PDB Short entry for 3ZE4 HEADER TRANSFERASE 03-DEC-12 3ZE4 TITLE CRYSTAL STRUCTURE OF THE INTEGRAL MEMBRANE DIACYLGLYCEROL KINASE - TITLE 2 WILD-TYPE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIACYLGLYCEROL KINASE; COMPND 3 CHAIN: A, B, C; COMPND 4 SYNONYM: DAGK, DIGLYCERIDE KINASE, DGK; COMPND 5 EC: 2.7.1.107; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI K-12; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: WH1061; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PTRCHISB; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PTRCHISB_DGKA_WILD-TYPE; SOURCE 10 OTHER_DETAILS: THE WILD-TYPE GENE WAS SYNTHESIZED BASED ON THE DGKA SOURCE 11 NUCLEOTIDE SEQUENCE OF ESCHERICHIA COLI K12, WITH ADDITIONAL SOURCE 12 NUCLEOTIDES ENCODING HIS TAG SEQUENCES AT THE N-TERMINUS. KEYWDS TRANSFERASE, LIPID METABOLISM, IN MESO CRYSTALLISATION, LIPID CUBIC KEYWDS 2 PHASE, LIPIDIC MESOPHASE, MEMBRANE PROTEIN, MONOACYLGLYCEROL, 7.8 KEYWDS 3 MAG EXPDTA X-RAY DIFFRACTION MDLTYP P ATOMS ONLY, CHAIN D, E, F AUTHOR D.LI,J.A.LYONS,V.E.PYE,L.VOGELEY,D.ARAGAO,M.CAFFREY REVDAT 7 07-FEB-24 3ZE4 1 REMARK REVDAT 6 29-MAR-23 3ZE4 1 AUTHOR REVDAT 5 03-APR-19 3ZE4 1 REMARK REVDAT 4 06-MAR-19 3ZE4 1 REMARK REVDAT 3 05-JUN-13 3ZE4 1 JRNL REVDAT 2 29-MAY-13 3ZE4 1 JRNL REVDAT 1 22-MAY-13 3ZE4 0 JRNL AUTH D.LI,J.A.LYONS,V.E.PYE,L.VOGELEY,D.ARAGAO,C.P.KENYON, JRNL AUTH 2 S.T.A.SHAH,C.DOHERTY,M.AHERNE,M.CAFFREY JRNL TITL CRYSTAL STRUCTURE OF THE INTEGRAL MEMBRANE DIACYLGLYCEROL JRNL TITL 2 KINASE. JRNL REF NATURE V. 497 521 2013 JRNL REFN ISSN 0028-0836 JRNL PMID 23676677 JRNL DOI 10.1038/NATURE12179 REMARK 2 REMARK 2 RESOLUTION. 3.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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) : 3.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.23 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.7 REMARK 3 NUMBER OF REFLECTIONS : 7069 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.286 REMARK 3 R VALUE (WORKING SET) : 0.285 REMARK 3 FREE R VALUE : 0.312 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.700 REMARK 3 FREE R VALUE TEST SET COUNT : 333 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 39.2278 - 4.6624 0.95 3373 176 0.2763 0.3063 REMARK 3 2 4.6624 - 3.7016 0.98 3363 157 0.3028 0.3250 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.30 REMARK 3 SHRINKAGE RADIUS : 1.10 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.390 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 37.450 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 130.2 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 150.0 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 : 0.005 2499 REMARK 3 ANGLE : 0.795 3405 REMARK 3 CHIRALITY : 0.052 431 REMARK 3 PLANARITY : 0.002 403 REMARK 3 DIHEDRAL : 13.044 850 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 7:17) REMARK 3 ORIGIN FOR THE GROUP (A): -69.1004 28.1841 15.9771 REMARK 3 T TENSOR REMARK 3 T11: 1.4275 T22: 1.4829 REMARK 3 T33: 1.4305 T12: 0.5253 REMARK 3 T13: 0.0174 T23: 0.3819 REMARK 3 L TENSOR REMARK 3 L11: 2.9160 L22: 0.8620 REMARK 3 L33: 0.6879 L12: 1.5870 REMARK 3 L13: 1.4313 L23: 0.7664 REMARK 3 S TENSOR REMARK 3 S11: -0.9293 S12: -0.6451 S13: 2.4374 REMARK 3 S21: -0.4690 S22: -0.5254 S23: 0.2201 REMARK 3 S31: -1.1222 S32: -0.7439 S33: -0.3126 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESID 18:27) REMARK 3 ORIGIN FOR THE GROUP (A): -63.1984 12.7771 15.0365 REMARK 3 T TENSOR REMARK 3 T11: 1.8479 T22: 1.5312 REMARK 3 T33: 1.0787 T12: 0.3162 REMARK 3 T13: -0.1006 T23: 0.0846 REMARK 3 L TENSOR REMARK 3 L11: 0.0359 L22: 0.1061 REMARK 3 L33: 0.0312 L12: -0.0601 REMARK 3 L13: 0.0331 L23: -0.0608 REMARK 3 S TENSOR REMARK 3 S11: 0.0786 S12: 0.2373 S13: -0.8514 REMARK 3 S21: -1.0608 S22: 1.2221 S23: 1.0523 REMARK 3 S31: 1.1092 S32: -0.9254 S33: 0.0126 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN A AND RESID 28:37) REMARK 3 ORIGIN FOR THE GROUP (A): -55.0282 7.1500 20.2831 REMARK 3 T TENSOR REMARK 3 T11: 1.9878 T22: 1.6765 REMARK 3 T33: 1.7010 T12: 0.2769 REMARK 3 T13: 0.1692 T23: 0.3733 REMARK 3 L TENSOR REMARK 3 L11: 0.3455 L22: 0.5269 REMARK 3 L33: 0.1831 L12: 0.4269 REMARK 3 L13: -0.2524 L23: -0.3134 REMARK 3 S TENSOR REMARK 3 S11: -1.3517 S12: 0.1189 S13: -0.7963 REMARK 3 S21: -1.3989 S22: 1.5755 S23: -0.4174 REMARK 3 S31: 0.6970 S32: 0.6337 S33: -0.0060 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN A AND RESID 38:57) REMARK 3 ORIGIN FOR THE GROUP (A): -54.3123 14.2812 39.3475 REMARK 3 T TENSOR REMARK 3 T11: 1.2348 T22: 1.0613 REMARK 3 T33: 1.6679 T12: 0.4822 REMARK 3 T13: 0.2496 T23: 0.1812 REMARK 3 L TENSOR REMARK 3 L11: 2.9750 L22: 0.4582 REMARK 3 L33: 1.8956 L12: 1.0642 REMARK 3 L13: -1.8491 L23: -0.8298 REMARK 3 S TENSOR REMARK 3 S11: -0.4091 S12: -1.6446 S13: -0.9914 REMARK 3 S21: 0.8465 S22: 0.6253 S23: 0.7133 REMARK 3 S31: -1.2961 S32: -0.1778 S33: -0.1582 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN A AND RESID 58:77) REMARK 3 ORIGIN FOR THE GROUP (A): -51.1688 16.9993 21.4484 REMARK 3 T TENSOR REMARK 3 T11: 0.9031 T22: 1.1110 REMARK 3 T33: 0.8159 T12: 0.4887 REMARK 3 T13: 0.2496 T23: 0.1650 REMARK 3 L TENSOR REMARK 3 L11: 0.0796 L22: 1.6242 REMARK 3 L33: 9.9206 L12: 0.1533 REMARK 3 L13: 0.0046 L23: -3.4985 REMARK 3 S TENSOR REMARK 3 S11: 0.1383 S12: -0.1791 S13: 0.1852 REMARK 3 S21: -0.7137 S22: 0.6136 S23: -0.5882 REMARK 3 S31: 1.6594 S32: -0.8447 S33: 0.2963 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: (CHAIN A AND RESID 78:87) REMARK 3 ORIGIN FOR THE GROUP (A): -49.3636 14.4590 -1.7017 REMARK 3 T TENSOR REMARK 3 T11: 1.6760 T22: 2.1565 REMARK 3 T33: 1.1111 T12: 0.1577 REMARK 3 T13: 0.0479 T23: -0.3554 REMARK 3 L TENSOR REMARK 3 L11: 1.3618 L22: 0.7043 REMARK 3 L33: 1.3759 L12: 0.9691 REMARK 3 L13: -1.3629 L23: -0.9559 REMARK 3 S TENSOR REMARK 3 S11: -1.4176 S12: 0.7891 S13: -2.3586 REMARK 3 S21: -1.5787 S22: 0.9573 S23: -0.6751 REMARK 3 S31: 2.2057 S32: 1.4440 S33: -0.0694 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: (CHAIN A AND RESID 88:97) REMARK 3 ORIGIN FOR THE GROUP (A): -40.6738 15.3635 7.2886 REMARK 3 T TENSOR REMARK 3 T11: 2.9975 T22: 1.6473 REMARK 3 T33: 1.4082 T12: 0.5029 REMARK 3 T13: 0.5096 T23: -0.2449 REMARK 3 L TENSOR REMARK 3 L11: 7.3223 L22: 0.4796 REMARK 3 L33: 0.3144 L12: 1.8729 REMARK 3 L13: 1.5199 L23: 0.3918 REMARK 3 S TENSOR REMARK 3 S11: 0.1004 S12: 2.2074 S13: 0.6042 REMARK 3 S21: -0.5639 S22: 1.1807 S23: -1.1984 REMARK 3 S31: -1.0134 S32: 0.2064 S33: 0.1544 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: (CHAIN A AND RESID 98:112) REMARK 3 ORIGIN FOR THE GROUP (A): -42.9454 14.0278 27.4080 REMARK 3 T TENSOR REMARK 3 T11: 0.8978 T22: 0.5646 REMARK 3 T33: 1.1679 T12: 1.3263 REMARK 3 T13: 0.0204 T23: -0.3170 REMARK 3 L TENSOR REMARK 3 L11: 0.9806 L22: 0.1078 REMARK 3 L33: 0.6172 L12: 0.0035 REMARK 3 L13: -0.0079 L23: -0.2502 REMARK 3 S TENSOR REMARK 3 S11: -0.0765 S12: 0.9188 S13: -0.6717 REMARK 3 S21: -0.5290 S22: -0.2627 S23: 0.1373 REMARK 3 S31: 0.2421 S32: 0.2054 S33: -1.5171 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: (CHAIN A AND RESID 113:120) REMARK 3 ORIGIN FOR THE GROUP (A): -42.9166 12.8390 43.3136 REMARK 3 T TENSOR REMARK 3 T11: 1.7539 T22: 0.0461 REMARK 3 T33: 0.7730 T12: 1.2023 REMARK 3 T13: -0.0571 T23: 0.7633 REMARK 3 L TENSOR REMARK 3 L11: 0.1106 L22: 1.0040 REMARK 3 L33: 1.7825 L12: 0.0928 REMARK 3 L13: 0.1323 L23: -1.0249 REMARK 3 S TENSOR REMARK 3 S11: -0.4401 S12: -0.1692 S13: -0.2539 REMARK 3 S21: -0.1766 S22: -0.3456 S23: 0.3792 REMARK 3 S31: 0.2005 S32: 0.2932 S33: -2.1656 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: (CHAIN B AND RESID 8:29) REMARK 3 ORIGIN FOR THE GROUP (A): -43.5985 39.4433 12.8263 REMARK 3 T TENSOR REMARK 3 T11: 1.4444 T22: 1.7915 REMARK 3 T33: 1.1720 T12: 0.2750 REMARK 3 T13: 0.0731 T23: 0.5111 REMARK 3 L TENSOR REMARK 3 L11: 0.2410 L22: 1.7073 REMARK 3 L33: 0.9535 L12: 0.3047 REMARK 3 L13: -0.2491 L23: 0.6327 REMARK 3 S TENSOR REMARK 3 S11: -0.1789 S12: -0.1396 S13: -0.5357 REMARK 3 S21: -0.9324 S22: -0.0006 S23: -0.5447 REMARK 3 S31: -1.4867 S32: 0.6251 S33: 0.0571 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: (CHAIN B AND RESID 30:51) REMARK 3 ORIGIN FOR THE GROUP (A): -55.5610 38.4799 30.7327 REMARK 3 T TENSOR REMARK 3 T11: 2.1584 T22: 0.5539 REMARK 3 T33: 0.8308 T12: 0.8686 REMARK 3 T13: -0.1583 T23: 0.1161 REMARK 3 L TENSOR REMARK 3 L11: 1.0967 L22: 1.5927 REMARK 3 L33: 2.9228 L12: -0.2334 REMARK 3 L13: 0.1274 L23: -0.1561 REMARK 3 S TENSOR REMARK 3 S11: 0.5172 S12: -0.0070 S13: -0.3747 REMARK 3 S21: 0.2569 S22: 0.7267 S23: 0.2144 REMARK 3 S31: 0.3498 S32: 0.2481 S33: 0.2260 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: (CHAIN B AND RESID 52:91) REMARK 3 ORIGIN FOR THE GROUP (A): -52.6914 27.9560 15.4786 REMARK 3 T TENSOR REMARK 3 T11: 1.2096 T22: 0.9308 REMARK 3 T33: 0.5875 T12: 0.4519 REMARK 3 T13: -0.0441 T23: 0.0212 REMARK 3 L TENSOR REMARK 3 L11: 2.0242 L22: 0.3019 REMARK 3 L33: 0.6453 L12: 0.2888 REMARK 3 L13: -0.6660 L23: -0.4618 REMARK 3 S TENSOR REMARK 3 S11: -0.4002 S12: -0.0140 S13: -0.0718 REMARK 3 S21: 0.5355 S22: 0.2351 S23: 0.3940 REMARK 3 S31: -0.2220 S32: -0.7418 S33: -0.0012 REMARK 3 TLS GROUP : 13 REMARK 3 SELECTION: (CHAIN B AND RESID 92:120) REMARK 3 ORIGIN FOR THE GROUP (A): -58.8382 25.0791 28.7914 REMARK 3 T TENSOR REMARK 3 T11: 1.3342 T22: 0.6132 REMARK 3 T33: 0.9720 T12: 0.4720 REMARK 3 T13: 0.2131 T23: 0.1234 REMARK 3 L TENSOR REMARK 3 L11: 2.3732 L22: 3.4491 REMARK 3 L33: 8.3477 L12: 0.9260 REMARK 3 L13: 2.6385 L23: 2.6336 REMARK 3 S TENSOR REMARK 3 S11: -0.1856 S12: -0.1535 S13: 0.2655 REMARK 3 S21: 1.4404 S22: -1.1235 S23: 0.5491 REMARK 3 S31: 1.1829 S32: -1.0276 S33: -0.4338 REMARK 3 TLS GROUP : 14 REMARK 3 SELECTION: (CHAIN C AND RESID 28:51) REMARK 3 ORIGIN FOR THE GROUP (A): -30.6461 24.5359 29.1579 REMARK 3 T TENSOR REMARK 3 T11: 1.2047 T22: 2.3538 REMARK 3 T33: 1.7000 T12: 0.2716 REMARK 3 T13: -0.0913 T23: 0.1034 REMARK 3 L TENSOR REMARK 3 L11: 0.5614 L22: 0.5918 REMARK 3 L33: 0.0569 L12: 0.5521 REMARK 3 L13: -0.0915 L23: -0.0470 REMARK 3 S TENSOR REMARK 3 S11: 0.6140 S12: 0.9956 S13: -0.9800 REMARK 3 S21: 0.0667 S22: 0.9218 S23: 0.4811 REMARK 3 S31: 0.6297 S32: 1.0462 S33: 0.0026 REMARK 3 TLS GROUP : 15 REMARK 3 SELECTION: (CHAIN C AND RESID 52:119) REMARK 3 ORIGIN FOR THE GROUP (A): -41.6678 28.9114 20.0409 REMARK 3 T TENSOR REMARK 3 T11: 0.9544 T22: 1.3640 REMARK 3 T33: 0.9091 T12: 0.3429 REMARK 3 T13: -0.0150 T23: 0.0173 REMARK 3 L TENSOR REMARK 3 L11: 3.3489 L22: 3.1697 REMARK 3 L33: 1.6821 L12: 0.2620 REMARK 3 L13: -0.8137 L23: -1.5285 REMARK 3 S TENSOR REMARK 3 S11: -1.0852 S12: 0.3597 S13: 0.2274 REMARK 3 S21: 0.5158 S22: -0.1178 S23: -0.8416 REMARK 3 S31: -1.0830 S32: 2.3514 S33: -0.0349 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : 1 REMARK 3 NCS GROUP : 1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: CHAIN A AND RESSEQ 11 OR CHAIN A AND REMARK 3 RESSEQ 13:15 OR CHAIN A AND RESSEQ 18:20 REMARK 3 OR CHAIN A AND RESSEQ 23:26 OR CHAIN A REMARK 3 AND RESSEQ 35 OR CHAIN A AND RESSEQ 37 OR REMARK 3 CHAIN A AND RESSEQ 39:46 OR CHAIN A AND REMARK 3 RESSEQ 52:54 OR CHAIN A AND RESSEQ 56:57 REMARK 3 OR CHAIN A AND RESSEQ 63:68 OR CHAIN A REMARK 3 AND RESSEQ 70:72 OR CHAIN A AND RESSEQ 74: REMARK 3 75 OR CHAIN A AND RESSEQ 77:80 OR CHAIN A REMARK 3 AND RESSEQ 97:118 REMARK 3 SELECTION : CHAIN B AND RESSEQ 11 OR CHAIN B AND REMARK 3 RESSEQ 13:15 OR CHAIN B AND RESSEQ 18:20 REMARK 3 OR CHAIN B AND RESSEQ 23:26 OR CHAIN B REMARK 3 AND RESSEQ 35 OR CHAIN B AND RESSEQ 37 OR REMARK 3 CHAIN B AND RESSEQ 39:46 OR CHAIN B AND REMARK 3 RESSEQ 52:54 OR CHAIN B AND RESSEQ 56:57 REMARK 3 OR CHAIN B AND RESSEQ 63:68 OR CHAIN B REMARK 3 AND RESSEQ 70:72 OR CHAIN B AND RESSEQ 74: REMARK 3 75 OR CHAIN B AND RESSEQ 77:80 OR CHAIN B REMARK 3 AND RESSEQ 97:118 REMARK 3 ATOM PAIRS NUMBER : 451 REMARK 3 RMSD : 0.022 REMARK 3 NCS OPERATOR : 2 REMARK 3 REFERENCE SELECTION: CHAIN A AND RESSEQ 11 OR CHAIN A AND REMARK 3 RESSEQ 13:15 OR CHAIN A AND RESSEQ 18:20 REMARK 3 OR CHAIN A AND RESSEQ 23:26 OR CHAIN A REMARK 3 AND RESSEQ 35 OR CHAIN A AND RESSEQ 37 OR REMARK 3 CHAIN A AND RESSEQ 39:46 OR CHAIN A AND REMARK 3 RESSEQ 52:54 OR CHAIN A AND RESSEQ 56:57 REMARK 3 OR CHAIN A AND RESSEQ 63:68 OR CHAIN A REMARK 3 AND RESSEQ 70:72 OR CHAIN A AND RESSEQ 74: REMARK 3 75 OR CHAIN A AND RESSEQ 77:80 OR CHAIN A REMARK 3 AND RESSEQ 97:118 REMARK 3 SELECTION : CHAIN C AND RESSEQ 11 OR CHAIN C AND REMARK 3 RESSEQ 13:15 OR CHAIN C AND RESSEQ 18:20 REMARK 3 OR CHAIN C AND RESSEQ 23:26 OR CHAIN C REMARK 3 AND RESSEQ 35 OR CHAIN C AND RESSEQ 37 OR REMARK 3 CHAIN C AND RESSEQ 39:46 OR CHAIN C AND REMARK 3 RESSEQ 52:54 OR CHAIN C AND RESSEQ 56:57 REMARK 3 OR CHAIN C AND RESSEQ 63:68 OR CHAIN C REMARK 3 AND RESSEQ 70:72 OR CHAIN C AND RESSEQ 74: REMARK 3 75 OR CHAIN AND RESSEQ 97:118 REMARK 3 ATOM PAIRS NUMBER : 343 REMARK 3 RMSD : 0.019 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3ZE4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 03-DEC-12. REMARK 100 THE DEPOSITION ID IS D_1290054574. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-JUN-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 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-B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.03306 REMARK 200 MONOCHROMATOR : SI(111) DOUBLE CRYSTAL REMARK 200 OPTICS : K-B PAIR OF BIOMORPH MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7069 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.700 REMARK 200 RESOLUTION RANGE LOW (A) : 39.230 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.7 REMARK 200 DATA REDUNDANCY : 4.800 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.70 REMARK 200 R MERGE FOR SHELL (I) : 0.72000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.000 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: PDB ENTRY 3ZE5 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 67.16 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.74 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 3-5 %(V/V) 2-METHYL-2, 4-PENTANEDIOL, REMARK 280 0.1 M SODIUM CHLORIDE, 0.1 M LITHIUM NITRATE, 0.1 M SODIUM REMARK 280 CITRATE/HCL PH 5.6. CRYSTALLIZED USING THE IN MESO (LIPIDIC REMARK 280 CUBIC PHASE) METHOD AT 4 DEGREE CELSIUS WITH THE 7.8 REMARK 280 MONOACYLGLYCEROL (7.8 MAG) AS THE HOSTING LIPID., TEMPERATURE REMARK 280 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 65.63333 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 131.26667 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 131.26667 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 65.63333 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7230 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16300 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -82.7 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 -8 REMARK 465 HIS A -7 REMARK 465 HIS A -6 REMARK 465 HIS A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 GLU A -1 REMARK 465 LEU A 0 REMARK 465 ALA A 1 REMARK 465 ASN A 2 REMARK 465 ASN A 3 REMARK 465 THR A 4 REMARK 465 THR A 5 REMARK 465 GLY A 6 REMARK 465 GLY A 121 REMARK 465 GLY B -8 REMARK 465 HIS B -7 REMARK 465 HIS B -6 REMARK 465 HIS B -5 REMARK 465 HIS B -4 REMARK 465 HIS B -3 REMARK 465 HIS B -2 REMARK 465 GLU B -1 REMARK 465 LEU B 0 REMARK 465 ALA B 1 REMARK 465 ASN B 2 REMARK 465 ASN B 3 REMARK 465 THR B 4 REMARK 465 THR B 5 REMARK 465 GLY B 121 REMARK 465 GLY C -8 REMARK 465 HIS C -7 REMARK 465 HIS C -6 REMARK 465 HIS C -5 REMARK 465 HIS C -4 REMARK 465 HIS C -3 REMARK 465 HIS C -2 REMARK 465 GLU C -1 REMARK 465 LEU C 0 REMARK 465 ALA C 1 REMARK 465 ASN C 2 REMARK 465 ASN C 3 REMARK 465 THR C 4 REMARK 465 THR C 5 REMARK 465 GLY C 6 REMARK 465 PHE C 7 REMARK 465 THR C 8 REMARK 465 ARG C 9 REMARK 465 ILE C 10 REMARK 465 ILE C 11 REMARK 465 LYS C 12 REMARK 465 ALA C 13 REMARK 465 ALA C 14 REMARK 465 GLY C 15 REMARK 465 TYR C 16 REMARK 465 SER C 17 REMARK 465 TRP C 18 REMARK 465 LYS C 19 REMARK 465 GLY C 20 REMARK 465 LEU C 21 REMARK 465 ARG C 22 REMARK 465 ALA C 23 REMARK 465 ALA C 24 REMARK 465 TRP C 25 REMARK 465 ILE C 26 REMARK 465 ASN C 27 REMARK 465 PHE C 120 REMARK 465 GLY C 121 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3ZE3 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE INTEGRAL MEMBRANE DIACYLGLYCEROL KINASE - REMARK 900 DELTA7 REMARK 900 RELATED ID: 3ZE5 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE INTEGRAL MEMBRANE DIACYLGLYCEROL KINASE - REMARK 900 DELTA4 DBREF 3ZE4 A 1 121 UNP P0ABN1 KDGL_ECOLI 2 122 DBREF 3ZE4 B 1 121 UNP P0ABN1 KDGL_ECOLI 2 122 DBREF 3ZE4 C 1 121 UNP P0ABN1 KDGL_ECOLI 2 122 SEQADV 3ZE4 GLY A -8 UNP P0ABN1 EXPRESSION TAG SEQADV 3ZE4 HIS A -7 UNP P0ABN1 EXPRESSION TAG SEQADV 3ZE4 HIS A -6 UNP P0ABN1 EXPRESSION TAG SEQADV 3ZE4 HIS A -5 UNP P0ABN1 EXPRESSION TAG SEQADV 3ZE4 HIS A -4 UNP P0ABN1 EXPRESSION TAG SEQADV 3ZE4 HIS A -3 UNP P0ABN1 EXPRESSION TAG SEQADV 3ZE4 HIS A -2 UNP P0ABN1 EXPRESSION TAG SEQADV 3ZE4 GLU A -1 UNP P0ABN1 EXPRESSION TAG SEQADV 3ZE4 LEU A 0 UNP P0ABN1 EXPRESSION TAG SEQADV 3ZE4 GLY B -8 UNP P0ABN1 EXPRESSION TAG SEQADV 3ZE4 HIS B -7 UNP P0ABN1 EXPRESSION TAG SEQADV 3ZE4 HIS B -6 UNP P0ABN1 EXPRESSION TAG SEQADV 3ZE4 HIS B -5 UNP P0ABN1 EXPRESSION TAG SEQADV 3ZE4 HIS B -4 UNP P0ABN1 EXPRESSION TAG SEQADV 3ZE4 HIS B -3 UNP P0ABN1 EXPRESSION TAG SEQADV 3ZE4 HIS B -2 UNP P0ABN1 EXPRESSION TAG SEQADV 3ZE4 GLU B -1 UNP P0ABN1 EXPRESSION TAG SEQADV 3ZE4 LEU B 0 UNP P0ABN1 EXPRESSION TAG SEQADV 3ZE4 GLY C -8 UNP P0ABN1 EXPRESSION TAG SEQADV 3ZE4 HIS C -7 UNP P0ABN1 EXPRESSION TAG SEQADV 3ZE4 HIS C -6 UNP P0ABN1 EXPRESSION TAG SEQADV 3ZE4 HIS C -5 UNP P0ABN1 EXPRESSION TAG SEQADV 3ZE4 HIS C -4 UNP P0ABN1 EXPRESSION TAG SEQADV 3ZE4 HIS C -3 UNP P0ABN1 EXPRESSION TAG SEQADV 3ZE4 HIS C -2 UNP P0ABN1 EXPRESSION TAG SEQADV 3ZE4 GLU C -1 UNP P0ABN1 EXPRESSION TAG SEQADV 3ZE4 LEU C 0 UNP P0ABN1 EXPRESSION TAG SEQRES 1 A 130 GLY HIS HIS HIS HIS HIS HIS GLU LEU ALA ASN ASN THR SEQRES 2 A 130 THR GLY PHE THR ARG ILE ILE LYS ALA ALA GLY TYR SER SEQRES 3 A 130 TRP LYS GLY LEU ARG ALA ALA TRP ILE ASN GLU ALA ALA SEQRES 4 A 130 PHE ARG GLN GLU GLY VAL ALA VAL LEU LEU ALA VAL VAL SEQRES 5 A 130 ILE ALA CYS TRP LEU ASP VAL ASP ALA ILE THR ARG VAL SEQRES 6 A 130 LEU LEU ILE SER SER VAL MET LEU VAL MET ILE VAL GLU SEQRES 7 A 130 ILE LEU ASN SER ALA ILE GLU ALA VAL VAL ASP ARG ILE SEQRES 8 A 130 GLY SER GLU TYR HIS GLU LEU SER GLY ARG ALA LYS ASP SEQRES 9 A 130 MET GLY SER ALA ALA VAL LEU ILE ALA ILE ILE VAL ALA SEQRES 10 A 130 VAL ILE THR TRP CYS ILE LEU LEU TRP SER HIS PHE GLY SEQRES 1 B 130 GLY HIS HIS HIS HIS HIS HIS GLU LEU ALA ASN ASN THR SEQRES 2 B 130 THR GLY PHE THR ARG ILE ILE LYS ALA ALA GLY TYR SER SEQRES 3 B 130 TRP LYS GLY LEU ARG ALA ALA TRP ILE ASN GLU ALA ALA SEQRES 4 B 130 PHE ARG GLN GLU GLY VAL ALA VAL LEU LEU ALA VAL VAL SEQRES 5 B 130 ILE ALA CYS TRP LEU ASP VAL ASP ALA ILE THR ARG VAL SEQRES 6 B 130 LEU LEU ILE SER SER VAL MET LEU VAL MET ILE VAL GLU SEQRES 7 B 130 ILE LEU ASN SER ALA ILE GLU ALA VAL VAL ASP ARG ILE SEQRES 8 B 130 GLY SER GLU TYR HIS GLU LEU SER GLY ARG ALA LYS ASP SEQRES 9 B 130 MET GLY SER ALA ALA VAL LEU ILE ALA ILE ILE VAL ALA SEQRES 10 B 130 VAL ILE THR TRP CYS ILE LEU LEU TRP SER HIS PHE GLY SEQRES 1 C 130 GLY HIS HIS HIS HIS HIS HIS GLU LEU ALA ASN ASN THR SEQRES 2 C 130 THR GLY PHE THR ARG ILE ILE LYS ALA ALA GLY TYR SER SEQRES 3 C 130 TRP LYS GLY LEU ARG ALA ALA TRP ILE ASN GLU ALA ALA SEQRES 4 C 130 PHE ARG GLN GLU GLY VAL ALA VAL LEU LEU ALA VAL VAL SEQRES 5 C 130 ILE ALA CYS TRP LEU ASP VAL ASP ALA ILE THR ARG VAL SEQRES 6 C 130 LEU LEU ILE SER SER VAL MET LEU VAL MET ILE VAL GLU SEQRES 7 C 130 ILE LEU ASN SER ALA ILE GLU ALA VAL VAL ASP ARG ILE SEQRES 8 C 130 GLY SER GLU TYR HIS GLU LEU SER GLY ARG ALA LYS ASP SEQRES 9 C 130 MET GLY SER ALA ALA VAL LEU ILE ALA ILE ILE VAL ALA SEQRES 10 C 130 VAL ILE THR TRP CYS ILE LEU LEU TRP SER HIS PHE GLY HELIX 1 1 PHE A 7 GLU A 28 1 22 HELIX 2 2 ALA A 30 LEU A 48 1 19 HELIX 3 3 ASP A 51 GLY A 83 1 33 HELIX 4 4 SER A 90 PHE A 120 1 31 HELIX 5 5 PHE B 7 ASN B 27 1 21 HELIX 6 6 ALA B 30 LEU B 48 1 19 HELIX 7 7 ASP B 51 TYR B 86 1 36 HELIX 8 8 GLY B 91 PHE B 120 1 30 HELIX 9 9 ALA C 30 LEU C 48 1 19 HELIX 10 10 ASP C 51 ILE C 82 1 32 HELIX 11 11 HIS C 87 HIS C 119 1 33 CRYST1 74.970 74.970 196.900 90.00 90.00 120.00 P 31 2 1 18 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 0.013339 0.007701 0.000000 0.00000 SCALE2 0.000000 0.015402 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005079 0.00000 MTRIX1 1 -0.514200 0.857600 0.009619 -93.03000 1 MTRIX2 1 -0.847100 -0.509600 0.151100 -8.11600 1 MTRIX3 1 0.134500 0.069540 0.988500 5.14300 1 MTRIX1 2 -0.489600 -0.861800 0.132600 -53.50000 1 MTRIX2 2 0.871900 -0.485300 0.065590 75.43000 1 MTRIX3 2 0.007839 0.147700 0.989000 -2.99600 1