HEADER PLANT PROTEIN/RNA 05-FEB-18 5Z9X TITLE ARABIDOPSIS SMALL RNA DEGRADING NUCLEASE 1 IN COMPLEX WITH AN RNA TITLE 2 SUBSTRATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: SMALL RNA DEGRADING NUCLEASE 1; COMPND 3 CHAIN: A; COMPND 4 EC: 3.1.-.-; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: RNA (5'-R(P*GP*CP*CP*CP*AP*UP*UP*AP*G)-3'); COMPND 8 CHAIN: R; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; SOURCE 3 ORGANISM_COMMON: MOUSE-EAR CRESS; SOURCE 4 ORGANISM_TAXID: 3702; SOURCE 5 GENE: SDN1, AT3G50100, F3A4.180; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; SOURCE 12 ORGANISM_TAXID: 3702 KEYWDS EXONUCLEASE, MICRORNA TURNOVER, PROTEIN-RNA COMPLEX, PLANT PROTEIN, KEYWDS 2 PLANT PROTEIN-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.CHEN,L.LIU,C.YOU,J.GU,W.RUAN,L.ZHANG,J.GAN,C.CAO,Y.HUANG,X.CHEN, AUTHOR 2 J.MA REVDAT 4 03-APR-24 5Z9X 1 REMARK REVDAT 3 27-MAR-24 5Z9X 1 LINK REVDAT 2 03-OCT-18 5Z9X 1 JRNL REVDAT 1 27-JUN-18 5Z9X 0 JRNL AUTH J.CHEN,L.LIU,C.YOU,J.GU,W.RUAN,L.ZHANG,J.GAN,C.CAO,Y.HUANG, JRNL AUTH 2 X.CHEN,J.MA JRNL TITL STRUCTURAL AND BIOCHEMICAL INSIGHTS INTO SMALL RNA 3' END JRNL TITL 2 TRIMMING BY ARABIDOPSIS SDN1. JRNL REF NAT COMMUN V. 9 3585 2018 JRNL REFN ESSN 2041-1723 JRNL PMID 30181559 JRNL DOI 10.1038/S41467-018-05942-7 REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.4_1496 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) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.99 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.430 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 20211 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.253 REMARK 3 R VALUE (WORKING SET) : 0.252 REMARK 3 FREE R VALUE : 0.261 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.850 REMARK 3 FREE R VALUE TEST SET COUNT : 1991 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 28.9877 - 6.7223 0.98 1382 158 0.2066 0.2103 REMARK 3 2 6.7223 - 5.3466 1.00 1366 141 0.2768 0.2462 REMARK 3 3 5.3466 - 4.6740 0.99 1317 146 0.2178 0.2316 REMARK 3 4 4.6740 - 4.2481 0.99 1294 140 0.2018 0.2284 REMARK 3 5 4.2481 - 3.9444 0.99 1321 150 0.2130 0.2324 REMARK 3 6 3.9444 - 3.7123 0.99 1286 137 0.2305 0.2563 REMARK 3 7 3.7123 - 3.5267 0.99 1271 138 0.2428 0.2736 REMARK 3 8 3.5267 - 3.3735 0.99 1289 139 0.2657 0.2846 REMARK 3 9 3.3735 - 3.2438 1.00 1293 142 0.3142 0.3235 REMARK 3 10 3.2438 - 3.1320 0.99 1280 139 0.3176 0.3365 REMARK 3 11 3.1320 - 3.0341 1.00 1291 137 0.3621 0.4193 REMARK 3 12 3.0341 - 2.9475 0.99 1275 143 0.3716 0.3510 REMARK 3 13 2.9475 - 2.8700 0.99 1294 142 0.3893 0.4278 REMARK 3 14 2.8700 - 2.8000 0.99 1261 139 0.4021 0.4695 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) : 0.540 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 33.370 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 : 0.015 2524 REMARK 3 ANGLE : 1.843 3453 REMARK 3 CHIRALITY : 0.082 413 REMARK 3 PLANARITY : 0.008 410 REMARK 3 DIHEDRAL : 17.381 970 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 27.4711 39.4699 74.1192 REMARK 3 T TENSOR REMARK 3 T11: -0.3478 T22: 1.4473 REMARK 3 T33: 0.3587 T12: 0.4217 REMARK 3 T13: 0.0417 T23: -0.0929 REMARK 3 L TENSOR REMARK 3 L11: 2.0859 L22: 1.0794 REMARK 3 L33: 2.2153 L12: 0.1644 REMARK 3 L13: -0.1775 L23: 0.1069 REMARK 3 S TENSOR REMARK 3 S11: -0.2119 S12: 1.0518 S13: -0.0148 REMARK 3 S21: -0.6498 S22: 0.3314 S23: -0.0360 REMARK 3 S31: 0.2255 S32: -0.2707 S33: -0.0826 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 5Z9X COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 14-FEB-18. REMARK 100 THE DEPOSITION ID IS D_1300006733. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-APR-13 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.987 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 0.98.699A REMARK 200 DATA SCALING SOFTWARE : HKL-2000 0.98.699A REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20440 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 26.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.90 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX 1.7.1_743 REMARK 200 STARTING MODEL: SDN1 DELTAC-SSRNA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 69.45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: LITHUM SULFATE, MAGNESIUM CHLORIDE, 2 REMARK 280 -(N-MORPHOLINO) ETHANESULFONIC ACID, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 290K 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 59.54633 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 119.09267 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 119.09267 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 59.54633 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: 1730 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16310 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -52.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, R 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 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 609 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 247 REMARK 465 TYR A 248 REMARK 465 PRO A 249 REMARK 465 ASN A 250 REMARK 465 THR A 251 REMARK 465 ARG A 252 REMARK 465 GLU A 270 REMARK 465 VAL A 271 REMARK 465 ARG A 272 REMARK 465 LYS A 273 REMARK 465 THR A 274 REMARK 465 THR A 301 REMARK 465 THR A 302 REMARK 465 ILE A 303 REMARK 465 LYS A 304 REMARK 465 PRO A 305 REMARK 465 SER A 306 REMARK 465 LYS A 307 REMARK 465 GLU A 308 REMARK 465 MET A 309 REMARK 465 LEU A 310 REMARK 465 GLU A 311 REMARK 465 VAL A 312 REMARK 465 GLU A 313 REMARK 465 LYS A 314 REMARK 465 ALA A 315 REMARK 465 LYS A 316 REMARK 465 LEU A 317 REMARK 465 PHE A 318 REMARK 465 LEU A 319 REMARK 465 HIS A 320 REMARK 465 LYS A 321 REMARK 465 ILE A 322 REMARK 465 PRO A 323 REMARK 465 ASN A 324 REMARK 465 ASN A 325 REMARK 465 VAL A 326 REMARK 465 PRO A 327 REMARK 465 SER A 328 REMARK 465 GLU A 329 REMARK 465 GLU A 330 REMARK 465 LEU A 331 REMARK 465 GLU A 332 REMARK 465 GLN A 333 REMARK 465 VAL A 334 REMARK 465 LEU A 335 REMARK 465 SER A 336 REMARK 465 GLY A 337 REMARK 465 LYS A 338 REMARK 465 PHE A 339 REMARK 465 THR A 340 REMARK 465 LEU A 341 REMARK 465 ASP A 342 REMARK 465 VAL A 343 REMARK 465 LYS A 344 REMARK 465 GLN A 345 REMARK 465 ALA A 346 REMARK 465 LYS A 347 REMARK 465 THR A 348 REMARK 465 GLN A 349 REMARK 465 GLY A 350 REMARK 465 ARG A 351 REMARK 465 TYR A 352 REMARK 465 TYR A 353 REMARK 465 CYS A 354 REMARK 465 ALA A 355 REMARK 465 PHE A 356 REMARK 465 ALA A 357 REMARK 465 LEU A 358 REMARK 465 PHE A 359 REMARK 465 HIS A 360 REMARK 465 SER A 361 REMARK 465 SER A 362 REMARK 465 GLU A 363 REMARK 465 ASP A 364 REMARK 465 ALA A 365 REMARK 465 ASP A 366 REMARK 465 GLN A 367 REMARK 465 ALA A 368 REMARK 465 PHE A 369 REMARK 465 GLU A 370 REMARK 465 HIS A 371 REMARK 465 ILE A 372 REMARK 465 ASP A 373 REMARK 465 GLY A 374 REMARK 465 ILE A 375 REMARK 465 GLU A 376 REMARK 465 MET A 377 REMARK 465 THR A 378 REMARK 465 ASP A 379 REMARK 465 SER A 380 REMARK 465 LEU A 381 REMARK 465 GLY A 382 REMARK 465 LEU A 383 REMARK 465 PRO A 384 REMARK 465 GLN A 385 REMARK 465 LYS A 386 REMARK 465 VAL A 387 REMARK 465 VAL A 388 REMARK 465 ILE A 389 REMARK 465 ILE A 390 REMARK 465 LYS A 391 REMARK 465 LEU A 392 REMARK 465 SER A 393 REMARK 465 SER A 394 REMARK 465 GLY A 395 REMARK 465 SER A 396 REMARK 465 ARG A 397 REMARK 465 ALA A 398 REMARK 465 SER A 399 REMARK 465 ILE A 400 REMARK 465 TYR A 401 REMARK 465 VAL A 402 REMARK 465 ARG A 403 REMARK 465 LYS A 404 REMARK 465 MET A 405 REMARK 465 VAL A 406 REMARK 465 GLN A 407 REMARK 465 ASP A 408 REMARK 465 GLU A 409 REMARK 465 A R 1 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 41 CG CD CE NZ REMARK 470 ASN A 42 CG OD1 ND2 REMARK 470 ASP A 44 CG OD1 OD2 REMARK 470 ASP A 91 CG OD1 OD2 REMARK 470 LYS A 253 CG CD CE NZ REMARK 470 LEU A 254 CG CD1 CD2 REMARK 470 ILE A 266 CG1 CG2 CD1 REMARK 470 LEU A 267 CG CD1 CD2 REMARK 470 ASP A 300 CG OD1 OD2 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 613 O HOH A 622 2.06 REMARK 500 O PHE A 60 OG1 THR A 63 2.14 REMARK 500 OG SER A 119 O HOH A 601 2.14 REMARK 500 O CYS A 263 N LEU A 267 2.15 REMARK 500 NH1 ARG A 23 O3 SO4 A 501 2.15 REMARK 500 O ASP A 48 N SER A 50 2.16 REMARK 500 NH2 ARG A 23 O HOH A 602 2.17 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 ARG A 255 CB ARG A 255 CG 0.248 REMARK 500 ARG A 255 CG ARG A 255 CD 0.221 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 LEU A 171 N - CA - C ANGL. DEV. = -22.5 DEGREES REMARK 500 ARG A 255 NE - CZ - NH1 ANGL. DEV. = -4.7 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 GLN A 87 7.61 -65.20 REMARK 500 HIS A 106 129.96 -38.80 REMARK 500 PRO A 180 -173.29 -64.63 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ARG A 51 ARG A 52 -134.38 REMARK 500 GLN A 90 ASP A 91 -148.14 REMARK 500 GLU A 120 ASP A 121 143.67 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 MG A 502 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 144 OD2 REMARK 620 2 HIS A 223 O 136.8 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 503 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 144 OD1 REMARK 620 2 GLU A 146 OE2 137.6 REMARK 620 3 ASP A 283 OD2 97.9 114.6 REMARK 620 4 G R 10 OP1 84.0 118.0 94.1 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 R 101 DBREF 5Z9X A 1 409 UNP A3KPE8 SDN1_ARATH 1 409 DBREF 5Z9X R 1 10 PDB 5Z9X 5Z9X 1 10 SEQRES 1 A 409 MET GLU LEU LYS LEU ALA THR ALA GLU LYS GLN VAL LEU SEQRES 2 A 409 ASP GLU LEU VAL LYS LEU LEU GLN SER ARG ASP LEU ARG SEQRES 3 A 409 GLY GLU ASN GLY ASN TRP LYS GLU PHE LEU HIS VAL TYR SEQRES 4 A 409 ASP LYS ASN ALA ASP SER PRO SER ASP PRO SER ARG ARG SEQRES 5 A 409 SER HIS GLU ASP LEU VAL GLN PHE LEU THR THR PHE LYS SEQRES 6 A 409 LYS LYS GLU ASP LEU GLN LEU LEU LYS CYS HIS ALA ASN SEQRES 7 A 409 HIS LEU LEU ILE GLU ASN LEU LYS GLN GLU SER GLN ASP SEQRES 8 A 409 GLU ASP THR PRO GLU GLN MET LEU VAL ARG LEU THR VAL SEQRES 9 A 409 GLU HIS PRO SER TYR SER LEU ASP TYR SER PHE LYS PRO SEQRES 10 A 409 TYR SER GLU ASP TRP PHE VAL SER ASP VAL GLY MET LYS SEQRES 11 A 409 MET LYS LYS VAL MET GLU SER THR ASN MET VAL ALA VAL SEQRES 12 A 409 ASP CYS GLU MET VAL LEU CYS GLU ASP GLY THR GLU GLY SEQRES 13 A 409 LEU VAL ARG VAL GLY VAL VAL ASP ARG ASP LEU LYS VAL SEQRES 14 A 409 ILE LEU ASP GLU PHE VAL LYS PRO ASN LYS PRO VAL VAL SEQRES 15 A 409 ASP TYR ARG THR ASP ILE THR GLY ILE THR ALA GLU ASP SEQRES 16 A 409 ILE GLU ASN ALA SER LEU SER VAL VAL ASP ILE GLN GLU SEQRES 17 A 409 THR LEU GLN PRO PHE LEU SER THR GLY THR ILE LEU VAL SEQRES 18 A 409 GLY HIS SER LEU ASN ARG ASP LEU GLU VAL LEU LYS ILE SEQRES 19 A 409 ASP HIS PRO LYS VAL ILE ASP THR ALA LEU VAL PHE LYS SEQRES 20 A 409 TYR PRO ASN THR ARG LYS LEU ARG ARG PRO SER LEU ASN SEQRES 21 A 409 ASN LEU CYS LYS SER ILE LEU GLY TYR GLU VAL ARG LYS SEQRES 22 A 409 THR GLY VAL PRO HIS ASP CYS VAL HIS ASP ALA SER ALA SEQRES 23 A 409 ALA MET LYS LEU ALA LEU ALA VAL VAL GLU LYS ARG VAL SEQRES 24 A 409 ASP THR THR ILE LYS PRO SER LYS GLU MET LEU GLU VAL SEQRES 25 A 409 GLU LYS ALA LYS LEU PHE LEU HIS LYS ILE PRO ASN ASN SEQRES 26 A 409 VAL PRO SER GLU GLU LEU GLU GLN VAL LEU SER GLY LYS SEQRES 27 A 409 PHE THR LEU ASP VAL LYS GLN ALA LYS THR GLN GLY ARG SEQRES 28 A 409 TYR TYR CYS ALA PHE ALA LEU PHE HIS SER SER GLU ASP SEQRES 29 A 409 ALA ASP GLN ALA PHE GLU HIS ILE ASP GLY ILE GLU MET SEQRES 30 A 409 THR ASP SER LEU GLY LEU PRO GLN LYS VAL VAL ILE ILE SEQRES 31 A 409 LYS LEU SER SER GLY SER ARG ALA SER ILE TYR VAL ARG SEQRES 32 A 409 LYS MET VAL GLN ASP GLU SEQRES 1 R 10 A G C C C A U U A G HET SO4 A 501 5 HET MG A 502 1 HET MG A 503 1 HET SO4 R 101 5 HETNAM SO4 SULFATE ION HETNAM MG MAGNESIUM ION FORMUL 3 SO4 2(O4 S 2-) FORMUL 4 MG 2(MG 2+) FORMUL 7 HOH *27(H2 O) HELIX 1 AA1 GLU A 9 ASP A 24 1 16 HELIX 2 AA2 ASN A 31 TYR A 39 1 9 HELIX 3 AA3 SER A 53 THR A 62 1 10 HELIX 4 AA4 LYS A 66 GLN A 87 1 22 HELIX 5 AA5 SER A 89 ASP A 93 5 5 HELIX 6 AA6 THR A 94 HIS A 106 1 13 HELIX 7 AA7 SER A 108 TYR A 113 1 6 HELIX 8 AA8 ASP A 126 LYS A 130 5 5 HELIX 9 AA9 MET A 131 GLU A 136 1 6 HELIX 10 AB1 ILE A 191 ASN A 198 1 8 HELIX 11 AB2 SER A 202 THR A 216 1 15 HELIX 12 AB3 SER A 224 LYS A 233 1 10 HELIX 13 AB4 THR A 242 PHE A 246 1 5 HELIX 14 AB5 SER A 258 LEU A 267 1 10 HELIX 15 AB6 ASP A 279 LYS A 297 1 19 SHEET 1 AA1 2 PHE A 123 VAL A 124 0 SHEET 2 AA1 2 ILE A 234 ASP A 235 1 O ASP A 235 N PHE A 123 SHEET 1 AA2 5 VAL A 169 PHE A 174 0 SHEET 2 AA2 5 GLU A 155 ASP A 164 -1 N VAL A 162 O LEU A 171 SHEET 3 AA2 5 MET A 140 LEU A 149 -1 N ASP A 144 O GLY A 161 SHEET 4 AA2 5 ILE A 219 GLY A 222 1 O ILE A 219 N VAL A 141 SHEET 5 AA2 5 VAL A 239 ASP A 241 1 O ILE A 240 N GLY A 222 LINK OD2 ASP A 144 MG MG A 502 1555 1555 2.17 LINK OD1 ASP A 144 MG MG A 503 1555 1555 2.15 LINK OE2BGLU A 146 MG MG A 503 1555 1555 2.17 LINK O HIS A 223 MG MG A 502 1555 1555 2.88 LINK OD2 ASP A 283 MG MG A 503 1555 1555 2.16 LINK MG MG A 503 OP1 G R 10 1555 1555 2.18 CISPEP 1 LYS A 116 PRO A 117 0 5.02 CISPEP 2 THR A 186 ASP A 187 0 28.24 SITE 1 AC1 4 ARG A 23 LEU A 72 LYS A 116 HOH A 618 SITE 1 AC2 4 ASP A 144 HIS A 223 ASP A 228 G R 10 SITE 1 AC3 6 ASP A 144 CYS A 145 GLU A 146 CYS A 280 SITE 2 AC3 6 ASP A 283 G R 10 SITE 1 AC4 2 A R 9 G R 10 CRYST1 87.993 87.993 178.639 90.00 90.00 120.00 P 31 2 1 6 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 0.011365 0.006561 0.000000 0.00000 SCALE2 0.000000 0.013123 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005598 0.00000