PDB Short entry for 4YMK HEADER OXIDOREDUCTASE 06-MAR-15 4YMK TITLE CRYSTAL STRUCTURE OF STEAROYL-COENZYME A DESATURASE 1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ACYL-COA DESATURASE 1; COMPND 3 CHAIN: A, D; COMPND 4 FRAGMENT: UNP RESIDUES 24-355; COMPND 5 SYNONYM: DELTA(9)-DESATURASE 1, DELTA-9 DESATURASE 1, FATTY ACID COMPND 6 DESATURASE 1, STEAROYL-COA DESATURASE 1; COMPND 7 EC: 1.14.19.1; COMPND 8 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: SCD1; SOURCE 6 EXPRESSION_SYSTEM: TRICHOPLUSIA NI; SOURCE 7 EXPRESSION_SYSTEM_COMMON: CABBAGE LOOPER; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 7111; SOURCE 9 EXPRESSION_SYSTEM_CELL_LINE: HIGH FIVE; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PFASTBACDUAL KEYWDS DIMETAL CENTER, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.BAI,J.G.MCCOY,K.R.RAJASHANKAR,M.ZHOU REVDAT 8 28-FEB-24 4YMK 1 LINK REVDAT 7 25-DEC-19 4YMK 1 REMARK REVDAT 6 22-NOV-17 4YMK 1 REMARK REVDAT 5 06-SEP-17 4YMK 1 REMARK REVDAT 4 08-JUN-16 4YMK 1 HETATM REVDAT 3 19-AUG-15 4YMK 1 JRNL REVDAT 2 08-JUL-15 4YMK 1 KEYWDS REVDAT 1 24-JUN-15 4YMK 0 JRNL AUTH Y.BAI,J.G.MCCOY,E.J.LEVIN,P.SOBRADO,K.R.RAJASHANKAR,B.G.FOX, JRNL AUTH 2 M.ZHOU JRNL TITL X-RAY STRUCTURE OF A MAMMALIAN STEAROYL-COA DESATURASE. JRNL REF NATURE V. 524 252 2015 JRNL REFN ESSN 1476-4687 JRNL PMID 26098370 JRNL DOI 10.1038/NATURE14549 REMARK 2 REMARK 2 RESOLUTION. 2.61 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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) : 2.61 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.41 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 3 NUMBER OF REFLECTIONS : 38016 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.204 REMARK 3 R VALUE (WORKING SET) : 0.203 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.260 REMARK 3 FREE R VALUE TEST SET COUNT : 1999 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 47.4188 - 6.2749 0.97 2731 152 0.1810 0.1835 REMARK 3 2 6.2749 - 4.9823 0.99 2667 147 0.2017 0.2181 REMARK 3 3 4.9823 - 4.3530 0.98 2600 145 0.2022 0.2664 REMARK 3 4 4.3530 - 3.9552 1.00 2626 145 0.2104 0.2261 REMARK 3 5 3.9552 - 3.6719 0.98 2549 142 0.2058 0.2276 REMARK 3 6 3.6719 - 3.4554 0.99 2617 145 0.2051 0.2433 REMARK 3 7 3.4554 - 3.2824 0.99 2581 144 0.2025 0.2468 REMARK 3 8 3.2824 - 3.1396 0.99 2583 143 0.2108 0.2260 REMARK 3 9 3.1396 - 3.0187 0.96 2512 139 0.2061 0.2757 REMARK 3 10 3.0187 - 2.9146 0.99 2550 141 0.2058 0.2400 REMARK 3 11 2.9146 - 2.8235 0.98 2554 142 0.1997 0.2632 REMARK 3 12 2.8235 - 2.7428 0.98 2520 141 0.2090 0.2790 REMARK 3 13 2.7428 - 2.6706 0.97 2509 139 0.2160 0.2407 REMARK 3 14 2.6706 - 2.6054 0.93 2418 134 0.2212 0.2650 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) : 0.250 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.550 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 43.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 46.86 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 : 0.002 5587 REMARK 3 ANGLE : 0.633 7565 REMARK 3 CHIRALITY : 0.030 779 REMARK 3 PLANARITY : 0.002 928 REMARK 3 DIHEDRAL : 14.087 2022 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 8 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 40 THROUGH 112 ) REMARK 3 ORIGIN FOR THE GROUP (A): -27.3078 -18.9639 15.0396 REMARK 3 T TENSOR REMARK 3 T11: 0.2731 T22: 0.2185 REMARK 3 T33: 0.3217 T12: 0.0499 REMARK 3 T13: 0.0079 T23: 0.0849 REMARK 3 L TENSOR REMARK 3 L11: 2.2029 L22: 1.5157 REMARK 3 L33: 4.9202 L12: 0.2101 REMARK 3 L13: 0.1334 L23: 0.7295 REMARK 3 S TENSOR REMARK 3 S11: -0.0316 S12: 0.0765 S13: -0.1567 REMARK 3 S21: -0.0305 S22: 0.0760 S23: 0.0620 REMARK 3 S31: -0.0392 S32: -0.3184 S33: -0.0362 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 113 THROUGH 361 ) REMARK 3 ORIGIN FOR THE GROUP (A): -20.1970 -18.5134 10.0211 REMARK 3 T TENSOR REMARK 3 T11: 0.2475 T22: 0.2961 REMARK 3 T33: 0.2688 T12: 0.0057 REMARK 3 T13: -0.0086 T23: 0.0133 REMARK 3 L TENSOR REMARK 3 L11: 1.7018 L22: 0.7804 REMARK 3 L33: 2.4939 L12: 0.0274 REMARK 3 L13: 0.2247 L23: 0.1906 REMARK 3 S TENSOR REMARK 3 S11: -0.0969 S12: 0.0361 S13: 0.0777 REMARK 3 S21: 0.0465 S22: 0.0200 S23: -0.0397 REMARK 3 S31: -0.0804 S32: -0.0658 S33: 0.0769 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'D' AND (RESID 41 THROUGH 68 ) REMARK 3 ORIGIN FOR THE GROUP (A): 13.6369 25.5101 -0.7659 REMARK 3 T TENSOR REMARK 3 T11: 0.6407 T22: 0.5580 REMARK 3 T33: 0.4491 T12: -0.1134 REMARK 3 T13: 0.0633 T23: -0.0994 REMARK 3 L TENSOR REMARK 3 L11: 2.3639 L22: 1.9354 REMARK 3 L33: 8.3357 L12: -1.7506 REMARK 3 L13: 0.4398 L23: -2.4849 REMARK 3 S TENSOR REMARK 3 S11: -0.0227 S12: 0.8318 S13: -0.0201 REMARK 3 S21: -0.2345 S22: 0.2654 S23: 0.1908 REMARK 3 S31: -0.4924 S32: 0.3880 S33: -0.3068 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'D' AND (RESID 69 THROUGH 141 ) REMARK 3 ORIGIN FOR THE GROUP (A): 1.8958 16.9368 21.5934 REMARK 3 T TENSOR REMARK 3 T11: 0.3835 T22: 0.3888 REMARK 3 T33: 0.2683 T12: -0.0669 REMARK 3 T13: 0.0177 T23: -0.0038 REMARK 3 L TENSOR REMARK 3 L11: 2.9909 L22: 1.4918 REMARK 3 L33: 2.1428 L12: 0.8060 REMARK 3 L13: 0.6683 L23: 0.8908 REMARK 3 S TENSOR REMARK 3 S11: 0.0843 S12: -0.4503 S13: -0.1632 REMARK 3 S21: 0.2436 S22: -0.1291 S23: 0.0641 REMARK 3 S31: 0.0774 S32: -0.0337 S33: 0.0370 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'D' AND (RESID 142 THROUGH 204 ) REMARK 3 ORIGIN FOR THE GROUP (A): 11.6672 25.6861 7.4232 REMARK 3 T TENSOR REMARK 3 T11: 0.4891 T22: 0.4078 REMARK 3 T33: 0.2885 T12: -0.1679 REMARK 3 T13: -0.0033 T23: 0.0101 REMARK 3 L TENSOR REMARK 3 L11: 8.9659 L22: 4.1565 REMARK 3 L33: 2.2281 L12: -2.5563 REMARK 3 L13: 0.9802 L23: 0.2785 REMARK 3 S TENSOR REMARK 3 S11: -0.0593 S12: -0.0431 S13: -0.0012 REMARK 3 S21: -0.3644 S22: 0.2409 S23: -0.0723 REMARK 3 S31: -0.4180 S32: 0.3431 S33: -0.1876 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'D' AND (RESID 205 THROUGH 246 ) REMARK 3 ORIGIN FOR THE GROUP (A): -0.1146 22.6651 30.1883 REMARK 3 T TENSOR REMARK 3 T11: 0.5368 T22: 0.6814 REMARK 3 T33: 0.3440 T12: -0.0825 REMARK 3 T13: 0.0673 T23: -0.1034 REMARK 3 L TENSOR REMARK 3 L11: 2.2016 L22: 3.0749 REMARK 3 L33: 5.7219 L12: -0.0345 REMARK 3 L13: 0.7513 L23: -0.6655 REMARK 3 S TENSOR REMARK 3 S11: -0.0169 S12: -0.8722 S13: 0.2203 REMARK 3 S21: 0.5781 S22: -0.2638 S23: -0.1632 REMARK 3 S31: -0.1031 S32: -0.1862 S33: 0.1596 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'D' AND (RESID 247 THROUGH 314 ) REMARK 3 ORIGIN FOR THE GROUP (A): 6.8169 9.4726 6.9211 REMARK 3 T TENSOR REMARK 3 T11: 0.3211 T22: 0.2950 REMARK 3 T33: 0.3312 T12: -0.0466 REMARK 3 T13: 0.0199 T23: 0.0142 REMARK 3 L TENSOR REMARK 3 L11: 2.1707 L22: 3.0609 REMARK 3 L33: 8.7452 L12: 0.9147 REMARK 3 L13: 2.2436 L23: 2.1361 REMARK 3 S TENSOR REMARK 3 S11: -0.0002 S12: 0.2179 S13: -0.1782 REMARK 3 S21: -0.2628 S22: 0.2080 S23: -0.2893 REMARK 3 S31: 0.3082 S32: 0.0955 S33: -0.1864 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'D' AND (RESID 315 THROUGH 352 ) REMARK 3 ORIGIN FOR THE GROUP (A): -4.4222 9.2266 0.0404 REMARK 3 T TENSOR REMARK 3 T11: 0.4189 T22: 0.2883 REMARK 3 T33: 0.3126 T12: -0.1349 REMARK 3 T13: -0.0086 T23: -0.0428 REMARK 3 L TENSOR REMARK 3 L11: 7.4725 L22: 3.2972 REMARK 3 L33: 7.9273 L12: -1.8133 REMARK 3 L13: -3.7885 L23: 1.5946 REMARK 3 S TENSOR REMARK 3 S11: -0.0492 S12: 0.6458 S13: -0.2494 REMARK 3 S21: -0.5550 S22: -0.1047 S23: 0.1719 REMARK 3 S31: 0.2565 S32: -0.6121 S33: 0.2445 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 4YMK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-MAR-15. REMARK 100 THE DEPOSITION ID IS D_1000207558. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-NOV-13; 08-MAR-14 REMARK 200 TEMPERATURE (KELVIN) : 93; 93 REMARK 200 PH : 6.9; 6.9 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : APS; APS REMARK 200 BEAMLINE : 24-ID-C; 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795; 1.2541 REMARK 200 MONOCHROMATOR : NULL; NULL REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL; PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F; DECTRIS REMARK 200 PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : XDS, AIMLESS, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 38065 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 6.200 REMARK 200 R MERGE (I) : 0.11100 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 6.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.64 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.00 REMARK 200 R MERGE FOR SHELL (I) : 0.53000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 27.30 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELXDE, PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 70.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 35% PEG400, 200 MM SODIUM CHLORIDE, 4% REMARK 280 ETHYLENE GLYCOL, 100 MM MES, PH 6.9, LIPIDIC CUBIC PHASE, REMARK 280 TEMPERATURE 298K. 35% PEG400, 200 MM SODIUM CHLORIDE, 4% REMARK 280 ETHYLENE GLYCOL, 100 MM MES, PH 6.9, LIPIDIC CUBIC PHASE, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 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 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 38.53050 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 70.84900 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 56.88300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 70.84900 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 38.53050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 56.88300 REMARK 290 SMTRY3 4 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: D 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 MET A 23 REMARK 465 SER A 24 REMARK 465 GLY A 25 REMARK 465 ASN A 26 REMARK 465 GLU A 27 REMARK 465 ARG A 28 REMARK 465 GLU A 29 REMARK 465 LYS A 30 REMARK 465 VAL A 31 REMARK 465 LYS A 32 REMARK 465 THR A 33 REMARK 465 VAL A 34 REMARK 465 PRO A 35 REMARK 465 LEU A 36 REMARK 465 HIS A 37 REMARK 465 LEU A 38 REMARK 465 GLU A 39 REMARK 465 MET D 23 REMARK 465 SER D 24 REMARK 465 GLY D 25 REMARK 465 ASN D 26 REMARK 465 GLU D 27 REMARK 465 ARG D 28 REMARK 465 GLU D 29 REMARK 465 LYS D 30 REMARK 465 VAL D 31 REMARK 465 LYS D 32 REMARK 465 THR D 33 REMARK 465 VAL D 34 REMARK 465 PRO D 35 REMARK 465 LEU D 36 REMARK 465 HIS D 37 REMARK 465 LEU D 38 REMARK 465 GLU D 39 REMARK 465 GLU D 40 REMARK 465 LYS D 353 REMARK 465 SER D 354 REMARK 465 SER D 355 REMARK 465 GLU D 356 REMARK 465 ASN D 357 REMARK 465 LEU D 358 REMARK 465 TYR D 359 REMARK 465 PHE D 360 REMARK 465 GLN D 361 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 LYS A 47 17.91 -145.54 REMARK 500 GLU A 58 34.39 -143.17 REMARK 500 HIS A 116 -76.90 -85.50 REMARK 500 ASN A 144 158.60 67.45 REMARK 500 HIS A 167 51.56 -118.59 REMARK 500 ASN A 168 106.83 -49.11 REMARK 500 VAL A 178 -23.69 -145.74 REMARK 500 PHE A 223 -55.34 -125.30 REMARK 500 THR A 246 -64.07 -131.50 REMARK 500 SER A 262 -72.03 -96.95 REMARK 500 LEU A 266 -45.78 -139.39 REMARK 500 VAL A 289 44.99 32.19 REMARK 500 HIS D 116 -75.73 -83.99 REMARK 500 ASN D 144 159.74 68.54 REMARK 500 HIS D 167 56.78 -118.84 REMARK 500 VAL D 178 -17.78 -144.59 REMARK 500 PHE D 223 -60.44 -122.21 REMARK 500 SER D 262 -73.33 -105.19 REMARK 500 LEU D 266 -49.82 -134.66 REMARK 500 VAL D 289 44.28 33.37 REMARK 500 GLU D 291 34.56 -94.48 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 116 NE2 REMARK 620 2 HIS A 121 NE2 98.2 REMARK 620 3 HIS A 153 NE2 91.0 90.6 REMARK 620 4 HIS A 157 NE2 161.4 100.3 90.4 REMARK 620 5 HIS A 297 NE2 80.3 99.1 167.8 95.0 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 402 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 156 NE2 REMARK 620 2 HIS A 265 NE2 109.3 REMARK 620 3 HIS A 294 NE2 151.0 94.9 REMARK 620 4 HIS A 298 NE2 94.1 108.9 92.9 REMARK 620 5 HOH A 542 O 84.3 94.4 77.9 155.6 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN D 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS D 116 NE2 REMARK 620 2 HIS D 121 NE2 92.7 REMARK 620 3 HIS D 153 NE2 87.2 93.1 REMARK 620 4 HIS D 157 NE2 160.9 106.4 91.3 REMARK 620 5 HIS D 297 NE2 83.3 108.6 156.6 90.8 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN D 402 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS D 156 NE2 REMARK 620 2 HIS D 265 NE2 114.8 REMARK 620 3 HIS D 294 NE2 139.8 98.3 REMARK 620 4 HIS D 298 NE2 95.0 114.4 91.3 REMARK 620 5 HOH D 530 O 86.4 90.2 70.5 151.7 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ST9 A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MPG A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN D 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN D 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ST9 D 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MPG D 404 DBREF 4YMK A 24 355 UNP P13516 ACOD1_MOUSE 24 355 DBREF 4YMK D 24 355 UNP P13516 ACOD1_MOUSE 24 355 SEQADV 4YMK MET A 23 UNP P13516 INITIATING METHIONINE SEQADV 4YMK GLU A 356 UNP P13516 EXPRESSION TAG SEQADV 4YMK ASN A 357 UNP P13516 EXPRESSION TAG SEQADV 4YMK LEU A 358 UNP P13516 EXPRESSION TAG SEQADV 4YMK TYR A 359 UNP P13516 EXPRESSION TAG SEQADV 4YMK PHE A 360 UNP P13516 EXPRESSION TAG SEQADV 4YMK GLN A 361 UNP P13516 EXPRESSION TAG SEQADV 4YMK MET D 23 UNP P13516 INITIATING METHIONINE SEQADV 4YMK GLU D 356 UNP P13516 EXPRESSION TAG SEQADV 4YMK ASN D 357 UNP P13516 EXPRESSION TAG SEQADV 4YMK LEU D 358 UNP P13516 EXPRESSION TAG SEQADV 4YMK TYR D 359 UNP P13516 EXPRESSION TAG SEQADV 4YMK PHE D 360 UNP P13516 EXPRESSION TAG SEQADV 4YMK GLN D 361 UNP P13516 EXPRESSION TAG SEQRES 1 A 339 MET SER GLY ASN GLU ARG GLU LYS VAL LYS THR VAL PRO SEQRES 2 A 339 LEU HIS LEU GLU GLU ASP ILE ARG PRO GLU MET LYS GLU SEQRES 3 A 339 ASP ILE HIS ASP PRO THR TYR GLN ASP GLU GLU GLY PRO SEQRES 4 A 339 PRO PRO LYS LEU GLU TYR VAL TRP ARG ASN ILE ILE LEU SEQRES 5 A 339 MET VAL LEU LEU HIS LEU GLY GLY LEU TYR GLY ILE ILE SEQRES 6 A 339 LEU VAL PRO SER CYS LYS LEU TYR THR CYS LEU PHE GLY SEQRES 7 A 339 ILE PHE TYR TYR MET THR SER ALA LEU GLY ILE THR ALA SEQRES 8 A 339 GLY ALA HIS ARG LEU TRP SER HIS ARG THR TYR LYS ALA SEQRES 9 A 339 ARG LEU PRO LEU ARG ILE PHE LEU ILE ILE ALA ASN THR SEQRES 10 A 339 MET ALA PHE GLN ASN ASP VAL TYR GLU TRP ALA ARG ASP SEQRES 11 A 339 HIS ARG ALA HIS HIS LYS PHE SER GLU THR HIS ALA ASP SEQRES 12 A 339 PRO HIS ASN SER ARG ARG GLY PHE PHE PHE SER HIS VAL SEQRES 13 A 339 GLY TRP LEU LEU VAL ARG LYS HIS PRO ALA VAL LYS GLU SEQRES 14 A 339 LYS GLY GLY LYS LEU ASP MET SER ASP LEU LYS ALA GLU SEQRES 15 A 339 LYS LEU VAL MET PHE GLN ARG ARG TYR TYR LYS PRO GLY SEQRES 16 A 339 LEU LEU LEU MET CYS PHE ILE LEU PRO THR LEU VAL PRO SEQRES 17 A 339 TRP TYR CYS TRP GLY GLU THR PHE VAL ASN SER LEU PHE SEQRES 18 A 339 VAL SER THR PHE LEU ARG TYR THR LEU VAL LEU ASN ALA SEQRES 19 A 339 THR TRP LEU VAL ASN SER ALA ALA HIS LEU TYR GLY TYR SEQRES 20 A 339 ARG PRO TYR ASP LYS ASN ILE GLN SER ARG GLU ASN ILE SEQRES 21 A 339 LEU VAL SER LEU GLY ALA VAL GLY GLU GLY PHE HIS ASN SEQRES 22 A 339 TYR HIS HIS THR PHE PRO PHE ASP TYR SER ALA SER GLU SEQRES 23 A 339 TYR ARG TRP HIS ILE ASN PHE THR THR PHE PHE ILE ASP SEQRES 24 A 339 CYS MET ALA ALA LEU GLY LEU ALA TYR ASP ARG LYS LYS SEQRES 25 A 339 VAL SER LYS ALA THR VAL LEU ALA ARG ILE LYS ARG THR SEQRES 26 A 339 GLY ASP GLY SER HIS LYS SER SER GLU ASN LEU TYR PHE SEQRES 27 A 339 GLN SEQRES 1 D 339 MET SER GLY ASN GLU ARG GLU LYS VAL LYS THR VAL PRO SEQRES 2 D 339 LEU HIS LEU GLU GLU ASP ILE ARG PRO GLU MET LYS GLU SEQRES 3 D 339 ASP ILE HIS ASP PRO THR TYR GLN ASP GLU GLU GLY PRO SEQRES 4 D 339 PRO PRO LYS LEU GLU TYR VAL TRP ARG ASN ILE ILE LEU SEQRES 5 D 339 MET VAL LEU LEU HIS LEU GLY GLY LEU TYR GLY ILE ILE SEQRES 6 D 339 LEU VAL PRO SER CYS LYS LEU TYR THR CYS LEU PHE GLY SEQRES 7 D 339 ILE PHE TYR TYR MET THR SER ALA LEU GLY ILE THR ALA SEQRES 8 D 339 GLY ALA HIS ARG LEU TRP SER HIS ARG THR TYR LYS ALA SEQRES 9 D 339 ARG LEU PRO LEU ARG ILE PHE LEU ILE ILE ALA ASN THR SEQRES 10 D 339 MET ALA PHE GLN ASN ASP VAL TYR GLU TRP ALA ARG ASP SEQRES 11 D 339 HIS ARG ALA HIS HIS LYS PHE SER GLU THR HIS ALA ASP SEQRES 12 D 339 PRO HIS ASN SER ARG ARG GLY PHE PHE PHE SER HIS VAL SEQRES 13 D 339 GLY TRP LEU LEU VAL ARG LYS HIS PRO ALA VAL LYS GLU SEQRES 14 D 339 LYS GLY GLY LYS LEU ASP MET SER ASP LEU LYS ALA GLU SEQRES 15 D 339 LYS LEU VAL MET PHE GLN ARG ARG TYR TYR LYS PRO GLY SEQRES 16 D 339 LEU LEU LEU MET CYS PHE ILE LEU PRO THR LEU VAL PRO SEQRES 17 D 339 TRP TYR CYS TRP GLY GLU THR PHE VAL ASN SER LEU PHE SEQRES 18 D 339 VAL SER THR PHE LEU ARG TYR THR LEU VAL LEU ASN ALA SEQRES 19 D 339 THR TRP LEU VAL ASN SER ALA ALA HIS LEU TYR GLY TYR SEQRES 20 D 339 ARG PRO TYR ASP LYS ASN ILE GLN SER ARG GLU ASN ILE SEQRES 21 D 339 LEU VAL SER LEU GLY ALA VAL GLY GLU GLY PHE HIS ASN SEQRES 22 D 339 TYR HIS HIS THR PHE PRO PHE ASP TYR SER ALA SER GLU SEQRES 23 D 339 TYR ARG TRP HIS ILE ASN PHE THR THR PHE PHE ILE ASP SEQRES 24 D 339 CYS MET ALA ALA LEU GLY LEU ALA TYR ASP ARG LYS LYS SEQRES 25 D 339 VAL SER LYS ALA THR VAL LEU ALA ARG ILE LYS ARG THR SEQRES 26 D 339 GLY ASP GLY SER HIS LYS SER SER GLU ASN LEU TYR PHE SEQRES 27 D 339 GLN HET ZN A 401 1 HET ZN A 402 1 HET ST9 A 403 67 HET MPG A 404 25 HET ZN D 401 1 HET ZN D 402 1 HET ST9 D 403 67 HET MPG D 404 25 HETNAM ZN ZINC ION HETNAM ST9 STEAROYL-COENZYME A HETNAM MPG [(Z)-OCTADEC-9-ENYL] (2R)-2,3-BIS(OXIDANYL)PROPANOATE FORMUL 3 ZN 4(ZN 2+) FORMUL 5 ST9 2(C39 H70 N7 O17 P3 S) FORMUL 6 MPG 2(C21 H40 O4) FORMUL 11 HOH *86(H2 O) HELIX 1 AA1 VAL A 68 ILE A 87 1 20 HELIX 2 AA2 LEU A 88 CYS A 92 5 5 HELIX 3 AA3 LYS A 93 ALA A 113 1 21 HELIX 4 AA4 ARG A 127 PHE A 142 1 16 HELIX 5 AA5 ASP A 145 PHE A 159 1 15 HELIX 6 AA6 ASN A 168 ARG A 171 5 4 HELIX 7 AA7 GLY A 172 VAL A 178 1 7 HELIX 8 AA8 GLY A 179 LEU A 182 5 4 HELIX 9 AA9 HIS A 186 GLY A 194 1 9 HELIX 10 AB1 MET A 198 ALA A 203 1 6 HELIX 11 AB2 GLU A 204 TYR A 213 1 10 HELIX 12 AB3 TYR A 213 PHE A 223 1 11 HELIX 13 AB4 ILE A 224 TRP A 234 1 11 HELIX 14 AB5 THR A 237 VAL A 244 1 8 HELIX 15 AB6 THR A 246 LEU A 259 1 14 HELIX 16 AB7 VAL A 260 ASN A 261 5 2 HELIX 17 AB8 SER A 262 LEU A 266 5 5 HELIX 18 AB9 ASN A 281 ALA A 288 1 8 HELIX 19 AC1 PHE A 293 PHE A 300 1 8 HELIX 20 AC2 ASN A 314 LEU A 326 1 13 HELIX 21 AC3 SER A 336 GLY A 348 1 13 HELIX 22 AC4 SER A 351 SER A 355 5 5 HELIX 23 AC5 VAL D 68 ILE D 87 1 20 HELIX 24 AC6 LEU D 88 CYS D 92 5 5 HELIX 25 AC7 LYS D 93 ALA D 113 1 21 HELIX 26 AC8 ARG D 127 PHE D 142 1 16 HELIX 27 AC9 ASP D 145 PHE D 159 1 15 HELIX 28 AD1 ASN D 168 ARG D 171 5 4 HELIX 29 AD2 GLY D 172 VAL D 178 1 7 HELIX 30 AD3 GLY D 179 LEU D 182 5 4 HELIX 31 AD4 HIS D 186 GLY D 194 1 9 HELIX 32 AD5 MET D 198 ALA D 203 1 6 HELIX 33 AD6 GLU D 204 TYR D 213 1 10 HELIX 34 AD7 TYR D 213 PHE D 223 1 11 HELIX 35 AD8 PHE D 223 CYS D 233 1 11 HELIX 36 AD9 THR D 237 VAL D 244 1 8 HELIX 37 AE1 THR D 246 LEU D 259 1 14 HELIX 38 AE2 VAL D 260 ASN D 261 5 2 HELIX 39 AE3 SER D 262 LEU D 266 5 5 HELIX 40 AE4 ASN D 281 ALA D 288 1 8 HELIX 41 AE5 PHE D 293 PHE D 300 1 8 HELIX 42 AE6 ASN D 314 LEU D 326 1 13 HELIX 43 AE7 SER D 336 GLY D 348 1 13 SHEET 1 AA1 2 LYS A 125 ALA A 126 0 SHEET 2 AA1 2 ALA A 329 TYR A 330 -1 O TYR A 330 N LYS A 125 SHEET 1 AA2 2 LYS D 125 ALA D 126 0 SHEET 2 AA2 2 ALA D 329 TYR D 330 -1 O TYR D 330 N LYS D 125 LINK NE2 HIS A 116 ZN ZN A 401 1555 1555 2.45 LINK NE2 HIS A 121 ZN ZN A 401 1555 1555 2.19 LINK NE2 HIS A 153 ZN ZN A 401 1555 1555 2.00 LINK NE2 HIS A 156 ZN ZN A 402 1555 1555 2.18 LINK NE2 HIS A 157 ZN ZN A 401 1555 1555 2.24 LINK NE2 HIS A 265 ZN ZN A 402 1555 1555 2.20 LINK NE2 HIS A 294 ZN ZN A 402 1555 1555 1.98 LINK NE2 HIS A 297 ZN ZN A 401 1555 1555 1.98 LINK NE2 HIS A 298 ZN ZN A 402 1555 1555 2.26 LINK ZN ZN A 402 O HOH A 542 1555 1555 2.20 LINK NE2 HIS D 116 ZN ZN D 401 1555 1555 2.34 LINK NE2 HIS D 121 ZN ZN D 401 1555 1555 2.16 LINK NE2 HIS D 153 ZN ZN D 401 1555 1555 2.09 LINK NE2 HIS D 156 ZN ZN D 402 1555 1555 2.13 LINK NE2 HIS D 157 ZN ZN D 401 1555 1555 2.21 LINK NE2 HIS D 265 ZN ZN D 402 1555 1555 2.21 LINK NE2 HIS D 294 ZN ZN D 402 1555 1555 2.02 LINK NE2 HIS D 297 ZN ZN D 401 1555 1555 2.02 LINK NE2 HIS D 298 ZN ZN D 402 1555 1555 2.19 LINK ZN ZN D 402 O HOH D 530 1555 1555 2.21 SITE 1 AC1 5 HIS A 116 HIS A 121 HIS A 153 HIS A 157 SITE 2 AC1 5 HIS A 297 SITE 1 AC2 5 HIS A 156 HIS A 265 HIS A 294 HIS A 298 SITE 2 AC2 5 HOH A 542 SITE 1 AC3 25 ASN A 71 ILE A 111 THR A 112 HIS A 116 SITE 2 AC3 25 PHE A 142 GLN A 143 ASN A 144 TRP A 149 SITE 3 AC3 25 ARG A 151 ASP A 152 HIS A 153 TRP A 180 SITE 4 AC3 25 LEU A 181 VAL A 183 ARG A 184 LYS A 185 SITE 5 AC3 25 VAL A 189 GLY A 193 GLY A 194 ARG A 211 SITE 6 AC3 25 THR A 257 TRP A 258 VAL A 260 ASN A 261 SITE 7 AC3 25 ALA A 288 SITE 1 AC4 5 GLY A 100 TYR A 104 MET A 105 LEU A 286 SITE 2 AC4 5 VAL A 289 SITE 1 AC5 5 HIS D 116 HIS D 121 HIS D 153 HIS D 157 SITE 2 AC5 5 HIS D 297 SITE 1 AC6 5 HIS D 156 HIS D 265 HIS D 294 HIS D 298 SITE 2 AC6 5 HOH D 530 SITE 1 AC7 27 ASN D 71 ILE D 111 THR D 112 HIS D 116 SITE 2 AC7 27 PHE D 142 GLN D 143 ASN D 144 TRP D 149 SITE 3 AC7 27 ARG D 151 ASP D 152 HIS D 153 TRP D 180 SITE 4 AC7 27 LEU D 181 VAL D 183 ARG D 184 LYS D 185 SITE 5 AC7 27 VAL D 189 LYS D 190 GLY D 193 GLY D 194 SITE 6 AC7 27 LEU D 254 THR D 257 TRP D 258 ASN D 261 SITE 7 AC7 27 GLY D 287 ALA D 288 HOH D 519 SITE 1 AC8 4 GLY D 100 TYR D 104 MET D 105 LEU D 286 CRYST1 77.061 113.766 141.698 90.00 90.00 90.00 P 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 0.012977 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008790 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007057 0.00000