HEADER DNA BINDING PROTEIN 19-OCT-22 8BDK TITLE STRUCTURE OF A NON-CANONICAL HISTONE FROM ARCHAEA COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA-BINDING PROTEIN HMVA; COMPND 3 CHAIN: A, B, D, E; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHANOCALDOCOCCUS JANNASCHII; SOURCE 3 ORGANISM_TAXID: 2190; SOURCE 4 GENE: HMVA, MJ1647; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HISTONE, DIMERISATION, TRANSCRIPTION, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.OFER,F.WERNER REVDAT 3 07-FEB-24 8BDK 1 REMARK REVDAT 2 04-OCT-23 8BDK 1 JRNL REVDAT 1 12-JUL-23 8BDK 0 JRNL AUTH S.OFER,F.BLOMBACH,A.M.ERKELENS,D.BARKER,Z.SOLOVIEV,S.SCHWAB, JRNL AUTH 2 K.SMOLLETT,D.MATELSKA,T.FOUQUEAU,N.VAN DER VIS,N.A.KENT, JRNL AUTH 3 K.THALASSINOS,R.T.DAME,F.WERNER JRNL TITL DNA-BRIDGING BY AN ARCHAEAL HISTONE VARIANT VIA A UNIQUE JRNL TITL 2 TETRAMERISATION INTERFACE. JRNL REF COMMUN BIOL V. 6 968 2023 JRNL REFN ESSN 2399-3642 JRNL PMID 37740023 JRNL DOI 10.1038/S42003-023-05348-2 REMARK 2 REMARK 2 RESOLUTION. 1.88 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.10.1_2155 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) : 1.88 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 52.93 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 28578 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.210 REMARK 3 R VALUE (WORKING SET) : 0.208 REMARK 3 FREE R VALUE : 0.253 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.920 REMARK 3 FREE R VALUE TEST SET COUNT : 1405 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 52.9250 - 4.0498 0.99 2800 134 0.1748 0.2012 REMARK 3 2 4.0498 - 3.2146 1.00 2763 142 0.1640 0.1899 REMARK 3 3 3.2146 - 2.8083 1.00 2722 145 0.2006 0.2572 REMARK 3 4 2.8083 - 2.5515 0.99 2750 142 0.2038 0.2525 REMARK 3 5 2.5515 - 2.3686 0.99 2732 133 0.2120 0.3011 REMARK 3 6 2.3686 - 2.2290 0.99 2694 154 0.2262 0.2794 REMARK 3 7 2.2290 - 2.1174 0.99 2728 126 0.2540 0.3141 REMARK 3 8 2.1174 - 2.0252 0.99 2692 143 0.2802 0.3173 REMARK 3 9 2.0252 - 1.9472 0.98 2666 147 0.3180 0.3958 REMARK 3 10 1.9472 - 1.8800 0.96 2626 139 0.3665 0.4082 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) : 0.310 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.510 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.57 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 : 0.006 3131 REMARK 3 ANGLE : 0.764 4178 REMARK 3 CHIRALITY : 0.043 503 REMARK 3 PLANARITY : 0.004 528 REMARK 3 DIHEDRAL : 12.411 2081 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 20 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 20 ) REMARK 3 ORIGIN FOR THE GROUP (A): 12.3385 34.2783 106.5636 REMARK 3 T TENSOR REMARK 3 T11: 0.3102 T22: 0.2746 REMARK 3 T33: 0.2931 T12: 0.0646 REMARK 3 T13: 0.0895 T23: -0.0539 REMARK 3 L TENSOR REMARK 3 L11: 3.9945 L22: 6.4654 REMARK 3 L33: 5.0457 L12: 1.6072 REMARK 3 L13: 1.5566 L23: 3.0572 REMARK 3 S TENSOR REMARK 3 S11: -0.0214 S12: -0.3645 S13: 0.0776 REMARK 3 S21: 0.4348 S22: -0.2247 S23: 0.7397 REMARK 3 S31: -0.1646 S32: -0.6536 S33: 0.2613 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 21 THROUGH 49 ) REMARK 3 ORIGIN FOR THE GROUP (A): 18.5350 22.3058 92.9009 REMARK 3 T TENSOR REMARK 3 T11: 0.2598 T22: 0.2201 REMARK 3 T33: 0.1739 T12: 0.0421 REMARK 3 T13: -0.0155 T23: 0.0180 REMARK 3 L TENSOR REMARK 3 L11: 1.3567 L22: 8.2920 REMARK 3 L33: 3.0434 L12: -1.4830 REMARK 3 L13: -0.8764 L23: 4.3810 REMARK 3 S TENSOR REMARK 3 S11: 0.2175 S12: 0.1821 S13: 0.1235 REMARK 3 S21: -0.6827 S22: -0.3800 S23: -0.0391 REMARK 3 S31: -0.2343 S32: -0.1673 S33: 0.1563 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 50 THROUGH 63 ) REMARK 3 ORIGIN FOR THE GROUP (A): 21.4023 7.5795 95.5228 REMARK 3 T TENSOR REMARK 3 T11: 0.2603 T22: 0.1372 REMARK 3 T33: 0.1535 T12: 0.0263 REMARK 3 T13: -0.0172 T23: 0.0037 REMARK 3 L TENSOR REMARK 3 L11: 6.5269 L22: 9.1411 REMARK 3 L33: 7.9299 L12: 0.7863 REMARK 3 L13: 1.6935 L23: 0.9759 REMARK 3 S TENSOR REMARK 3 S11: -0.0354 S12: -0.2323 S13: -0.0481 REMARK 3 S21: -0.1736 S22: -0.1532 S23: -0.0226 REMARK 3 S31: -0.4682 S32: -0.1534 S33: 0.1905 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 64 THROUGH 76 ) REMARK 3 ORIGIN FOR THE GROUP (A): 38.1672 18.1702 95.5559 REMARK 3 T TENSOR REMARK 3 T11: 0.4248 T22: 0.4189 REMARK 3 T33: 0.6315 T12: 0.1746 REMARK 3 T13: 0.0207 T23: 0.0492 REMARK 3 L TENSOR REMARK 3 L11: 7.7210 L22: 7.0892 REMARK 3 L33: 3.7397 L12: 5.9549 REMARK 3 L13: -1.2792 L23: 1.9462 REMARK 3 S TENSOR REMARK 3 S11: 0.2502 S12: 0.3951 S13: 0.4081 REMARK 3 S21: 0.2068 S22: -0.2918 S23: -1.5814 REMARK 3 S31: 1.0596 S32: 0.9492 S33: 0.0745 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 77 THROUGH 82 ) REMARK 3 ORIGIN FOR THE GROUP (A): 32.6290 28.9220 87.1017 REMARK 3 T TENSOR REMARK 3 T11: 0.6151 T22: 0.4165 REMARK 3 T33: 0.4547 T12: 0.1620 REMARK 3 T13: 0.1537 T23: 0.1069 REMARK 3 L TENSOR REMARK 3 L11: 2.3064 L22: 5.4781 REMARK 3 L33: 3.3351 L12: -1.3697 REMARK 3 L13: 2.7315 L23: -0.9087 REMARK 3 S TENSOR REMARK 3 S11: -0.6254 S12: 0.4511 S13: -0.6066 REMARK 3 S21: 0.0629 S22: -0.3617 S23: -1.2763 REMARK 3 S31: 0.0330 S32: 0.5633 S33: 0.9265 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 83 THROUGH 96 ) REMARK 3 ORIGIN FOR THE GROUP (A): 28.2928 30.2856 98.8306 REMARK 3 T TENSOR REMARK 3 T11: 0.2833 T22: 0.2352 REMARK 3 T33: 0.2986 T12: 0.0331 REMARK 3 T13: -0.0216 T23: -0.0171 REMARK 3 L TENSOR REMARK 3 L11: 8.0558 L22: 2.1669 REMARK 3 L33: 6.9989 L12: -0.9288 REMARK 3 L13: 3.5764 L23: 0.0824 REMARK 3 S TENSOR REMARK 3 S11: 0.0030 S12: -0.3454 S13: 0.6999 REMARK 3 S21: 0.3058 S22: 0.0299 S23: -0.4483 REMARK 3 S31: 0.0905 S32: 0.0098 S33: 0.0049 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1 THROUGH 20 ) REMARK 3 ORIGIN FOR THE GROUP (A): 9.6826 17.0110 94.2009 REMARK 3 T TENSOR REMARK 3 T11: 0.2523 T22: 0.2538 REMARK 3 T33: 0.3794 T12: 0.0525 REMARK 3 T13: -0.1214 T23: -0.0427 REMARK 3 L TENSOR REMARK 3 L11: 5.9142 L22: 7.2628 REMARK 3 L33: 5.0163 L12: -1.4763 REMARK 3 L13: -2.7724 L23: 1.4694 REMARK 3 S TENSOR REMARK 3 S11: 0.1039 S12: -0.0222 S13: 0.3923 REMARK 3 S21: -0.3655 S22: -0.3183 S23: 0.8419 REMARK 3 S31: -0.5125 S32: -0.3711 S33: 0.1110 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 21 THROUGH 55 ) REMARK 3 ORIGIN FOR THE GROUP (A): 20.4807 30.3472 106.0345 REMARK 3 T TENSOR REMARK 3 T11: 0.2635 T22: 0.2267 REMARK 3 T33: 0.1371 T12: 0.0432 REMARK 3 T13: -0.0156 T23: 0.0036 REMARK 3 L TENSOR REMARK 3 L11: 2.6884 L22: 7.0010 REMARK 3 L33: 3.2636 L12: 2.7085 REMARK 3 L13: 1.3327 L23: 3.7871 REMARK 3 S TENSOR REMARK 3 S11: 0.0998 S12: -0.2868 S13: -0.0096 REMARK 3 S21: 0.6195 S22: -0.2559 S23: 0.0821 REMARK 3 S31: 0.0743 S32: -0.1009 S33: 0.1525 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 56 THROUGH 63 ) REMARK 3 ORIGIN FOR THE GROUP (A): 27.6025 39.8668 98.1483 REMARK 3 T TENSOR REMARK 3 T11: 0.5271 T22: 0.4429 REMARK 3 T33: 0.3965 T12: -0.0573 REMARK 3 T13: -0.0279 T23: -0.0465 REMARK 3 L TENSOR REMARK 3 L11: 2.3968 L22: 8.6661 REMARK 3 L33: 7.2210 L12: 2.0431 REMARK 3 L13: -3.0521 L23: -3.6742 REMARK 3 S TENSOR REMARK 3 S11: -0.6355 S12: 0.4219 S13: -0.0043 REMARK 3 S21: -1.0742 S22: 0.0640 S23: -1.1981 REMARK 3 S31: -0.4193 S32: 1.1370 S33: 0.7974 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 64 THROUGH 77 ) REMARK 3 ORIGIN FOR THE GROUP (A): 39.0533 29.4020 98.7477 REMARK 3 T TENSOR REMARK 3 T11: 0.3170 T22: 0.6365 REMARK 3 T33: 1.4065 T12: 0.0274 REMARK 3 T13: -0.1186 T23: 0.0497 REMARK 3 L TENSOR REMARK 3 L11: 2.4942 L22: 2.1754 REMARK 3 L33: 9.7382 L12: -0.5493 REMARK 3 L13: -4.0287 L23: 1.8545 REMARK 3 S TENSOR REMARK 3 S11: 0.1750 S12: -0.7106 S13: 2.2208 REMARK 3 S21: 0.0718 S22: -0.0732 S23: -1.2913 REMARK 3 S31: -1.1913 S32: 1.5305 S33: -0.0802 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 78 THROUGH 96 ) REMARK 3 ORIGIN FOR THE GROUP (A): 28.9950 19.0274 100.0278 REMARK 3 T TENSOR REMARK 3 T11: 0.2711 T22: 0.2003 REMARK 3 T33: 0.2877 T12: 0.0521 REMARK 3 T13: -0.0004 T23: 0.0238 REMARK 3 L TENSOR REMARK 3 L11: 9.3405 L22: 2.7194 REMARK 3 L33: 8.1862 L12: 1.8744 REMARK 3 L13: -1.0451 L23: 1.8607 REMARK 3 S TENSOR REMARK 3 S11: -0.1422 S12: -0.3269 S13: -0.2255 REMARK 3 S21: -0.0108 S22: 0.2127 S23: -0.3822 REMARK 3 S31: 0.3481 S32: 0.6565 S33: -0.0736 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: CHAIN 'D' AND (RESID 1 THROUGH 55 ) REMARK 3 ORIGIN FOR THE GROUP (A): 39.6163 14.6320 78.4366 REMARK 3 T TENSOR REMARK 3 T11: 0.2092 T22: 0.1959 REMARK 3 T33: 0.1678 T12: 0.0189 REMARK 3 T13: 0.0301 T23: 0.0059 REMARK 3 L TENSOR REMARK 3 L11: 2.0634 L22: 8.5634 REMARK 3 L33: 1.7302 L12: 2.4533 REMARK 3 L13: -0.5853 L23: -2.5131 REMARK 3 S TENSOR REMARK 3 S11: 0.0428 S12: -0.1428 S13: -0.0526 REMARK 3 S21: 0.4074 S22: -0.1917 S23: -0.3715 REMARK 3 S31: -0.0919 S32: 0.0845 S33: 0.1271 REMARK 3 TLS GROUP : 13 REMARK 3 SELECTION: CHAIN 'D' AND (RESID 56 THROUGH 63 ) REMARK 3 ORIGIN FOR THE GROUP (A): 30.2871 0.6228 71.4368 REMARK 3 T TENSOR REMARK 3 T11: 0.4244 T22: 0.4027 REMARK 3 T33: 0.3849 T12: 0.0086 REMARK 3 T13: -0.0231 T23: 0.0138 REMARK 3 L TENSOR REMARK 3 L11: 6.5917 L22: 6.9853 REMARK 3 L33: 8.0537 L12: 3.0532 REMARK 3 L13: -0.6020 L23: 1.4112 REMARK 3 S TENSOR REMARK 3 S11: -0.2669 S12: 1.1624 S13: 0.6986 REMARK 3 S21: -1.0622 S22: -0.1650 S23: 1.2041 REMARK 3 S31: -0.0238 S32: -0.7654 S33: -0.0521 REMARK 3 TLS GROUP : 14 REMARK 3 SELECTION: CHAIN 'D' AND (RESID 64 THROUGH 96 ) REMARK 3 ORIGIN FOR THE GROUP (A): 23.9598 16.9598 70.6672 REMARK 3 T TENSOR REMARK 3 T11: 0.2472 T22: 0.3750 REMARK 3 T33: 0.4638 T12: -0.0368 REMARK 3 T13: 0.0164 T23: -0.0905 REMARK 3 L TENSOR REMARK 3 L11: 2.7797 L22: 6.2490 REMARK 3 L33: 5.9348 L12: 1.8190 REMARK 3 L13: 1.5073 L23: 1.1114 REMARK 3 S TENSOR REMARK 3 S11: 0.0902 S12: 0.1589 S13: -0.3463 REMARK 3 S21: 0.0587 S22: -0.2538 S23: 0.8880 REMARK 3 S31: 0.2424 S32: -1.1650 S33: 0.0993 REMARK 3 TLS GROUP : 15 REMARK 3 SELECTION: CHAIN 'E' AND (RESID 1 THROUGH 20 ) REMARK 3 ORIGIN FOR THE GROUP (A): 42.0200 6.0790 84.1750 REMARK 3 T TENSOR REMARK 3 T11: 0.3181 T22: 0.1952 REMARK 3 T33: 0.1669 T12: 0.0285 REMARK 3 T13: -0.0488 T23: 0.0300 REMARK 3 L TENSOR REMARK 3 L11: 9.6493 L22: 9.4114 REMARK 3 L33: 2.6988 L12: 2.7491 REMARK 3 L13: -0.2778 L23: 1.1838 REMARK 3 S TENSOR REMARK 3 S11: -0.1071 S12: -0.4209 S13: -0.0416 REMARK 3 S21: 0.3043 S22: -0.0447 S23: -0.2310 REMARK 3 S31: 0.1259 S32: 0.2959 S33: 0.2289 REMARK 3 TLS GROUP : 16 REMARK 3 SELECTION: CHAIN 'E' AND (RESID 21 THROUGH 49 ) REMARK 3 ORIGIN FOR THE GROUP (A): 40.6912 18.1304 69.2425 REMARK 3 T TENSOR REMARK 3 T11: 0.1751 T22: 0.2110 REMARK 3 T33: 0.1745 T12: 0.0180 REMARK 3 T13: 0.0391 T23: -0.0020 REMARK 3 L TENSOR REMARK 3 L11: 0.3654 L22: 4.6821 REMARK 3 L33: 6.3275 L12: -0.4493 REMARK 3 L13: 0.8808 L23: -5.4523 REMARK 3 S TENSOR REMARK 3 S11: 0.1399 S12: 0.0587 S13: -0.0432 REMARK 3 S21: -0.8603 S22: -0.2697 S23: 0.0109 REMARK 3 S31: 0.3992 S32: 0.2421 S33: 0.2015 REMARK 3 TLS GROUP : 17 REMARK 3 SELECTION: CHAIN 'E' AND (RESID 50 THROUGH 63 ) REMARK 3 ORIGIN FOR THE GROUP (A): 37.2022 32.8720 70.7677 REMARK 3 T TENSOR REMARK 3 T11: 0.2628 T22: 0.1736 REMARK 3 T33: 0.2029 T12: 0.0175 REMARK 3 T13: 0.0475 T23: 0.0131 REMARK 3 L TENSOR REMARK 3 L11: 5.0273 L22: 7.7877 REMARK 3 L33: 8.0236 L12: -1.1238 REMARK 3 L13: -1.4979 L23: -0.8254 REMARK 3 S TENSOR REMARK 3 S11: 0.1127 S12: -0.1787 S13: -0.0286 REMARK 3 S21: 0.2579 S22: -0.2259 S23: 0.1199 REMARK 3 S31: -0.4281 S32: -0.0518 S33: 0.0458 REMARK 3 TLS GROUP : 18 REMARK 3 SELECTION: CHAIN 'E' AND (RESID 64 THROUGH 76 ) REMARK 3 ORIGIN FOR THE GROUP (A): 21.4356 22.6992 64.9676 REMARK 3 T TENSOR REMARK 3 T11: 0.4329 T22: 0.4730 REMARK 3 T33: 0.5687 T12: 0.1795 REMARK 3 T13: -0.0858 T23: -0.0879 REMARK 3 L TENSOR REMARK 3 L11: 6.9214 L22: 4.2965 REMARK 3 L33: 7.6441 L12: -1.8697 REMARK 3 L13: -1.2899 L23: -0.5896 REMARK 3 S TENSOR REMARK 3 S11: 0.3250 S12: 1.3662 S13: 0.4858 REMARK 3 S21: -0.6327 S22: -0.7942 S23: 0.9822 REMARK 3 S31: -1.3399 S32: -0.8681 S33: 0.3685 REMARK 3 TLS GROUP : 19 REMARK 3 SELECTION: CHAIN 'E' AND (RESID 77 THROUGH 82 ) REMARK 3 ORIGIN FOR THE GROUP (A): 28.9780 11.4578 59.1861 REMARK 3 T TENSOR REMARK 3 T11: 0.4284 T22: 0.2959 REMARK 3 T33: 0.3434 T12: -0.0047 REMARK 3 T13: -0.0197 T23: -0.0386 REMARK 3 L TENSOR REMARK 3 L11: 7.9432 L22: 5.1267 REMARK 3 L33: 2.4635 L12: -2.1793 REMARK 3 L13: -3.0812 L23: -1.5497 REMARK 3 S TENSOR REMARK 3 S11: -0.6269 S12: 0.2029 S13: 0.4572 REMARK 3 S21: -0.7292 S22: -0.2169 S23: 0.6414 REMARK 3 S31: 0.0106 S32: -0.4689 S33: 0.3922 REMARK 3 TLS GROUP : 20 REMARK 3 SELECTION: CHAIN 'E' AND (RESID 83 THROUGH 96 ) REMARK 3 ORIGIN FOR THE GROUP (A): 29.4778 10.0339 71.8730 REMARK 3 T TENSOR REMARK 3 T11: 0.2931 T22: 0.1940 REMARK 3 T33: 0.2941 T12: 0.0321 REMARK 3 T13: -0.0273 T23: 0.0250 REMARK 3 L TENSOR REMARK 3 L11: 6.7598 L22: 2.1495 REMARK 3 L33: 6.4902 L12: -0.1354 REMARK 3 L13: -2.7880 L23: -0.2519 REMARK 3 S TENSOR REMARK 3 S11: 0.1192 S12: -0.0761 S13: -0.0432 REMARK 3 S21: -0.0457 S22: 0.1695 S23: 0.4488 REMARK 3 S31: 0.4184 S32: -0.3176 S33: -0.2925 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 8BDK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 19-OCT-22. REMARK 100 THE DEPOSITION ID IS D_1292126172. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-JUL-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I02 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : POINTLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28933 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.880 REMARK 200 RESOLUTION RANGE LOW (A) : 80.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.09900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.88 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.91 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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: 1B67 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.81 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M NAOAC PH 4.6, 10% (W/V) PEG 3350 REMARK 280 AND 5% (W/V) TACSIMATE PH 4.6, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 40.57700 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: 6760 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9660 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -64.0 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 350 REMARK 350 BIOMOLECULE: 2 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: 6600 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9670 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -63.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: D, E 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 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 B 55 CD CE NZ REMARK 470 ASP D 16 CG OD1 OD2 REMARK 470 GLU D 95 CG CD OE1 OE2 REMARK 470 LEU D 96 CG CD1 CD2 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 O HOH D 101 O HOH D 121 1.92 REMARK 500 O GLU B 95 O HOH B 101 1.95 REMARK 500 O HOH D 144 O HOH D 145 1.95 REMARK 500 O HOH A 118 O HOH A 146 2.08 REMARK 500 O HOH A 161 O HOH B 159 2.12 REMARK 500 O ILE D 59 O HOH D 101 2.13 REMARK 500 OD2 ASP E 63 O HOH E 101 2.14 REMARK 500 O HOH B 155 O HOH B 157 2.15 REMARK 500 ND1 HIS D 14 O HOH D 102 2.16 REMARK 500 O HOH D 136 O HOH D 157 2.17 REMARK 500 NZ LYS D 70 O HOH D 103 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH D 137 O HOH D 144 1455 1.86 REMARK 500 O HOH D 137 O HOH D 145 1455 2.02 REMARK 500 O HOH D 126 O HOH E 146 2748 2.07 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 CYS B 62 -133.24 -83.30 REMARK 500 GLU B 95 -106.62 -81.16 REMARK 500 GLU D 95 69.81 -68.07 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 161 DISTANCE = 6.31 ANGSTROMS REMARK 525 HOH B 159 DISTANCE = 6.37 ANGSTROMS DBREF 8BDK A 1 96 UNP Q59041 HMVA_METJA 1 96 DBREF 8BDK B 1 96 UNP Q59041 HMVA_METJA 1 96 DBREF 8BDK D 1 96 UNP Q59041 HMVA_METJA 1 96 DBREF 8BDK E 1 96 UNP Q59041 HMVA_METJA 1 96 SEQRES 1 A 96 MET LEU PRO LYS ALA THR VAL LYS ARG ILE MET LYS GLN SEQRES 2 A 96 HIS THR ASP PHE ASN ILE SER ALA GLU ALA VAL ASP GLU SEQRES 3 A 96 LEU CYS ASN MET LEU GLU GLU ILE ILE LYS ILE THR THR SEQRES 4 A 96 GLU VAL ALA GLU GLN ASN ALA ARG LYS GLU GLY ARG LYS SEQRES 5 A 96 THR ILE LYS ALA ARG ASP ILE LYS GLN CYS ASP ASP GLU SEQRES 6 A 96 ARG LEU LYS ARG LYS ILE MET GLU LEU SER GLU ARG THR SEQRES 7 A 96 ASP LYS MET PRO ILE LEU ILE LYS GLU MET LEU ASN VAL SEQRES 8 A 96 ILE THR SER GLU LEU SEQRES 1 B 96 MET LEU PRO LYS ALA THR VAL LYS ARG ILE MET LYS GLN SEQRES 2 B 96 HIS THR ASP PHE ASN ILE SER ALA GLU ALA VAL ASP GLU SEQRES 3 B 96 LEU CYS ASN MET LEU GLU GLU ILE ILE LYS ILE THR THR SEQRES 4 B 96 GLU VAL ALA GLU GLN ASN ALA ARG LYS GLU GLY ARG LYS SEQRES 5 B 96 THR ILE LYS ALA ARG ASP ILE LYS GLN CYS ASP ASP GLU SEQRES 6 B 96 ARG LEU LYS ARG LYS ILE MET GLU LEU SER GLU ARG THR SEQRES 7 B 96 ASP LYS MET PRO ILE LEU ILE LYS GLU MET LEU ASN VAL SEQRES 8 B 96 ILE THR SER GLU LEU SEQRES 1 D 96 MET LEU PRO LYS ALA THR VAL LYS ARG ILE MET LYS GLN SEQRES 2 D 96 HIS THR ASP PHE ASN ILE SER ALA GLU ALA VAL ASP GLU SEQRES 3 D 96 LEU CYS ASN MET LEU GLU GLU ILE ILE LYS ILE THR THR SEQRES 4 D 96 GLU VAL ALA GLU GLN ASN ALA ARG LYS GLU GLY ARG LYS SEQRES 5 D 96 THR ILE LYS ALA ARG ASP ILE LYS GLN CYS ASP ASP GLU SEQRES 6 D 96 ARG LEU LYS ARG LYS ILE MET GLU LEU SER GLU ARG THR SEQRES 7 D 96 ASP LYS MET PRO ILE LEU ILE LYS GLU MET LEU ASN VAL SEQRES 8 D 96 ILE THR SER GLU LEU SEQRES 1 E 96 MET LEU PRO LYS ALA THR VAL LYS ARG ILE MET LYS GLN SEQRES 2 E 96 HIS THR ASP PHE ASN ILE SER ALA GLU ALA VAL ASP GLU SEQRES 3 E 96 LEU CYS ASN MET LEU GLU GLU ILE ILE LYS ILE THR THR SEQRES 4 E 96 GLU VAL ALA GLU GLN ASN ALA ARG LYS GLU GLY ARG LYS SEQRES 5 E 96 THR ILE LYS ALA ARG ASP ILE LYS GLN CYS ASP ASP GLU SEQRES 6 E 96 ARG LEU LYS ARG LYS ILE MET GLU LEU SER GLU ARG THR SEQRES 7 E 96 ASP LYS MET PRO ILE LEU ILE LYS GLU MET LEU ASN VAL SEQRES 8 E 96 ILE THR SER GLU LEU FORMUL 5 HOH *240(H2 O) HELIX 1 AA1 PRO A 3 LYS A 12 1 10 HELIX 2 AA2 SER A 20 GLU A 49 1 30 HELIX 3 AA3 LYS A 55 ILE A 59 5 5 HELIX 4 AA4 ASP A 63 SER A 75 1 13 HELIX 5 AA5 PRO A 82 LEU A 96 1 15 HELIX 6 AA6 PRO B 3 LYS B 12 1 10 HELIX 7 AA7 SER B 20 GLU B 49 1 30 HELIX 8 AA8 LYS B 55 ILE B 59 5 5 HELIX 9 AA9 ASP B 63 GLU B 76 1 14 HELIX 10 AB1 ARG B 77 MET B 81 5 5 HELIX 11 AB2 PRO B 82 GLU B 95 1 14 HELIX 12 AB3 PRO D 3 LYS D 12 1 10 HELIX 13 AB4 SER D 20 GLU D 49 1 30 HELIX 14 AB5 LYS D 55 ILE D 59 5 5 HELIX 15 AB6 ASP D 63 ARG D 77 1 15 HELIX 16 AB7 PRO D 82 GLU D 95 1 14 HELIX 17 AB8 PRO E 3 LYS E 12 1 10 HELIX 18 AB9 SER E 20 GLU E 49 1 30 HELIX 19 AC1 LYS E 55 ILE E 59 5 5 HELIX 20 AC2 ASP E 63 SER E 75 1 13 HELIX 21 AC3 PRO E 82 LEU E 96 1 15 SHEET 1 AA1 2 ASN A 18 ILE A 19 0 SHEET 2 AA1 2 THR B 53 ILE B 54 1 O ILE B 54 N ASN A 18 SHEET 1 AA2 2 THR A 53 ILE A 54 0 SHEET 2 AA2 2 ASN B 18 ILE B 19 1 O ASN B 18 N ILE A 54 SHEET 1 AA3 2 ASN D 18 ILE D 19 0 SHEET 2 AA3 2 THR E 53 ILE E 54 1 O ILE E 54 N ASN D 18 SHEET 1 AA4 2 THR D 53 ILE D 54 0 SHEET 2 AA4 2 ASN E 18 ILE E 19 1 O ASN E 18 N ILE D 54 CRYST1 42.016 81.154 53.543 90.00 98.71 90.00 P 1 21 1 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 0.023801 0.000000 0.003646 0.00000 SCALE2 0.000000 0.012322 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018895 0.00000