.00 2619 138 0.1863 0.2225 REMARK 3 9 2.5500 - 2.4500 1.00 2599 136 0.1966 0.2425 REMARK 3 10 2.4500 - 2.3700 1.00 2634 139 0.2115 0.2623 REMARK 3 11 2.3700 - 2.3000 1.00 2617 138 0.2230 0.2516 REMARK 3 12 2.3000 - 2.2300 1.00 2571 135 0.2318 0.2856 REMARK 3 13 2.2300 - 2.1700 1.00 2621 138 0.2509 0.2729 REMARK 3 14 2.1700 - 2.1200 1.00 2569 135 0.2599 0.2585 REMARK 3 15 2.1200 - 2.0700 1.00 2653 140 0.2931 0.3353 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.253 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.048 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 43.71 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 58.40 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 3513 REMARK 3 ANGLE : 0.690 4790 REMARK 3 CHIRALITY : 0.047 560 REMARK 3 PLANARITY : 0.004 571 REMARK 3 DIHEDRAL : 14.260 1400 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 52 THROUGH 64 ) REMARK 3 ORIGIN FOR THE GROUP (A): -1.5891 22.6057 -71.1536 REMARK 3 T TENSOR REMARK 3 T11: 1.4149 T22: 0.9370 REMARK 3 T33: 1.0244 T12: 0.1781 REMARK 3 T13: -0.2471 T23: 0.1495 REMARK 3 L TENSOR REMARK 3 L11: 0.0060 L22: 0.0117 REMARK 3 L33: -0.0034 L12: -0.0149 REMARK 3 L13: 0.0054 L23: -0.0002 REMARK 3 S TENSOR REMARK 3 S11: 0.3028 S12: 0.3913 S13: 0.4062 REMARK 3 S21: -1.5315 S22: -0.8949 S23: 0.5507 REMARK 3 S31: -0.8561 S32: 0.0878 S33: 0.5554 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 65 THROUGH 95 ) REMARK 3 ORIGIN FOR THE GROUP (A): -2.2398 30.2151 -48.4470 REMARK 3 T TENSOR REMARK 3 T11: 0.5628 T22: 0.2601 REMARK 3 T33: 0.5140 T12: -0.0099 REMARK 3 T13: -0.0596 T23: -0.0198 REMARK 3 L TENSOR REMARK 3 L11: 3.1013 L22: 3.2198 REMARK 3 L33: 8.0669 L12: 0.3273 REMARK 3 L13: 2.9077 L23: -0.5687 REMARK 3 S TENSOR REMARK 3 S11: -0.5399 S12: 0.1773 S13: 0.4895 REMARK 3 S21: -0.0861 S22: -0.0706 S23: -0.0475 REMARK 3 S31: -1.3043 S32: 0.2895 S33: 0.6762 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 96 THROUGH 180 ) REMARK 3 ORIGIN FOR THE GROUP (A): 3.0657 16.6333 -44.1704 REMARK 3 T TENSOR REMARK 3 T11: 0.3192 T22: 0.2630 REMARK 3 T33: 0.3367 T12: -0.0254 REMARK 3 T13: -0.0213 T23: -0.0156 REMARK 3 L TENSOR REMARK 3 L11: 1.3828 L22: 2.6820 REMARK 3 L33: 4.0029 L12: 0.8204 REMARK 3 L13: -0.9788 L23: -1.0480 REMARK 3 S TENSOR REMARK 3 S11: -0.0634 S12: -0.0164 S13: 0.1631 REMARK 3 S21: -0.0691 S22: 0.0875 S23: -0.1017 REMARK 3 S31: -0.4743 S32: 0.0467 S33: 0.0059 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 181 THROUGH 211 ) REMARK 3 ORIGIN FOR THE GROUP (A): 10.8718 11.2197 -49.9976 REMARK 3 T TENSOR REMARK 3 T11: 0.2869 T22: 0.3015 REMARK 3 T33: 0.4301 T12: -0.0028 REMARK 3 T13: 0.0533 T23: -0.0456 REMARK 3 L TENSOR REMARK 3 L11: 2.7531 L22: 1.8425 REMARK 3 L33: 8.9793 L12: 0.1796 REMARK 3 L13: -1.1970 L23: 0.0508 REMARK 3 S TENSOR REMARK 3 S11: 0.1032 S12: 0.0509 S13: -0.0446 REMARK 3 S21: -0.1784 S22: -0.0122 S23: -0.2427 REMARK 3 S31: -0.4123 S32: 0.1724 S33: -0.0400 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 212 THROUGH 241 ) REMARK 3 ORIGIN FOR THE GROUP (A): 4.8969 7.5274 -63.8304 REMARK 3 T TENSOR REMARK 3 T11: 0.5378 T22: 0.3389 REMARK 3 T33: 0.2828 T12: -0.0556 REMARK 3 T13: -0.0062 T23: 0.0046 REMARK 3 L TENSOR REMARK 3 L11: 3.7710 L22: 2.6801 REMARK 3 L33: 1.8496 L12: -0.1972 REMARK 3 L13: -0.3744 L23: 0.7723 REMARK 3 S TENSOR REMARK 3 S11: -0.0020 S12: 0.1045 S13: 0.0363 REMARK 3 S21: -0.1801 S22: -0.1025 S23: 0.0251 REMARK 3 S31: -1.0530 S32: 0.2528 S33: 0.0930 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 242 THROUGH 267 ) REMARK 3 ORIGIN FOR THE GROUP (A): -14.7318 3.1503 -33.5235 REMARK 3 T TENSOR REMARK 3 T11: 0.3483 T22: 0.4357 REMARK 3 T33: 0.4408 T12: 0.0253 REMARK 3 T13: 0.0048 T23: -0.0202 REMARK 3 L TENSOR REMARK 3 L11: 2.3875 L22: 4.4261 REMARK 3 L33: 7.5216 L12: 0.4843 REMARK 3 L13: 0.4549 L23: -0.1986 REMARK 3 S TENSOR REMARK 3 S11: -0.2308 S12: -0.3768 S13: -0.2054 REMARK 3 S21: 0.1917 S22: -0.0009 S23: 0.2801 REMARK 3 S31: 0.2651 S32: -0.8508 S33: 0.1903 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 268 THROUGH 311 ) REMARK 3 ORIGIN FOR THE GROUP (A): -13.3365 12.7969 -48.9402 REMARK 3 T TENSOR REMARK 3 T11: 0.2376 T22: 0.2754 REMARK 3 T33: 0.3915 T12: 0.0346 REMARK 3 T13: -0.0663 T23: -0.0207 REMARK 3 L TENSOR REMARK 3 L11: 3.1989 L22: 3.2274 REMARK 3 L33: 4.7548 L12: -0.1670 REMARK 3 L13: -0.4240 L23: 0.9065 REMARK 3 S TENSOR REMARK 3 S11: 0.0121 S12: -0.2381 S13: -0.0726 REMARK 3 S21: -0.2136 S22: -0.1219 S23: 0.2198 REMARK 3 S31: -1.1015 S32: -0.1917 S33: 0.0825 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 312 THROUGH 347 ) REMARK 3 ORIGIN FOR THE GROUP (A): -7.3435 22.0563 -46.4059 REMARK 3 T TENSOR REMARK 3 T11: 0.4761 T22: 0.2846 REMARK 3 T33: 0.4341 T12: 0.0369 REMARK 3 T13: -0.0269 T23: 0.0023 REMARK 3 L TENSOR REMARK 3 L11: 3.4697 L22: 2.6680 REMARK 3 L33: 2.0100 L12: 0.0381 REMARK 3 L13: -0.0602 L23: -1.4810 REMARK 3 S TENSOR REMARK 3 S11: 0.0284 S12: -0.1886 S13: 0.1845 REMARK 3 S21: 0.0969 S22: 0.3256 S23: 0.0630 REMARK 3 S31: -0.6201 S32: -0.0427 S33: -0.2463 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 3 THROUGH 9 ) REMARK 3 ORIGIN FOR THE GROUP (A): -12.4486 3.9078 -5.1278 REMARK 3 T TENSOR REMARK 3 T11: 0.6782 T22: 1.0219 REMARK 3 T33: 0.4988 T12: -0.0879 REMARK 3 T13: 0.1389 T23: -0.0516 REMARK 3 L TENSOR REMARK 3 L11: 4.6372 L22: 8.0480 REMARK 3 L33: 4.5779 L12: -5.7587 REMARK 3 L13: -3.1603 L23: 2.4421 REMARK 3 S TENSOR REMARK 3 S11: -0.7480 S12: -1.6370 S13: -0.8629 REMARK 3 S21: 0.8400 S22: 0.0511 S23: 0.9206 REMARK 3 S31: 0.3766 S32: -1.0408 S33: 0.6809 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 10 THROUGH 19 ) REMARK 3 ORIGIN FOR THE GROUP (A): 10.4005 2.6080 -8.6559 REMARK 3 T TENSOR REMARK 3 T11: 0.5308 T22: 1.2515 REMARK 3 T33: 0.5907 T12: 0.1796 REMARK 3 T13: -0.0319 T23: -0.0104 REMARK 3 L TENSOR REMARK 3 L11: 4.5026 L22: 5.8531 REMARK 3 L33: 1.9206 L12: 5.1320 REMARK 3 L13: -1.2400 L23: -1.3171 REMARK 3 S TENSOR REMARK 3 S11: 0.2846 S12: -0.0241 S13: -1.6935 REMARK 3 S21: -0.0163 S22: -0.1807 S23: -0.6660 REMARK 3 S31: 0.6751 S32: 1.9366 S33: -0.2132 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 20 THROUGH 30 ) REMARK 3 ORIGIN FOR THE GROUP (A): -10.2361 1.9030 -11.6962 REMARK 3 T TENSOR REMARK 3 T11: 0.4557 T22: 0.7102 REMARK 3 T33: 0.7206 T12: -0.0006 REMARK 3 T13: 0.0638 T23: 0.0848 REMARK 3 L TENSOR REMARK 3 L11: 9.8419 L22: 4.7221 REMARK 3 L33: 4.9911 L12: -0.8418 REMARK 3 L13: -2.4360 L23: 0.4217 REMARK 3 S TENSOR REMARK 3 S11: 0.5188 S12: -0.0506 S13: -0.8622 REMARK 3 S21: 0.6608 S22: -0.1890 S23: 1.2019 REMARK 3 S31: 0.2478 S32: -0.8319 S33: -0.2978 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 31 THROUGH 39 ) REMARK 3 ORIGIN FOR THE GROUP (A): -7.4457 11.4887 -10.7871 REMARK 3 T TENSOR REMARK 3 T11: 0.3459 T22: 0.6991 REMARK 3 T33: 0.2118 T12: 0.0475 REMARK 3 T13: -0.0002 T23: -0.0944 REMARK 3 L TENSOR REMARK 3 L11: 2.5958 L22: 4.2995 REMARK 3 L33: 2.3041 L12: 0.3775 REMARK 3 L13: -0.8360 L23: -0.5040 REMARK 3 S TENSOR REMARK 3 S11: 0.2115 S12: -1.6132 S13: 0.3036 REMARK 3 S21: 0.2319 S22: -0.4213 S23: 0.1600 REMARK 3 S31: -0.6267 S32: -0.9913 S33: 0.2115 REMARK 3 TLS GROUP : 13 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 40 THROUGH 51 ) REMARK 3 ORIGIN FOR THE GROUP (A): -0.9366 17.4698 -8.0685 REMARK 3 T TENSOR REMARK 3 T11: 0.7108 T22: 0.7285 REMARK 3 T33: 0.5553 T12: -0.0264 REMARK 3 T13: -0.0924 T23: -0.1922 REMARK 3 L TENSOR REMARK 3 L11: 7.9923 L22: 3.8306 REMARK 3 L33: 4.1181 L12: 1.9293 REMARK 3 L13: 5.5580 L23: 2.2469 REMARK 3 S TENSOR REMARK 3 S11: -0.4369 S12: -1.4584 S13: 1.6318 REMARK 3 S21: 0.8269 S22: -0.3606 S23: -0.0019 REMARK 3 S31: -0.4863 S32: -0.5620 S33: 0.7491 REMARK 3 TLS GROUP : 14 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 52 THROUGH 73 ) REMARK 3 ORIGIN FOR THE GROUP (A): -3.0909 11.6223 -20.5209 REMARK 3 T TENSOR REMARK 3 T11: 0.4543 T22: 0.5188 REMARK 3 T33: 0.3366 T12: 0.0161 REMARK 3 T13: 0.0409 T23: -0.0111 REMARK 3 L TENSOR REMARK 3 L11: 3.2477 L22: 3.9858 REMARK 3 L33: 5.8077 L12: -0.6185 REMARK 3 L13: 2.0907 L23: 1.3572 REMARK 3 S TENSOR REMARK 3 S11: -0.2209 S12: 0.0845 S13: 0.2728 REMARK 3 S21: -0.1136 S22: -0.1570 S23: 0.0891 REMARK 3 S31: -0.4519 S32: 0.0330 S33: 0.3518 REMARK 3 TLS GROUP : 15 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 74 THROUGH 83 ) REMARK 3 ORIGIN FOR THE GROUP (A): -7.2438 3.1689 -16.7487 REMARK 3 T TENSOR REMARK 3 T11: 0.3699 T22: 0.5660 REMARK 3 T33: 0.3249 T12: -0.0754 REMARK 3 T13: 0.0545 T23: -0.0120 REMARK 3 L TENSOR REMARK 3 L11: 4.9126 L22: 2.9980 REMARK 3 L33: 4.3866 L12: -0.3547 REMARK 3 L13: 0.7290 L23: 0.0016 REMARK 3 S TENSOR REMARK 3 S11: 0.1583 S12: -1.2029 S13: -0.1933 REMARK 3 S21: 0.0645 S22: -0.3439 S23: -0.0090 REMARK 3 S31: 0.4944 S32: -0.3991 S33: 0.1944 REMARK 3 TLS GROUP : 16 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 84 THROUGH 127 ) REMARK 3 ORIGIN FOR THE GROUP (A): -1.2932 10.2307 -7.4414 REMARK 3 T TENSOR REMARK 3 T11: 0.3739 T22: 0.7268 REMARK 3 T33: 0.3089 T12: -0.0017 REMARK 3 T13: -0.0189 T23: -0.0123 REMARK 3 L TENSOR REMARK 3 L11: 8.3032 L22: 3.2579 REMARK 3 L33: 4.5278 L12: 0.3011 REMARK 3 L13: 0.2393 L23: 0.5296 REMARK 3 S TENSOR REMARK 3 S11: -0.1699 S12: -0.1189 S13: 0.5013 REMARK 3 S21: 0.1838 S22: -0.0583 S23: -0.0232 REMARK 3 S31: -0.5458 S32: 0.1071 S33: 0.1972 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 5C1M COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-JUN-15. REMARK 100 THE DEPOSITION ID IS D_1000210873. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-NOV-14 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : 7.0-7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 23-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0332 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 41704 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.070 REMARK 200 RESOLUTION RANGE LOW (A) : 43.470 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 8.600 REMARK 200 R MERGE (I) : 0.11200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.07 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.12 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 1.53600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.700 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: 4DKL, 3P0G REMARK 200 REMARK 200 REMARK: CUBIC REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 65.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.54 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: RECONSTITUTED IN 10:1 REMARK 280 MONOOLEIN:CHOLESTEROL MIX. PRECIPITANT SOLUTION:15-25% PEG300, REMARK 280 100 MM HEPES PH 7.0-7.5, 1% 1,2,3-HEPTANETRIOL, 0.5-1.0% REMARK 280 POLYPROPYLENE GLYCOL P 400, 100-300 MM (NH4)2HPO4, PH 7.5, REMARK 280 LIPIDIC CUBIC PHASE, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X,-Y+1/2,Z REMARK 290 7555 -X+1/2,Y,-Z REMARK 290 8555 X,-Y,-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 -1.000000 0.000000 0.000000 22.21500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 104.95000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 72.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 104.95000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.21500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 72.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 22.21500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 72.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 104.95000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 72.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 22.21500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 104.95000 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: 4210 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19460 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -27.0 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 B 103 REMARK 465 GLN B 104 REMARK 465 SER B 105 REMARK 465 SER B 106 REMARK 465 SER B 107 REMARK 465 PRO B 108 REMARK 465 TYR B 109 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 269 CG CD CE NZ REMARK 470 GLU A 270 CG CD OE1 OE2 REMARK 470 ARG A 273 CG CD NE CZ NH1 NH2 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 HIS A 54 -88.98 -131.93 REMARK 500 PRO A 58 97.19 -60.26 REMARK 500 THR A 60 128.41 -37.40 REMARK 500 ARG A 179 44.86 -92.61 REMARK 500 PHE A 241 -60.00 -126.81 REMARK 500 LEU A 265 -12.61 -43.91 REMARK 500 SER A 266 -76.91 -122.79 REMARK 500 ARG B 29 16.27 57.12 REMARK 500 MET B 34 -9.39 -141.20 REMARK 500 VAL B 48 -60.89 -109.32 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 OLC A 401 REMARK 610 OLC A 402 REMARK 610 P6G A 406 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4DKL RELATED DB: PDB REMARK 900 4DKL CONTAINS THE SAME PROTEIN BOUND TO A MORPHINAN ANTAGONIST DBREF 5C1M A 52 347 UNP P42866 OPRM_MOUSE 52 347 DBREF 5C1M B 3 127 PDB 5C1M 5C1M 3 127 SEQRES 1 A 296 GLY SER HIS SER LEU YCM PRO GLN THR GLY SER PRO SER SEQRES 2 A 296 MET VAL THR ALA ILE THR ILE MET ALA LEU TYR SER ILE SEQRES 3 A 296 VAL CYS VAL VAL GLY LEU PHE GLY ASN PHE LEU VAL MET SEQRES 4 A 296 TYR VAL ILE VAL ARG TYR THR LYS MET LYS THR ALA THR SEQRES 5 A 296 ASN ILE TYR ILE PHE ASN LEU ALA LEU ALA ASP ALA LEU SEQRES 6 A 296 ALA THR SER THR LEU PRO PHE GLN SER VAL ASN TYR LEU SEQRES 7 A 296 MET GLY THR TRP PRO PHE GLY ASN ILE LEU CYS LYS ILE SEQRES 8 A 296 VAL ILE SER ILE ASP TYR TYR ASN MET PHE THR SER ILE SEQRES 9 A 296 PHE THR LEU CYS THR MET SER VAL ASP ARG TYR ILE ALA SEQRES 10 A 296 VAL CYS HIS PRO VAL LYS ALA LEU ASP PHE ARG THR PRO SEQRES 11 A 296 ARG ASN ALA LYS ILE VAL ASN VAL CYS ASN TRP ILE LEU SEQRES 12 A 296 SER SER ALA ILE GLY LEU PRO VAL MET PHE MET ALA THR SEQRES 13 A 296 THR LYS TYR ARG GLN GLY SER ILE ASP CYS THR LEU THR SEQRES 14 A 296 PHE SER HIS PRO THR TRP TYR TRP GLU ASN LEU LEU LYS SEQRES 15 A 296 ILE CYS VAL PHE ILE PHE ALA PHE ILE MET PRO VAL LEU SEQRES 16 A 296 ILE ILE THR VAL CYS TYR GLY LEU MET ILE LEU ARG LEU SEQRES 17 A 296 LYS SER VAL ARG MET LEU SER GLY SER LYS GLU LYS ASP SEQRES 18 A 296 ARG ASN LEU ARG ARG ILE THR ARG MET VAL LEU VAL VAL SEQRES 19 A 296 VAL ALA VAL PHE ILE VAL CYS TRP THR PRO ILE HIS ILE SEQRES 20 A 296 TYR VAL ILE ILE LYS ALA LEU ILE THR ILE PRO GLU THR SEQRES 21 A 296 THR PHE GLN THR VAL SER TRP HIS PHE CYS ILE ALA LEU SEQRES 22 A 296 GLY TYR THR ASN SER CYS LEU ASN PRO VAL LEU TYR ALA SEQRES 23 A 296 PHE LEU ASP GLU ASN PHE LYS ARG CYS PHE SEQRES 1 B 125 GLN VAL GLN LEU VAL GLU SER GLY GLY GLY LEU VAL ARG SEQRES 2 B 125 PRO GLY GLY SER LEU ARG LEU SER CYS VAL ASP SER GLU SEQRES 3 B 125 ARG THR SER TYR PRO MET GLY TRP PHE ARG ARG ALA PRO SEQRES 4 B 125 GLY LYS GLU ARG GLU PHE VAL ALA SER ILE THR TRP SER SEQRES 5 B 125 GLY ILE ASP PRO THR TYR ALA ASP SER VAL ALA ASP ARG SEQRES 6 B 125 PHE THR THR SER ARG ASP VAL ALA ASN ASN THR LEU TYR SEQRES 7 B 125 LEU GLN MET ASN SER LEU LYS HIS GLU ASP THR ALA VAL SEQRES 8 B 125 TYR TYR CYS ALA ALA ARG ALA PRO VAL GLY GLN SER SER SEQRES 9 B 125 SER PRO TYR ASP TYR ASP TYR TRP GLY GLN GLY THR GLN SEQRES 10 B 125 VAL THR VAL SER SER ALA ALA ALA MODRES 5C1M YCM A 57 CYS MODIFIED RESIDUE HET YCM A 57 10 HET OLC A 401 16 HET OLC A 402 18 HET CLR A 403 28 HET PO4 A 404 5 HET P6G A 405 19 HET P6G A 406 13 HET VF1 A 407 32 HETNAM YCM S-(2-AMINO-2-OXOETHYL)-L-CYSTEINE HETNAM OLC (2R)-2,3-DIHYDROXYPROPYL (9Z)-OCTADEC-9-ENOATE HETNAM CLR CHOLESTEROL HETNAM PO4 PHOSPHATE ION HETNAM P6G HEXAETHYLENE GLYCOL HETNAM VF1 (2R,3S,3AR,5AR,6R,11BR,11CS)-3A-METHOXY-3,14-DIMETHYL- HETNAM 2 VF1 2-PHENYL-2,3,3A,6,7,11C-HEXAHYDRO-1H-6,11B- HETNAM 3 VF1 (EPIMINOETHANO)-3,5A-METHANONAPHTHO[2,1-G]INDOL-10-OL HETSYN YCM CYSTEINE-S-ACETAMIDE HETSYN OLC 1-OLEOYL-R-GLYCEROL HETSYN P6G POLYETHYLENE GLYCOL PEG400 HETSYN VF1 BU72 FORMUL 1 YCM C5 H10 N2 O3 S FORMUL 3 OLC 2(C21 H40 O4) FORMUL 5 CLR C27 H46 O FORMUL 6 PO4 O4 P 3- FORMUL 7 P6G 2(C12 H26 O7) FORMUL 9 VF1 C28 H32 N2 O2 FORMUL 10 HOH *94(H2 O) HELIX 1 AA1 SER A 64 TYR A 96 1 33 HELIX 2 AA2 THR A 101 SER A 119 1 19 HELIX 3 AA3 THR A 120 MET A 130 1 11 HELIX 4 AA4 PHE A 135 HIS A 171 1 37 HELIX 5 AA5 HIS A 171 ARG A 179 1 9 HELIX 6 AA6 THR A 180 MET A 205 1 26 HELIX 7 AA7 PRO A 224 PHE A 241 1 18 HELIX 8 AA8 PHE A 241 VAL A 262 1 22 HELIX 9 AA9 GLY A 267 ILE A 306 1 40 HELIX 10 AB1 THR A 311 ALA A 337 1 27 HELIX 11 AB2 ASP A 340 PHE A 347 1 8 HELIX 12 AB3 LYS B 87 THR B 91 5 5 SHEET 1 AA1 2 ALA A 206 ARG A 211 0 SHEET 2 AA1 2 SER A 214 LEU A 219 -1 O SER A 214 N ARG A 211 SHEET 1 AA2 4 VAL B 7 SER B 9 0 SHEET 2 AA2 4 LEU B 20 VAL B 25 -1 O SER B 23 N SER B 9 SHEET 3 AA2 4 THR B 78 MET B 83 -1 O MET B 83 N LEU B 20 SHEET 4 AA2 4 PHE B 68 ASP B 73 -1 N THR B 69 O GLN B 82 SHEET 1 AA3 6 GLY B 12 VAL B 14 0 SHEET 2 AA3 6 THR B 118 VAL B 122 1 O THR B 121 N GLY B 12 SHEET 3 AA3 6 ALA B 92 ARG B 99 -1 N TYR B 94 O THR B 118 SHEET 4 AA3 6 TYR B 32 ARG B 39 -1 N PHE B 37 O TYR B 95 SHEET 5 AA3 6 ARG B 45 ILE B 51 -1 O ALA B 49 N TRP B 36 SHEET 6 AA3 6 PRO B 58 TYR B 60 -1 O THR B 59 N SER B 50 SHEET 1 AA4 4 GLY B 12 VAL B 14 0 SHEET 2 AA4 4 THR B 118 VAL B 122 1 O THR B 121 N GLY B 12 SHEET 3 AA4 4 ALA B 92 ARG B 99 -1 N TYR B 94 O THR B 118 SHEET 4 AA4 4 TYR B 113 TRP B 114 -1 O TYR B 113 N ALA B 98 SSBOND 1 CYS A 140 CYS A 217 1555 1555 2.04 SSBOND 2 CYS B 24 CYS B 96 1555 1555 2.04 LINK C LEU A 56 N YCM A 57 1555 1555 1.33 LINK C YCM A 57 N PRO A 58 1555 1555 1.34 CISPEP 1 HIS A 223 PRO A 224 0 -6.96 CRYST1 44.430 144.000 209.900 90.00 90.00 90.00 I 21 21 21 8 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 0.022507 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006944 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004764 0.00000