HEADER OXIDOREDUCTASE 23-OCT-12 4HP8 TITLE CRYSTAL STRUCTURE OF A PUTATIVE 2-DEOXY-D-GLUCONATE 3-DEHYDROGENASE TITLE 2 FROM AGROBACTERIUM TUMEFACIENS (TARGET EFI-506435) WITH BOUND NADP COMPND MOL_ID: 1; COMPND 2 MOLECULE: 2-DEOXY-D-GLUCONATE 3-DEHYDROGENASE; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AGROBACTERIUM TUMEFACIENS; SOURCE 3 ORGANISM_TAXID: 176299; SOURCE 4 STRAIN: C58 / ATCC 33970; SOURCE 5 GENE: KDUD, ATU3141; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET KEYWDS ENZYME FUNCTION INITIATIVE, EFI, STRUCTURAL GENOMICS, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR M.W.VETTING,J.T.BOUVIER,F.GRONINGER-POE,L.L.MORISCO,S.R.WASSERMAN, AUTHOR 2 S.SOJITRA,H.J.IMKER,J.A.GERLT,S.C.ALMO,ENZYME FUNCTION INITIATIVE AUTHOR 3 (EFI) REVDAT 2 20-SEP-23 4HP8 1 REMARK REVDAT 1 07-NOV-12 4HP8 0 JRNL AUTH M.W.VETTING,J.T.BOUVIER,F.GRONINGER-POE,L.L.MORISCO, JRNL AUTH 2 S.R.WASSERMAN,S.SOJITRA,H.J.IMKER,J.A.GERLT,S.C.ALMO JRNL TITL CRYSTAL STRUCTURE OF A PUTATIVE 2-DEOXY-D-GLUCONATE JRNL TITL 2 3-DEHYDROGENASE FROM AGROBACTERIUM TUMEFACIENS (TARGET JRNL TITL 3 EFI-506435) WITH BOUND NADP JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.1_1168 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) : 1.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.80 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 105176 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.140 REMARK 3 R VALUE (WORKING SET) : 0.139 REMARK 3 FREE R VALUE : 0.156 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 5254 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 25.8043 - 4.1890 1.00 3609 204 0.1499 0.1572 REMARK 3 2 4.1890 - 3.3272 1.00 3456 177 0.1334 0.1358 REMARK 3 3 3.3272 - 2.9072 1.00 3409 178 0.1436 0.1659 REMARK 3 4 2.9072 - 2.6417 1.00 3400 166 0.1474 0.1580 REMARK 3 5 2.6417 - 2.4525 1.00 3341 188 0.1388 0.1579 REMARK 3 6 2.4525 - 2.3080 1.00 3376 176 0.1384 0.1697 REMARK 3 7 2.3080 - 2.1925 1.00 3340 176 0.1338 0.1364 REMARK 3 8 2.1925 - 2.0971 1.00 3361 171 0.1261 0.1451 REMARK 3 9 2.0971 - 2.0164 1.00 3324 184 0.1362 0.1656 REMARK 3 10 2.0164 - 1.9469 1.00 3313 180 0.1282 0.1445 REMARK 3 11 1.9469 - 1.8860 1.00 3331 176 0.1294 0.1489 REMARK 3 12 1.8860 - 1.8321 1.00 3324 181 0.1283 0.1603 REMARK 3 13 1.8321 - 1.7839 1.00 3316 162 0.1287 0.1431 REMARK 3 14 1.7839 - 1.7404 1.00 3325 165 0.1260 0.1350 REMARK 3 15 1.7404 - 1.7008 1.00 3318 190 0.1209 0.1383 REMARK 3 16 1.7008 - 1.6646 1.00 3296 170 0.1269 0.1554 REMARK 3 17 1.6646 - 1.6313 1.00 3272 188 0.1260 0.1556 REMARK 3 18 1.6313 - 1.6006 1.00 3336 157 0.1243 0.1611 REMARK 3 19 1.6006 - 1.5720 1.00 3321 156 0.1282 0.1608 REMARK 3 20 1.5720 - 1.5453 1.00 3286 173 0.1303 0.1605 REMARK 3 21 1.5453 - 1.5204 1.00 3319 178 0.1289 0.1436 REMARK 3 22 1.5204 - 1.4970 1.00 3270 174 0.1321 0.1634 REMARK 3 23 1.4970 - 1.4750 1.00 3275 189 0.1498 0.1817 REMARK 3 24 1.4750 - 1.4542 1.00 3293 179 0.1553 0.1785 REMARK 3 25 1.4542 - 1.4346 1.00 3294 156 0.1554 0.1847 REMARK 3 26 1.4346 - 1.4159 1.00 3293 162 0.1570 0.1658 REMARK 3 27 1.4159 - 1.3982 1.00 3292 181 0.1653 0.1879 REMARK 3 28 1.3982 - 1.3814 1.00 3253 186 0.1723 0.1862 REMARK 3 29 1.3814 - 1.3653 1.00 3268 172 0.1766 0.1863 REMARK 3 30 1.3653 - 1.3500 1.00 3311 159 0.1901 0.2035 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) : 0.090 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 13.390 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.51 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 : 0.015 3840 REMARK 3 ANGLE : 1.722 5239 REMARK 3 CHIRALITY : 0.100 598 REMARK 3 PLANARITY : 0.009 681 REMARK 3 DIHEDRAL : 19.302 1364 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 3:53) REMARK 3 ORIGIN FOR THE GROUP (A): 32.5481 1.4108 16.3028 REMARK 3 T TENSOR REMARK 3 T11: 0.0512 T22: 0.0563 REMARK 3 T33: 0.0640 T12: -0.0031 REMARK 3 T13: -0.0143 T23: 0.0016 REMARK 3 L TENSOR REMARK 3 L11: 0.3941 L22: 0.1495 REMARK 3 L33: 0.1719 L12: 0.1624 REMARK 3 L13: 0.0577 L23: -0.0273 REMARK 3 S TENSOR REMARK 3 S11: 0.0219 S12: -0.0732 S13: -0.0282 REMARK 3 S21: 0.0546 S22: -0.0187 S23: -0.0408 REMARK 3 S31: 0.0020 S32: 0.0244 S33: 0.0000 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN A AND (RESID 54:128) REMARK 3 ORIGIN FOR THE GROUP (A): 29.7525 14.1759 6.0229 REMARK 3 T TENSOR REMARK 3 T11: 0.0336 T22: 0.0482 REMARK 3 T33: 0.0519 T12: -0.0051 REMARK 3 T13: 0.0038 T23: -0.0056 REMARK 3 L TENSOR REMARK 3 L11: 0.2029 L22: 0.3248 REMARK 3 L33: 0.2434 L12: -0.0182 REMARK 3 L13: 0.2245 L23: -0.0468 REMARK 3 S TENSOR REMARK 3 S11: -0.0170 S12: -0.0317 S13: 0.0182 REMARK 3 S21: 0.0201 S22: 0.0004 S23: -0.0603 REMARK 3 S31: -0.0024 S32: 0.0365 S33: -0.0007 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN A AND (RESID 129:247) REMARK 3 ORIGIN FOR THE GROUP (A): 16.8508 6.1313 9.6729 REMARK 3 T TENSOR REMARK 3 T11: 0.0384 T22: 0.0396 REMARK 3 T33: 0.0340 T12: 0.0021 REMARK 3 T13: 0.0041 T23: -0.0119 REMARK 3 L TENSOR REMARK 3 L11: 0.4344 L22: 0.1555 REMARK 3 L33: -0.0380 L12: 0.1410 REMARK 3 L13: 0.0969 L23: -0.2111 REMARK 3 S TENSOR REMARK 3 S11: 0.0179 S12: -0.0836 S13: 0.0237 REMARK 3 S21: 0.0412 S22: 0.0078 S23: -0.0030 REMARK 3 S31: -0.0115 S32: 0.0006 S33: 0.0003 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN B AND (RESID 2:54) REMARK 3 ORIGIN FOR THE GROUP (A): 13.3510 -23.9466 8.7572 REMARK 3 T TENSOR REMARK 3 T11: 0.1530 T22: 0.0353 REMARK 3 T33: 0.0927 T12: 0.0144 REMARK 3 T13: 0.0164 T23: 0.0057 REMARK 3 L TENSOR REMARK 3 L11: 0.2748 L22: 0.2919 REMARK 3 L33: 0.2324 L12: -0.1324 REMARK 3 L13: -0.0760 L23: -0.2651 REMARK 3 S TENSOR REMARK 3 S11: 0.0266 S12: -0.0549 S13: -0.0844 REMARK 3 S21: -0.0930 S22: -0.0886 S23: -0.0929 REMARK 3 S31: 0.1878 S32: 0.0229 S33: -0.0140 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN B AND (RESID 55:128) REMARK 3 ORIGIN FOR THE GROUP (A): -2.7965 -18.2101 5.3470 REMARK 3 T TENSOR REMARK 3 T11: 0.0970 T22: 0.0557 REMARK 3 T33: 0.0613 T12: -0.0322 REMARK 3 T13: 0.0074 T23: 0.0021 REMARK 3 L TENSOR REMARK 3 L11: 0.4060 L22: 0.3567 REMARK 3 L33: 0.0854 L12: -0.0686 REMARK 3 L13: 0.1978 L23: 0.0229 REMARK 3 S TENSOR REMARK 3 S11: 0.0295 S12: -0.0331 S13: -0.0867 REMARK 3 S21: -0.0277 S22: -0.0056 S23: 0.0315 REMARK 3 S31: 0.1533 S32: -0.0738 S33: -0.0200 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN B AND (RESID 129:196) REMARK 3 ORIGIN FOR THE GROUP (A): 4.5539 -9.2714 1.7871 REMARK 3 T TENSOR REMARK 3 T11: 0.0614 T22: 0.0406 REMARK 3 T33: 0.0405 T12: -0.0093 REMARK 3 T13: 0.0085 T23: -0.0069 REMARK 3 L TENSOR REMARK 3 L11: 0.3182 L22: 0.2189 REMARK 3 L33: 0.0133 L12: -0.0379 REMARK 3 L13: 0.0182 L23: -0.1086 REMARK 3 S TENSOR REMARK 3 S11: 0.0045 S12: 0.0079 S13: -0.0359 REMARK 3 S21: -0.0211 S22: -0.0016 S23: 0.0104 REMARK 3 S31: 0.0488 S32: -0.0301 S33: 0.0000 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN B AND (RESID 197:214) REMARK 3 ORIGIN FOR THE GROUP (A): 16.6465 -9.3005 -13.4347 REMARK 3 T TENSOR REMARK 3 T11: 0.0823 T22: 0.0534 REMARK 3 T33: 0.0617 T12: 0.0082 REMARK 3 T13: 0.0048 T23: -0.0195 REMARK 3 L TENSOR REMARK 3 L11: 0.0384 L22: 0.0840 REMARK 3 L33: 0.0477 L12: -0.0574 REMARK 3 L13: -0.0519 L23: 0.0784 REMARK 3 S TENSOR REMARK 3 S11: 0.0289 S12: 0.0221 S13: 0.0153 REMARK 3 S21: -0.1128 S22: -0.0411 S23: -0.0345 REMARK 3 S31: 0.0738 S32: 0.0047 S33: -0.0000 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN B AND (RESID 215:247) REMARK 3 ORIGIN FOR THE GROUP (A): 14.3723 -7.0364 4.8510 REMARK 3 T TENSOR REMARK 3 T11: 0.0554 T22: 0.0386 REMARK 3 T33: 0.0539 T12: 0.0001 REMARK 3 T13: 0.0064 T23: -0.0027 REMARK 3 L TENSOR REMARK 3 L11: 0.2047 L22: 0.0725 REMARK 3 L33: 0.0485 L12: 0.0371 REMARK 3 L13: 0.1054 L23: -0.0300 REMARK 3 S TENSOR REMARK 3 S11: 0.0040 S12: 0.0040 S13: -0.0078 REMARK 3 S21: 0.0044 S22: -0.0198 S23: -0.0406 REMARK 3 S31: 0.0456 S32: -0.0149 S33: 0.0000 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 4HP8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-OCT-12. REMARK 100 THE DEPOSITION ID IS D_1000075747. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-OCT-12 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 : APS REMARK 200 BEAMLINE : 31-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9793 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX225HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.20 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 105259 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.350 REMARK 200 RESOLUTION RANGE LOW (A) : 109.285 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 14.50 REMARK 200 R MERGE (I) : 0.11600 REMARK 200 R SYM (I) : 0.11600 REMARK 200 FOR THE DATA SET : 15.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.42 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 14.40 REMARK 200 R MERGE FOR SHELL (I) : 0.75500 REMARK 200 R SYM FOR SHELL (I) : 0.75500 REMARK 200 FOR SHELL : 1.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 3UF0 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.36 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.29 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN (10MM TRIS, PH 7.9), RESERVOIR REMARK 280 (0.1 M BIS-TRIS:HCL, PH 6.5, 2.0 M AMMONIUM SULFATE, 10 MM NADP), REMARK 280 CRYOPROTECTION (RESERVOIR + 20% ETHYLENE GLYCOL), VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 54.64250 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 46.51100 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 46.51100 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 81.96375 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 46.51100 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 46.51100 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 27.32125 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 46.51100 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 46.51100 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 81.96375 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 46.51100 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 46.51100 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 27.32125 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 54.64250 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 18090 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 31510 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -86.0 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 BIOMT1 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 506 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 602 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 492 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 581 LIES ON A SPECIAL POSITION. 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 1 REMARK 465 LYS A 2 REMARK 465 MET B 1 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 B 559 O HOH B 700 2.14 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 NZ LYS B 173 O HOH A 697 8555 2.16 REMARK 500 O HOH A 492 O HOH B 640 4555 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 169 CD GLU A 169 OE2 -0.077 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ASP A 231 CB - CG - OD1 ANGL. DEV. = 6.6 DEGREES 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 LEU A 111 -59.02 -125.68 REMARK 500 ALA A 138 -142.87 -90.69 REMARK 500 LEU B 111 -57.76 -126.12 REMARK 500 ALA B 138 -138.10 -94.01 REMARK 500 ASP B 241 13.22 -142.29 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAP A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAP B 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EFI-506435 RELATED DB: TARGETTRACK DBREF 4HP8 A 1 247 UNP A9CEQ9 A9CEQ9_AGRT5 1 247 DBREF 4HP8 B 1 247 UNP A9CEQ9 A9CEQ9_AGRT5 1 247 SEQRES 1 A 247 MET LYS ASN PRO PHE SER LEU GLU GLY ARG LYS ALA LEU SEQRES 2 A 247 VAL THR GLY ALA ASN THR GLY LEU GLY GLN ALA ILE ALA SEQRES 3 A 247 VAL GLY LEU ALA ALA ALA GLY ALA GLU VAL VAL CYS ALA SEQRES 4 A 247 ALA ARG ARG ALA PRO ASP GLU THR LEU ASP ILE ILE ALA SEQRES 5 A 247 LYS ASP GLY GLY ASN ALA SER ALA LEU LEU ILE ASP PHE SEQRES 6 A 247 ALA ASP PRO LEU ALA ALA LYS ASP SER PHE THR ASP ALA SEQRES 7 A 247 GLY PHE ASP ILE LEU VAL ASN ASN ALA GLY ILE ILE ARG SEQRES 8 A 247 ARG ALA ASP SER VAL GLU PHE SER GLU LEU ASP TRP ASP SEQRES 9 A 247 GLU VAL MET ASP VAL ASN LEU LYS ALA LEU PHE PHE THR SEQRES 10 A 247 THR GLN ALA PHE ALA LYS GLU LEU LEU ALA LYS GLY ARG SEQRES 11 A 247 SER GLY LYS VAL VAL ASN ILE ALA SER LEU LEU SER PHE SEQRES 12 A 247 GLN GLY GLY ILE ARG VAL PRO SER TYR THR ALA ALA LYS SEQRES 13 A 247 HIS GLY VAL ALA GLY LEU THR LYS LEU LEU ALA ASN GLU SEQRES 14 A 247 TRP ALA ALA LYS GLY ILE ASN VAL ASN ALA ILE ALA PRO SEQRES 15 A 247 GLY TYR ILE GLU THR ASN ASN THR GLU ALA LEU ARG ALA SEQRES 16 A 247 ASP ALA ALA ARG ASN LYS ALA ILE LEU GLU ARG ILE PRO SEQRES 17 A 247 ALA GLY ARG TRP GLY HIS SER GLU ASP ILE ALA GLY ALA SEQRES 18 A 247 ALA VAL PHE LEU SER SER ALA ALA ALA ASP TYR VAL HIS SEQRES 19 A 247 GLY ALA ILE LEU ASN VAL ASP GLY GLY TRP LEU ALA ARG SEQRES 1 B 247 MET LYS ASN PRO PHE SER LEU GLU GLY ARG LYS ALA LEU SEQRES 2 B 247 VAL THR GLY ALA ASN THR GLY LEU GLY GLN ALA ILE ALA SEQRES 3 B 247 VAL GLY LEU ALA ALA ALA GLY ALA GLU VAL VAL CYS ALA SEQRES 4 B 247 ALA ARG ARG ALA PRO ASP GLU THR LEU ASP ILE ILE ALA SEQRES 5 B 247 LYS ASP GLY GLY ASN ALA SER ALA LEU LEU ILE ASP PHE SEQRES 6 B 247 ALA ASP PRO LEU ALA ALA LYS ASP SER PHE THR ASP ALA SEQRES 7 B 247 GLY PHE ASP ILE LEU VAL ASN ASN ALA GLY ILE ILE ARG SEQRES 8 B 247 ARG ALA ASP SER VAL GLU PHE SER GLU LEU ASP TRP ASP SEQRES 9 B 247 GLU VAL MET ASP VAL ASN LEU LYS ALA LEU PHE PHE THR SEQRES 10 B 247 THR GLN ALA PHE ALA LYS GLU LEU LEU ALA LYS GLY ARG SEQRES 11 B 247 SER GLY LYS VAL VAL ASN ILE ALA SER LEU LEU SER PHE SEQRES 12 B 247 GLN GLY GLY ILE ARG VAL PRO SER TYR THR ALA ALA LYS SEQRES 13 B 247 HIS GLY VAL ALA GLY LEU THR LYS LEU LEU ALA ASN GLU SEQRES 14 B 247 TRP ALA ALA LYS GLY ILE ASN VAL ASN ALA ILE ALA PRO SEQRES 15 B 247 GLY TYR ILE GLU THR ASN ASN THR GLU ALA LEU ARG ALA SEQRES 16 B 247 ASP ALA ALA ARG ASN LYS ALA ILE LEU GLU ARG ILE PRO SEQRES 17 B 247 ALA GLY ARG TRP GLY HIS SER GLU ASP ILE ALA GLY ALA SEQRES 18 B 247 ALA VAL PHE LEU SER SER ALA ALA ALA ASP TYR VAL HIS SEQRES 19 B 247 GLY ALA ILE LEU ASN VAL ASP GLY GLY TRP LEU ALA ARG HET NAP A 301 48 HET ACT A 302 4 HET NAP B 301 48 HETNAM NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE HETNAM ACT ACETATE ION HETSYN NAP 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE FORMUL 3 NAP 2(C21 H28 N7 O17 P3) FORMUL 4 ACT C2 H3 O2 1- FORMUL 6 HOH *601(H2 O) HELIX 1 1 THR A 19 ALA A 32 1 14 HELIX 2 2 PRO A 44 ASP A 54 1 11 HELIX 3 3 ASP A 94 PHE A 98 5 5 HELIX 4 4 SER A 99 LEU A 111 1 13 HELIX 5 5 LEU A 111 GLY A 129 1 19 HELIX 6 6 SER A 139 PHE A 143 5 5 HELIX 7 7 VAL A 149 ALA A 171 1 23 HELIX 8 8 THR A 187 ASN A 189 5 3 HELIX 9 9 THR A 190 ALA A 195 1 6 HELIX 10 10 ASP A 196 GLU A 205 1 10 HELIX 11 11 SER A 215 SER A 226 1 12 HELIX 12 12 SER A 227 ASP A 231 5 5 HELIX 13 13 GLY A 243 ARG A 247 5 5 HELIX 14 14 THR B 19 ALA B 32 1 14 HELIX 15 15 PRO B 44 ASP B 54 1 11 HELIX 16 16 ASP B 94 PHE B 98 5 5 HELIX 17 17 SER B 99 LEU B 111 1 13 HELIX 18 18 LEU B 111 GLY B 129 1 19 HELIX 19 19 SER B 139 PHE B 143 5 5 HELIX 20 20 VAL B 149 ALA B 171 1 23 HELIX 21 21 THR B 187 ASN B 189 5 3 HELIX 22 22 THR B 190 ALA B 195 1 6 HELIX 23 23 ASP B 196 ARG B 206 1 11 HELIX 24 24 HIS B 214 SER B 226 1 13 HELIX 25 25 SER B 227 ASP B 231 5 5 HELIX 26 26 GLY B 243 ARG B 247 5 5 SHEET 1 A 7 ALA A 58 LEU A 62 0 SHEET 2 A 7 GLU A 35 ALA A 40 1 N CYS A 38 O SER A 59 SHEET 3 A 7 LYS A 11 VAL A 14 1 N ALA A 12 O VAL A 37 SHEET 4 A 7 ILE A 82 ASN A 85 1 O VAL A 84 N LEU A 13 SHEET 5 A 7 GLY A 132 ILE A 137 1 O VAL A 135 N LEU A 83 SHEET 6 A 7 ILE A 175 PRO A 182 1 O ASN A 176 N VAL A 134 SHEET 7 A 7 ILE A 237 VAL A 240 1 O LEU A 238 N ALA A 179 SHEET 1 B 7 ALA B 58 LEU B 62 0 SHEET 2 B 7 GLU B 35 ALA B 40 1 N CYS B 38 O SER B 59 SHEET 3 B 7 LYS B 11 VAL B 14 1 N ALA B 12 O VAL B 37 SHEET 4 B 7 ILE B 82 ASN B 85 1 O VAL B 84 N LEU B 13 SHEET 5 B 7 GLY B 132 ILE B 137 1 O VAL B 135 N LEU B 83 SHEET 6 B 7 ILE B 175 PRO B 182 1 O ASN B 176 N VAL B 134 SHEET 7 B 7 ILE B 237 VAL B 240 1 O LEU B 238 N ALA B 179 SITE 1 AC1 38 GLY A 16 ASN A 18 THR A 19 GLY A 20 SITE 2 AC1 38 LEU A 21 ARG A 41 ARG A 42 ILE A 63 SITE 3 AC1 38 ASP A 64 PHE A 65 ALA A 66 ASN A 86 SITE 4 AC1 38 ALA A 87 GLY A 88 ILE A 89 ILE A 137 SITE 5 AC1 38 ALA A 138 TYR A 152 LYS A 156 PRO A 182 SITE 6 AC1 38 GLY A 183 TYR A 184 ILE A 185 THR A 187 SITE 7 AC1 38 ASN A 188 ASN A 189 THR A 190 HOH A 403 SITE 8 AC1 38 HOH A 434 HOH A 457 HOH A 471 HOH A 491 SITE 9 AC1 38 HOH A 511 HOH A 512 HOH A 520 HOH A 564 SITE 10 AC1 38 HOH A 578 HOH A 676 SITE 1 AC2 5 ILE A 90 ARG A 92 TYR A 184 HOH A 437 SITE 2 AC2 5 HOH A 443 SITE 1 AC3 40 GLY B 16 ASN B 18 THR B 19 GLY B 20 SITE 2 AC3 40 LEU B 21 ARG B 41 ARG B 42 ILE B 63 SITE 3 AC3 40 ASP B 64 PHE B 65 ALA B 66 ASN B 86 SITE 4 AC3 40 ALA B 87 GLY B 88 ILE B 89 ILE B 137 SITE 5 AC3 40 ALA B 138 TYR B 152 LYS B 156 PRO B 182 SITE 6 AC3 40 GLY B 183 ILE B 185 THR B 187 ASN B 189 SITE 7 AC3 40 THR B 190 HOH B 404 HOH B 444 HOH B 447 SITE 8 AC3 40 HOH B 449 HOH B 450 HOH B 493 HOH B 498 SITE 9 AC3 40 HOH B 545 HOH B 551 HOH B 555 HOH B 580 SITE 10 AC3 40 HOH B 586 HOH B 611 HOH B 672 HOH B 673 CRYST1 93.022 93.022 109.285 90.00 90.00 90.00 P 43 21 2 16 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 0.010750 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010750 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009150 0.00000