10 20 30 40 50 60 70 80 4YU7 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER TOXIN 18-MAR-15 4YU7
TITLE CRYSTAL STRUCTURE OF PIRATOXIN I (PRTX-I) COMPLEXED TO CAFFEIC ACID
COMPND MOL_ID: 1; COMPND 2 MOLECULE: BASIC PHOSPHOLIPASE A2 HOMOLOG PIRATOXIN-1; COMPND 3 CHAIN: B, A; COMPND 4 SYNONYM: SVPLA2 HOMOLOG,MYOTOXIN SIV-SP5,PIRATOXIN-I,PRTX-I
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOTHROPS PIRAJAI; SOURCE 3 ORGANISM_COMMON: PIRAJA'S LANCE HEAD; SOURCE 4 ORGANISM_TAXID: 113192
KEYWDS PHOSPHOLIPASE A2 PHOSPHOLIPASE A2-LIKE BOTHROPS SNAKE VENOM KEYWDS 2 INHIBITOR, TOXIN
EXPDTA X-RAY DIFFRACTION
AUTHOR C.A.H.FERNANDES,M.R.M.FONTES
REVDAT 2 30-SEP-15 4YU7 1 JRNL REVDAT 1 05-AUG-15 4YU7 0
JRNL AUTH C.A.FERNANDES,F.F.CARDOSO,W.G.CAVALCANTE,A.M.SOARES, JRNL AUTH 2 M.DAL-PAI,M.GALLACCI,M.R.FONTES JRNL TITL STRUCTURAL BASIS FOR THE INHIBITION OF A PHOSPHOLIPASE JRNL TITL 2 A2-LIKE TOXIN BY CAFFEIC AND ARISTOLOCHIC ACIDS. JRNL REF PLOS ONE V. 10 33370 2015 JRNL REFN ESSN 1932-6203 JRNL PMID 26192963 JRNL DOI 10.1371/JOURNAL.PONE.0133370
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH P.S.SHIMABUKU,C.A.FERNANDES,A.J.MAGRO,T.R.COSTA,A.M.SOARES, REMARK 1 AUTH 2 M.R.FONTES REMARK 1 TITL CRYSTALLIZATION AND PRELIMINARY X-RAY DIFFRACTION ANALYSIS REMARK 1 TITL 2 OF A LYS49-PHOSPHOLIPASE A2 COMPLEXED WITH CAFFEIC ACID, A REMARK 1 TITL 3 MOLECULE WITH INHIBITORY PROPERTIES AGAINST SNAKE VENOMS. REMARK 1 REF ACTA CRYSTALLOGR.,SECT.F V. 67 249 2011 REMARK 1 REFN ESSN 1744-3091 REMARK 1 PMID 21301098 REMARK 1 DOI 10.1107/S1744309110051407
REMARK 2 REMARK 2 RESOLUTION. 1.65 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.2_1309) 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) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.34 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.010 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.5 REMARK 3 NUMBER OF REFLECTIONS : 27807 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.090 REMARK 3 FREE R VALUE TEST SET COUNT : 1414 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 37.3506 - 3.5469 0.86 2429 148 0.1705 0.1961 REMARK 3 2 3.5469 - 2.8156 0.94 2619 140 0.1755 0.2183 REMARK 3 3 2.8156 - 2.4598 0.94 2649 149 0.1837 0.2315 REMARK 3 4 2.4598 - 2.2349 0.96 2711 116 0.1701 0.2196 REMARK 3 5 2.2349 - 2.0747 0.97 2695 153 0.1644 0.2427 REMARK 3 6 2.0747 - 1.9524 0.97 2682 144 0.1843 0.2485 REMARK 3 7 1.9524 - 1.8546 0.96 2699 145 0.1959 0.2556 REMARK 3 8 1.8546 - 1.7739 0.96 2684 147 0.2293 0.2974 REMARK 3 9 1.7739 - 1.7056 0.95 2637 142 0.2621 0.3237 REMARK 3 10 1.7056 - 1.6468 0.92 2588 130 0.2706 0.3109 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.910 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.007 2004 REMARK 3 ANGLE : 1.178 2659 REMARK 3 CHIRALITY : 0.079 266 REMARK 3 PLANARITY : 0.006 337 REMARK 3 DIHEDRAL : 16.332 765 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 18 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1 THROUGH 13 ) REMARK 3 ORIGIN FOR THE GROUP (A): -8.5779 -20.8254 6.0161 REMARK 3 T TENSOR REMARK 3 T11: 0.1734 T22: 0.1986 REMARK 3 T33: 0.2223 T12: 0.0084 REMARK 3 T13: 0.0157 T23: -0.0011 REMARK 3 L TENSOR REMARK 3 L11: 2.9825 L22: 3.3789 REMARK 3 L33: 3.0165 L12: 0.5925 REMARK 3 L13: 0.9692 L23: 1.4192 REMARK 3 S TENSOR REMARK 3 S11: -0.1335 S12: 0.2265 S13: 0.0079 REMARK 3 S21: -0.2859 S22: 0.1087 S23: -0.1342 REMARK 3 S31: -0.2169 S32: 0.0847 S33: -0.0278 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 14 THROUGH 21 ) REMARK 3 ORIGIN FOR THE GROUP (A): -0.2068 -26.7645 6.6488 REMARK 3 T TENSOR REMARK 3 T11: 0.2131 T22: 0.2962 REMARK 3 T33: 0.2428 T12: 0.0207 REMARK 3 T13: 0.0075 T23: -0.0363 REMARK 3 L TENSOR REMARK 3 L11: 0.7460 L22: 6.7655 REMARK 3 L33: 3.6089 L12: -0.2991 REMARK 3 L13: -0.9942 L23: 1.9932 REMARK 3 S TENSOR REMARK 3 S11: 0.1249 S12: 0.0594 S13: 0.1128 REMARK 3 S21: -0.0890 S22: 0.2620 S23: -0.3663 REMARK 3 S31: -0.0968 S32: 0.5557 S33: -0.1368 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 22 THROUGH 38 ) REMARK 3 ORIGIN FOR THE GROUP (A): -7.7444 -38.8331 9.2466 REMARK 3 T TENSOR REMARK 3 T11: 0.2493 T22: 0.1996 REMARK 3 T33: 0.2249 T12: 0.0073 REMARK 3 T13: -0.0231 T23: -0.0213 REMARK 3 L TENSOR REMARK 3 L11: 3.6284 L22: 2.9423 REMARK 3 L33: 2.6859 L12: 1.7075 REMARK 3 L13: -0.9019 L23: -0.3439 REMARK 3 S TENSOR REMARK 3 S11: -0.0012 S12: 0.2678 S13: 0.0557 REMARK 3 S21: -0.2508 S22: 0.0049 S23: 0.2326 REMARK 3 S31: 0.2061 S32: -0.2228 S33: -0.0148 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 39 THROUGH 65 ) REMARK 3 ORIGIN FOR THE GROUP (A): -17.0014 -29.5141 7.1644 REMARK 3 T TENSOR REMARK 3 T11: 0.1410 T22: 0.1999 REMARK 3 T33: 0.2170 T12: -0.0071 REMARK 3 T13: -0.0105 T23: -0.0131 REMARK 3 L TENSOR REMARK 3 L11: 2.0238 L22: 2.4216 REMARK 3 L33: 1.6648 L12: -1.0848 REMARK 3 L13: 0.8230 L23: -0.2980 REMARK 3 S TENSOR REMARK 3 S11: 0.0192 S12: 0.1153 S13: -0.1374 REMARK 3 S21: -0.1291 S22: 0.0484 S23: 0.3389 REMARK 3 S31: -0.0328 S32: -0.2630 S33: -0.0529 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 66 THROUGH 79 ) REMARK 3 ORIGIN FOR THE GROUP (A): -15.6001 -13.4727 10.9792 REMARK 3 T TENSOR REMARK 3 T11: 0.1412 T22: 0.2341 REMARK 3 T33: 0.2841 T12: 0.0140 REMARK 3 T13: -0.0303 T23: -0.0421 REMARK 3 L TENSOR REMARK 3 L11: 5.8770 L22: 0.4561 REMARK 3 L33: 1.1020 L12: 0.3420 REMARK 3 L13: 1.5370 L23: -0.3884 REMARK 3 S TENSOR REMARK 3 S11: -0.0388 S12: -0.3132 S13: 0.4912 REMARK 3 S21: 0.0272 S22: -0.2546 S23: 0.4402 REMARK 3 S31: -0.1182 S32: -0.3827 S33: 0.3215 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 80 THROUGH 102 ) REMARK 3 ORIGIN FOR THE GROUP (A): -13.5139 -24.5767 12.8778 REMARK 3 T TENSOR REMARK 3 T11: 0.2008 T22: 0.1989 REMARK 3 T33: 0.2241 T12: -0.0101 REMARK 3 T13: 0.0317 T23: -0.0100 REMARK 3 L TENSOR REMARK 3 L11: 6.6380 L22: 2.5668 REMARK 3 L33: 2.9721 L12: -3.0289 REMARK 3 L13: 3.6929 L23: -1.1951 REMARK 3 S TENSOR REMARK 3 S11: -0.1185 S12: -0.2874 S13: -0.2545 REMARK 3 S21: 0.0900 S22: 0.1459 S23: 0.2314 REMARK 3 S31: -0.1413 S32: -0.2568 S33: 0.0065 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 103 THROUGH 114 ) REMARK 3 ORIGIN FOR THE GROUP (A): 0.2763 -39.6757 8.3055 REMARK 3 T TENSOR REMARK 3 T11: 0.2055 T22: 0.2054 REMARK 3 T33: 0.2287 T12: 0.0388 REMARK 3 T13: 0.0455 T23: -0.0171 REMARK 3 L TENSOR REMARK 3 L11: 3.2869 L22: 5.6440 REMARK 3 L33: 5.5090 L12: -0.7670 REMARK 3 L13: -0.3983 L23: 0.8467 REMARK 3 S TENSOR REMARK 3 S11: -0.2185 S12: 0.2065 S13: -0.1243 REMARK 3 S21: -0.2659 S22: -0.0024 S23: 0.0357 REMARK 3 S31: 0.4921 S32: 0.2883 S33: 0.2159 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 115 THROUGH 121 ) REMARK 3 ORIGIN FOR THE GROUP (A): -15.5965 -44.8498 12.0573 REMARK 3 T TENSOR REMARK 3 T11: 0.4222 T22: 0.3554 REMARK 3 T33: 0.4791 T12: -0.0063 REMARK 3 T13: 0.1237 T23: 0.0235 REMARK 3 L TENSOR REMARK 3 L11: 2.1546 L22: 8.0687 REMARK 3 L33: 2.8571 L12: -1.8086 REMARK 3 L13: 2.4209 L23: -2.6372 REMARK 3 S TENSOR REMARK 3 S11: -0.1508 S12: -0.1915 S13: -0.8498 REMARK 3 S21: 0.4549 S22: 0.3081 S23: 1.1434 REMARK 3 S31: 0.0928 S32: -0.7750 S33: 0.0508 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 13 ) REMARK 3 ORIGIN FOR THE GROUP (A): -3.3783 -43.5782 -9.3095 REMARK 3 T TENSOR REMARK 3 T11: 0.1306 T22: 0.2003 REMARK 3 T33: 0.1927 T12: -0.0140 REMARK 3 T13: -0.0032 T23: -0.0050 REMARK 3 L TENSOR REMARK 3 L11: 4.5527 L22: 2.7374 REMARK 3 L33: 2.7870 L12: 0.7576 REMARK 3 L13: -1.4492 L23: -0.3165 REMARK 3 S TENSOR REMARK 3 S11: -0.1453 S12: 0.2081 S13: -0.2395 REMARK 3 S21: 0.2911 S22: 0.0596 S23: -0.1312 REMARK 3 S31: 0.2422 S32: 0.1084 S33: -0.0410 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 14 THROUGH 21 ) REMARK 3 ORIGIN FOR THE GROUP (A): 3.3639 -37.7388 -4.8728 REMARK 3 T TENSOR REMARK 3 T11: 0.1847 T22: 0.2747 REMARK 3 T33: 0.2239 T12: 0.0046 REMARK 3 T13: -0.0446 T23: -0.0235 REMARK 3 L TENSOR REMARK 3 L11: 1.7546 L22: 5.4307 REMARK 3 L33: 4.3712 L12: -0.7900 REMARK 3 L13: -0.5708 L23: 1.9152 REMARK 3 S TENSOR REMARK 3 S11: -0.0390 S12: -0.5286 S13: -0.3942 REMARK 3 S21: 0.2247 S22: 0.2644 S23: -0.3406 REMARK 3 S31: 0.2263 S32: 0.1194 S33: -0.0353 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 22 THROUGH 38 ) REMARK 3 ORIGIN FOR THE GROUP (A): -2.3946 -25.8940 -10.1097 REMARK 3 T TENSOR REMARK 3 T11: 0.2535 T22: 0.1961 REMARK 3 T33: 0.2192 T12: -0.0032 REMARK 3 T13: -0.0060 T23: -0.0218 REMARK 3 L TENSOR REMARK 3 L11: 2.7876 L22: 2.2878 REMARK 3 L33: 1.8850 L12: -0.3246 REMARK 3 L13: 0.4795 L23: -0.2897 REMARK 3 S TENSOR REMARK 3 S11: -0.0876 S12: -0.1836 S13: 0.3434 REMARK 3 S21: 0.1990 S22: 0.0667 S23: 0.0981 REMARK 3 S31: -0.2042 S32: -0.1841 S33: -0.0088 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 39 THROUGH 53 ) REMARK 3 ORIGIN FOR THE GROUP (A): -6.2086 -30.4954 -16.0573 REMARK 3 T TENSOR REMARK 3 T11: 0.1625 T22: 0.2167 REMARK 3 T33: 0.2236 T12: 0.0202 REMARK 3 T13: -0.0215 T23: -0.0062 REMARK 3 L TENSOR REMARK 3 L11: 7.8856 L22: 3.5206 REMARK 3 L33: 2.6389 L12: 1.8192 REMARK 3 L13: 0.7437 L23: -0.1745 REMARK 3 S TENSOR REMARK 3 S11: -0.2731 S12: 0.2724 S13: 0.2362 REMARK 3 S21: -0.2499 S22: 0.2293 S23: 0.3902 REMARK 3 S31: -0.3054 S32: -0.3954 S33: 0.0432 REMARK 3 TLS GROUP : 13 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 54 THROUGH 65 ) REMARK 3 ORIGIN FOR THE GROUP (A): -16.5160 -41.4193 -10.5813 REMARK 3 T TENSOR REMARK 3 T11: 0.2485 T22: 0.4203 REMARK 3 T33: 0.3688 T12: -0.0563 REMARK 3 T13: 0.0656 T23: -0.0298 REMARK 3 L TENSOR REMARK 3 L11: 1.8299 L22: 3.5999 REMARK 3 L33: 3.3008 L12: 0.5132 REMARK 3 L13: -0.7779 L23: 1.0147 REMARK 3 S TENSOR REMARK 3 S11: -0.0092 S12: -0.2202 S13: 0.1429 REMARK 3 S21: 0.4022 S22: 0.2181 S23: 0.4554 REMARK 3 S31: -0.1390 S32: -0.4549 S33: -0.2687 REMARK 3 TLS GROUP : 14 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 66 THROUGH 79 ) REMARK 3 ORIGIN FOR THE GROUP (A): -6.8553 -50.6221 -17.2060 REMARK 3 T TENSOR REMARK 3 T11: 0.1798 T22: 0.2525 REMARK 3 T33: 0.2960 T12: -0.0128 REMARK 3 T13: -0.0246 T23: -0.0460 REMARK 3 L TENSOR REMARK 3 L11: 9.5316 L22: 1.1767 REMARK 3 L33: 1.0942 L12: -2.2555 REMARK 3 L13: 0.5975 L23: -0.7127 REMARK 3 S TENSOR REMARK 3 S11: 0.2945 S12: 0.5589 S13: -0.6604 REMARK 3 S21: -0.1636 S22: -0.2142 S23: 0.4240 REMARK 3 S31: 0.2673 S32: -0.2819 S33: 0.0090 REMARK 3 TLS GROUP : 15 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 80 THROUGH 98 ) REMARK 3 ORIGIN FOR THE GROUP (A): -7.0024 -40.7520 -17.5234 REMARK 3 T TENSOR REMARK 3 T11: 0.1700 T22: 0.2547 REMARK 3 T33: 0.2318 T12: -0.0214 REMARK 3 T13: 0.0001 T23: 0.0019 REMARK 3 L TENSOR REMARK 3 L11: 9.7191 L22: 1.6457 REMARK 3 L33: 0.9931 L12: 2.4366 REMARK 3 L13: -0.0991 L23: 0.1871 REMARK 3 S TENSOR REMARK 3 S11: -0.0145 S12: 0.2138 S13: 0.1447 REMARK 3 S21: 0.0271 S22: 0.0433 S23: 0.1829 REMARK 3 S31: 0.0647 S32: -0.1919 S33: -0.0021 REMARK 3 TLS GROUP : 16 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 99 THROUGH 107 ) REMARK 3 ORIGIN FOR THE GROUP (A): 8.7725 -29.9771 -10.4390 REMARK 3 T TENSOR REMARK 3 T11: 0.1486 T22: 0.2576 REMARK 3 T33: 0.1808 T12: -0.0458 REMARK 3 T13: -0.0602 T23: 0.0027 REMARK 3 L TENSOR REMARK 3 L11: 1.8405 L22: 4.3277 REMARK 3 L33: 5.4772 L12: -0.0156 REMARK 3 L13: -0.7940 L23: 2.2633 REMARK 3 S TENSOR REMARK 3 S11: -0.0974 S12: -0.5904 S13: 0.0357 REMARK 3 S21: 0.4546 S22: 0.0592 S23: -0.2247 REMARK 3 S31: -0.0167 S32: 0.8029 S33: 0.0410 REMARK 3 TLS GROUP : 17 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 108 THROUGH 114 ) REMARK 3 ORIGIN FOR THE GROUP (A): 0.8140 -23.0517 -3.3241 REMARK 3 T TENSOR REMARK 3 T11: 0.4451 T22: 0.1976 REMARK 3 T33: 0.3372 T12: -0.0004 REMARK 3 T13: -0.0858 T23: -0.0591 REMARK 3 L TENSOR REMARK 3 L11: 3.6524 L22: 2.6692 REMARK 3 L33: 2.6185 L12: -1.1143 REMARK 3 L13: -0.1962 L23: 0.8185 REMARK 3 S TENSOR REMARK 3 S11: -0.3945 S12: -0.1755 S13: 0.3284 REMARK 3 S21: 0.5847 S22: 0.1783 S23: 0.4862 REMARK 3 S31: -0.5533 S32: 0.0758 S33: -0.0689 REMARK 3 TLS GROUP : 18 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 115 THROUGH 121 ) REMARK 3 ORIGIN FOR THE GROUP (A): -7.2558 -19.3694 -16.3493 REMARK 3 T TENSOR REMARK 3 T11: 0.4238 T22: 0.3008 REMARK 3 T33: 0.4775 T12: -0.0652 REMARK 3 T13: -0.0244 T23: 0.1250 REMARK 3 L TENSOR REMARK 3 L11: 0.9117 L22: 5.0316 REMARK 3 L33: 1.1757 L12: 0.8828 REMARK 3 L13: -0.9888 L23: -0.3381 REMARK 3 S TENSOR REMARK 3 S11: -0.2266 S12: 0.3543 S13: 0.4116 REMARK 3 S21: -0.2280 S22: 0.4524 S23: 0.7240 REMARK 3 S31: -0.6995 S32: 0.3530 S33: 0.1587 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 4YU7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-MAR-15. REMARK 100 THE DEPOSITION ID IS D_1000208111.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-NOV-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.1 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : LNLS REMARK 200 BEAMLINE : W01B-MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.45680 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29444 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.647 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.5 REMARK 200 DATA REDUNDANCY : 2.800 REMARK 200 R MERGE (I) : 0.06500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 27.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.71 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 <I/SIGMA(I)> 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: MOLREP REMARK 200 STARTING MODEL: 3IQ3 REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG4000, TRIS HCL PH 8.1, LITHIUM REMARK 280 SULFATE., VAPOR DIFFUSION, SITTING DROP, 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 36.04100 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL
REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA.
REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 890 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12720 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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 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 LEU B 31 CG CD1 CD2 REMARK 470 LYS B 52 CG CD CE NZ REMARK 470 LYS B 53 CG CD CE NZ REMARK 470 LYS B 60 CG CD CE NZ REMARK 470 LYS B 61 CG CD CE NZ REMARK 470 LYS B 116 CG CD CE NZ REMARK 470 PHE A 3 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS A 35 CG CD CE NZ REMARK 470 LYS A 53 CG CD CE NZ REMARK 470 THR A 55 OG1 CG2 REMARK 470 LYS A 60 CG CD CE NZ REMARK 470 LYS A 61 CG CD CE NZ REMARK 470 LYS A 69 CG CD CE NZ REMARK 470 LYS A 117 CG CD CE NZ
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 A 437 O HOH A 443 1.91 REMARK 500 O HOH A 339 O HOH A 420 1.94 REMARK 500 O HOH A 398 O HOH A 427 1.96 REMARK 500 CD2 LEU A 106 O HOH A 419 1.97 REMARK 500 OE2 GLU B 98 O HOH B 301 2.03 REMARK 500 O HOH A 433 O HOH A 436 2.04 REMARK 500 O HOH B 437 O HOH B 440 2.07 REMARK 500 OH TYR B 109 O HOH B 302 2.08 REMARK 500 O HOH A 367 O HOH A 409 2.08 REMARK 500 O HOH B 321 O HOH B 345 2.10 REMARK 500 O HOH A 374 O HOH A 401 2.12 REMARK 500 CD1 LEU A 106 O HOH A 419 2.13 REMARK 500 OH TYR B 109 OH TYR A 109 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 B 403 O HOH A 370 1455 1.87 REMARK 500 O HOH B 357 O HOH A 409 2555 1.91 REMARK 500 O HOH B 401 O HOH A 411 2455 1.93 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 ALA B 23 29.92 -150.57 REMARK 500 LEU B 31 46.60 73.46 REMARK 500 ASP B 38 -169.20 -165.04 REMARK 500 ALA A 23 15.43 -146.21 REMARK 500 LEU A 31 30.00 71.10 REMARK 500 ASN A 78 -120.75 46.08 REMARK 500 PHE A 114 52.52 -101.18 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 B 436 DISTANCE = 6.09 ANGSTROMS REMARK 525 HOH B 437 DISTANCE = 6.36 ANGSTROMS REMARK 525 HOH B 438 DISTANCE = 6.69 ANGSTROMS REMARK 525 HOH B 439 DISTANCE = 6.75 ANGSTROMS REMARK 525 HOH B 440 DISTANCE = 7.04 ANGSTROMS REMARK 525 HOH B 441 DISTANCE = 7.45 ANGSTROMS REMARK 525 HOH A 447 DISTANCE = 5.87 ANGSTROMS REMARK 525 HOH A 448 DISTANCE = 6.39 ANGSTROMS
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 PE4 B 201 REMARK 610 PE4 A 201
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PE4 B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PE4 B 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DHC B 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DHC B 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PE4 A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DHC A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DHC A 204
DBREF 4YU7 B 1 121 UNP P58399 PA2H1_BOTPI 1 121 DBREF 4YU7 A 1 121 UNP P58399 PA2H1_BOTPI 1 121
SEQRES 1 B 121 SER LEU PHE GLU LEU GLY LYS MET ILE LEU GLN GLU THR SEQRES 2 B 121 GLY LYS ASN PRO ALA LYS SER TYR GLY ALA TYR GLY CYS SEQRES 3 B 121 ASN CYS GLY VAL LEU GLY ARG GLY LYS PRO LYS ASP ALA SEQRES 4 B 121 THR ASP ARG CYS CYS TYR VAL HIS LYS CYS CYS TYR LYS SEQRES 5 B 121 LYS LEU THR GLY CYS ASN PRO LYS LYS ASP ARG TYR SER SEQRES 6 B 121 TYR SER TRP LYS ASP LYS THR ILE VAL CYS GLY GLU ASN SEQRES 7 B 121 ASN PRO CYS LEU LYS GLU LEU CYS GLU CYS ASP LYS ALA SEQRES 8 B 121 VAL ALA ILE CYS LEU ARG GLU ASN LEU GLY THR TYR ASN SEQRES 9 B 121 LYS LEU TYR ARG TYR HIS LEU LYS PRO PHE CYS LYS LYS SEQRES 10 B 121 ALA ASP ASP CYS SEQRES 1 A 121 SER LEU PHE GLU LEU GLY LYS MET ILE LEU GLN GLU THR SEQRES 2 A 121 GLY LYS ASN PRO ALA LYS SER TYR GLY ALA TYR GLY CYS SEQRES 3 A 121 ASN CYS GLY VAL LEU GLY ARG GLY LYS PRO LYS ASP ALA SEQRES 4 A 121 THR ASP ARG CYS CYS TYR VAL HIS LYS CYS CYS TYR LYS SEQRES 5 A 121 LYS LEU THR GLY CYS ASN PRO LYS LYS ASP ARG TYR SER SEQRES 6 A 121 TYR SER TRP LYS ASP LYS THR ILE VAL CYS GLY GLU ASN SEQRES 7 A 121 ASN PRO CYS LEU LYS GLU LEU CYS GLU CYS ASP LYS ALA SEQRES 8 A 121 VAL ALA ILE CYS LEU ARG GLU ASN LEU GLY THR TYR ASN SEQRES 9 A 121 LYS LEU TYR ARG TYR HIS LEU LYS PRO PHE CYS LYS LYS SEQRES 10 A 121 ALA ASP ASP CYS
HET PE4 B 201 13 HET PE4 B 202 24 HET DHC B 203 13 HET DHC B 204 13 HET PE4 A 201 14 HET SO4 A 202 5 HET DHC A 203 13 HET DHC A 204 13
HETNAM PE4 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}- HETNAM 2 PE4 ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL HETNAM DHC CAFFEIC ACID HETNAM SO4 SULFATE ION
HETSYN PE4 POLYETHYLENE GLYCOL PEG4000 HETSYN DHC 3,4-DIHYDROXYCINNAMIC ACID
FORMUL 3 PE4 3(C16 H34 O8) FORMUL 5 DHC 4(C9 H8 O4) FORMUL 8 SO4 O4 S 2- FORMUL 11 HOH *289(H2 O)
HELIX 1 AA1 SER B 1 GLY B 14 1 14 HELIX 2 AA2 ASN B 16 GLY B 22 1 7 HELIX 3 AA3 ASP B 38 LYS B 53 1 16 HELIX 4 AA4 ASN B 79 ASN B 99 1 21 HELIX 5 AA5 LEU B 100 TYR B 103 5 4 HELIX 6 AA6 ASN B 104 ARG B 108 5 5 HELIX 7 AA7 LEU B 111 CYS B 115 5 5 HELIX 8 AA8 LEU A 2 GLY A 14 1 13 HELIX 9 AA9 ASN A 16 GLY A 22 1 7 HELIX 10 AB1 ASP A 38 LYS A 53 1 16 HELIX 11 AB2 ASN A 79 ASN A 99 1 21 HELIX 12 AB3 LEU A 100 TYR A 103 5 4 HELIX 13 AB4 ASN A 104 ARG A 108 5 5 HELIX 14 AB5 LEU A 111 CYS A 115 5 5
SHEET 1 AA1 2 TYR B 66 LYS B 69 0 SHEET 2 AA1 2 THR B 72 CYS B 75 -1 O VAL B 74 N SER B 67 SHEET 1 AA2 2 TYR A 66 LYS A 69 0 SHEET 2 AA2 2 THR A 72 CYS A 75 -1 O VAL A 74 N SER A 67
SSBOND 1 CYS B 26 CYS B 115 1555 1555 2.05 SSBOND 2 CYS B 28 CYS B 44 1555 1555 2.06 SSBOND 3 CYS B 43 CYS B 95 1555 1555 2.03 SSBOND 4 CYS B 49 CYS B 121 1555 1555 2.17 SSBOND 5 CYS B 50 CYS B 88 1555 1555 2.03 SSBOND 6 CYS B 57 CYS B 81 1555 1555 2.03 SSBOND 7 CYS B 75 CYS B 86 1555 1555 2.03 SSBOND 8 CYS A 26 CYS A 115 1555 1555 2.03 SSBOND 9 CYS A 28 CYS A 44 1555 1555 2.05 SSBOND 10 CYS A 43 CYS A 95 1555 1555 2.04 SSBOND 11 CYS A 49 CYS A 121 1555 1555 2.20 SSBOND 12 CYS A 50 CYS A 88 1555 1555 2.04 SSBOND 13 CYS A 57 CYS A 81 1555 1555 2.04 SSBOND 14 CYS A 75 CYS A 86 1555 1555 2.04
SITE 1 AC1 4 PRO A 113 GLY B 6 PRO B 17 TYR B 21 SITE 1 AC2 6 PHE B 3 LYS B 7 LEU B 10 GLN B 11 SITE 2 AC2 6 TYR B 66 TRP B 68 SITE 1 AC3 7 LEU A 111 LYS B 15 ASN B 16 PRO B 80 SITE 2 AC3 7 HOH B 307 HOH B 314 HOH B 357 SITE 1 AC4 5 LYS B 19 THR B 55 LYS B 105 ARG B 108 SITE 2 AC4 5 HOH B 307 SITE 1 AC5 5 LEU A 2 GLY A 6 PRO A 17 TYR A 21 SITE 2 AC5 5 HOH A 307 SITE 1 AC6 6 GLY A 32 ARG A 33 LYS A 52 HOH A 343 SITE 2 AC6 6 HOH A 346 HOH A 364 SITE 1 AC7 10 THR A 72 ILE A 94 ARG A 97 GLU A 98 SITE 2 AC7 10 HOH A 303 HOH A 309 HOH A 359 LYS B 35 SITE 3 AC7 10 PRO B 36 ARG B 42 SITE 1 AC8 8 LYS A 15 LYS A 19 LYS A 105 ARG A 108 SITE 2 AC8 8 HOH A 301 HOH A 370 THR B 55 GLY B 56
CRYST1 39.233 72.082 44.644 90.00 102.08 90.00 P 1 21 1 4
ORIGX1 1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 0.025489 0.000000 0.005455 0.00000
SCALE2 0.000000 0.013873 0.000000 0.00000
SCALE3 0.000000 0.000000 0.022907 0.00000