HEADER LYASE 14-JUN-18 6DSR TITLE RE-REFINEMENT OF P. FALCIPARUM OROTIDINE 5'-MONOPHOSPHATE TITLE 2 DECARBOXYLASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE; COMPND 3 CHAIN: A, B; COMPND 4 EC: 4.1.1.23; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PLASMODIUM FALCIPARUM; SOURCE 3 ORGANISM_TAXID: 5833; SOURCE 4 GENE: OMPDC; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS COMPLEX, P FALCIPARUM, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR G.S.BRANDT,W.R.P.NOVAK REVDAT 2 11-OCT-23 6DSR 1 REMARK REVDAT 1 17-OCT-18 6DSR 0 JRNL AUTH W.R.P.NOVAK,K.H.J.WEST,L.M.D.KIRKMAN,G.S.BRANDT JRNL TITL RE-REFINEMENT OF PLASMODIUM FALCIPARUM OROTIDINE JRNL TITL 2 5'-MONOPHOSPHATE DECARBOXYLASE PROVIDES A CLEARER PICTURE OF JRNL TITL 3 AN IMPORTANT MALARIAL DRUG TARGET. JRNL REF ACTA CRYSTALLOGR F STRUCT V. 74 664 2018 JRNL REF 2 BIOL COMMUN JRNL REFN ESSN 2053-230X JRNL PMID 30279319 JRNL DOI 10.1107/S2053230X18010610 REMARK 0 REMARK 0 THIS ENTRY 6DSR REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL REMARK 0 DATA IN 2ZA1 DETERMINED BY AUTHOR: TOKUOKA, K., INOUE, T. REMARK 0 ORIGINAL DATA REFERENCE 1 REMARK 0 PDB ID: 2ZA1 REMARK 0 AUTH K.TOKUOKA,Y.KUSAKARI,S.R.KRUNGKRAI,H.MATSUMURA,Y.KAI, REMARK 0 AUTH 2 J.KRUNGKRAI,T.HORII,T.INOUE REMARK 0 TITL STRUCTURAL BASIS FOR THE DECARBOXYLATION OF OROTIDINE REMARK 0 TITL 2 5'-MONOPHOSPHATE (OMP) BY PLASMODIUM FALCIPARUM OMP REMARK 0 TITL 3 DECARBOXYLASE. REMARK 0 REF J. BIOCHEM. V. 143 69 2008 REMARK 0 REFN ISSN 0021-924X REMARK 0 PMID 17981823 REMARK 0 DOI 10.1093/JB/MVM193 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.10.1_2155 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.73 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.030 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 20423 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.224 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.140 REMARK 3 FREE R VALUE TEST SET COUNT : 1049 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 36.7375 - 4.9640 0.98 2765 138 0.1640 0.1781 REMARK 3 2 4.9640 - 3.9416 1.00 2799 150 0.1546 0.1834 REMARK 3 3 3.9416 - 3.4437 1.00 2771 162 0.1760 0.2239 REMARK 3 4 3.4437 - 3.1291 0.98 2805 133 0.2087 0.2942 REMARK 3 5 3.1291 - 2.9049 0.98 2746 161 0.2253 0.2801 REMARK 3 6 2.9049 - 2.7337 0.98 2736 154 0.2301 0.3012 REMARK 3 7 2.7337 - 2.5968 0.98 2752 151 0.2426 0.3246 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.380 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.830 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 53.30 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 : 0.004 5149 REMARK 3 ANGLE : 0.715 6973 REMARK 3 CHIRALITY : 0.050 762 REMARK 3 PLANARITY : 0.005 894 REMARK 3 DIHEDRAL : 12.508 3057 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 ((RESID 1 AND (NAME N OR REMARK 3 NAME CA OR NAME CB OR NAME C OR NAME O )) REMARK 3 OR RESSEQ 2:8 OR (RESID 9 AND (NAME N OR REMARK 3 NAME CA OR NAME CB OR NAME C OR NAME O )) REMARK 3 OR RESSEQ 10:29 OR (RESID 30 AND (NAME N REMARK 3 OR NAME CA OR NAME CB OR NAME C OR NAME O REMARK 3 )) OR RESSEQ 31:41 OR (RESID 42 AND (NAME REMARK 3 N OR NAME CA OR NAME CB OR NAME C OR NAME REMARK 3 O )) OR RESSEQ 43:44 OR (RESID 45 AND REMARK 3 (NAME N OR NAME CA OR NAME CB OR NAME C REMARK 3 OR NAME O )) OR RESSEQ 46:48 OR (RESID 49 REMARK 3 AND (NAME N OR NAME CA OR NAME CB OR NAME REMARK 3 C OR NAME O )) OR RESSEQ 50 OR (RESID 51 REMARK 3 AND (NAME N OR NAME CA OR NAME CB OR NAME REMARK 3 C OR NAME O )) OR (RESID 52 AND (NAME N REMARK 3 OR NAME CA OR NAME CB OR NAME C OR NAME O REMARK 3 )) OR RESSEQ 53 OR RESSEQ 55:60 OR RESSEQ REMARK 3 62:67 OR (RESID 75 AND (NAME N OR NAME CA REMARK 3 OR NAME CB OR NAME C OR NAME O )) OR REMARK 3 RESSEQ 76:95 OR RESSEQ 97:179 OR (RESID REMARK 3 180 AND (NAME N OR NAME CA OR NAME CB OR REMARK 3 NAME C OR NAME O )) OR (RESID 181 AND REMARK 3 (NAME N OR NAME CA OR NAME CB OR NAME C REMARK 3 OR NAME O )) OR RESSEQ 183:249 OR RESSEQ REMARK 3 251:268 OR (RESID 269 AND (NAME N OR NAME REMARK 3 CA OR NAME CB OR NAME CG OR NAME CD OR REMARK 3 NAME OE1 OR NAME NE2)) OR RESSEQ 270:316)) REMARK 3 SELECTION : (CHAIN B AND (RESSEQ 1:38 OR (RESID 39 REMARK 3 AND (NAME N OR NAME CA OR NAME CB OR NAME REMARK 3 C OR NAME O )) OR RESSEQ 40:45 OR (RESID REMARK 3 46 AND (NAME N OR NAME CA OR NAME CB OR REMARK 3 NAME C OR NAME O )) OR RESSEQ 47:53 OR REMARK 3 RESSEQ 55:60 OR RESSEQ 62:67 OR RESSEQ 75: REMARK 3 95 OR RESSEQ 97:181 OR RESSEQ 183:208 OR REMARK 3 (RESID 209 AND (NAME N OR NAME CA OR NAME REMARK 3 CB OR NAME C OR NAME O )) OR (RESID 210 REMARK 3 AND (NAME N OR NAME CA OR NAME CB OR NAME REMARK 3 C OR NAME O )) OR RESSEQ 211:249 OR REMARK 3 RESSEQ 251:268 OR (RESID 269 AND (NAME N REMARK 3 OR NAME CA OR NAME CB OR NAME CG OR NAME REMARK 3 CD OR NAME OE1 OR NAME NE2)) OR RESSEQ REMARK 3 270:271 OR (RESID 272 AND (NAME N OR NAME REMARK 3 CA OR NAME CB OR NAME C OR NAME O )) OR REMARK 3 RESSEQ 273:274 OR (RESID 275 AND (NAME N REMARK 3 OR NAME CA OR NAME CB OR NAME C OR NAME O REMARK 3 )) OR RESSEQ 276:316)) REMARK 3 ATOM PAIRS NUMBER : 2734 REMARK 3 RMSD : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6DSR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB. REMARK 100 THE DEPOSITION ID IS D_1000234475. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-NOV-06 REMARK 200 TEMPERATURE (KELVIN) : 93 REMARK 200 PH : 9.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL38B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20677 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.597 REMARK 200 RESOLUTION RANGE LOW (A) : 36.734 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 4.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL 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 REMARK 200 STARTING MODEL: 3N3M REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.91 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 23% PEG 3000, PH 9.5, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 X+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,Z+2/3 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 0.00000 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 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 100.93950 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 58.27745 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 14.73033 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 100.93950 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 58.27745 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 14.73033 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 100.93950 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 58.27745 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 14.73033 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 116.55489 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 29.46067 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 116.55489 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 29.46067 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 116.55489 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 29.46067 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: 6210 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22380 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -35.0 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 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 ASP A 68 REMARK 465 ASN A 69 REMARK 465 ILE A 70 REMARK 465 ILE A 71 REMARK 465 ARG A 72 REMARK 465 GLU A 73 REMARK 465 MET A 321 REMARK 465 GLU A 322 REMARK 465 SER A 323 REMARK 465 ASN B 69 REMARK 465 ILE B 70 REMARK 465 ILE B 71 REMARK 465 ARG B 72 REMARK 465 GLU B 73 REMARK 465 GLU B 74 REMARK 465 LYS B 318 REMARK 465 GLN B 319 REMARK 465 ASN B 320 REMARK 465 MET B 321 REMARK 465 GLU B 322 REMARK 465 SER B 323 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 9 CD CE NZ REMARK 470 LYS A 34 CG CD CE NZ REMARK 470 ASN A 39 CG OD1 ND2 REMARK 470 LYS A 46 CG CD CE NZ REMARK 470 GLU A 74 CG CD OE1 OE2 REMARK 470 LYS A 184 CG CD CE NZ REMARK 470 ILE A 201 CG1 CG2 CD1 REMARK 470 ASP A 209 CG OD1 OD2 REMARK 470 ASN A 210 CG OD1 ND2 REMARK 470 TYR A 255 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ASN A 270 CG OD1 ND2 REMARK 470 ASP A 272 CG OD1 OD2 REMARK 470 LYS A 275 CG CD CE NZ REMARK 470 LYS A 283 CG CD CE NZ REMARK 470 LYS A 304 CG CD CE NZ REMARK 470 ASN A 314 CG OD1 ND2 REMARK 470 LYS A 318 CG CD CE NZ REMARK 470 GLN A 319 CG CD OE1 NE2 REMARK 470 MET B 1 CG SD CE REMARK 470 LYS B 9 CG CD CE NZ REMARK 470 GLU B 30 CG CD OE1 OE2 REMARK 470 LYS B 34 CG CD CE NZ REMARK 470 ASN B 42 CG OD1 ND2 REMARK 470 LYS B 45 CG CD CE NZ REMARK 470 LYS B 49 CG CD CE NZ REMARK 470 LYS B 51 CG CD CE NZ REMARK 470 TYR B 52 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS B 75 CG CD CE NZ REMARK 470 GLU B 180 CG CD OE1 OE2 REMARK 470 GLU B 181 CG CD OE1 OE2 REMARK 470 LYS B 184 CG CD CE NZ REMARK 470 ILE B 201 CG1 CG2 CD1 REMARK 470 TYR B 255 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ASN B 270 CG OD1 ND2 REMARK 470 LYS B 283 CG CD CE NZ REMARK 470 LYS B 304 CG CD CE NZ REMARK 470 ASN B 314 CG OD1 ND2 REMARK 470 LEU B 317 CG CD1 CD2 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 OH TYR A 186 O HOH A 501 1.81 REMARK 500 OH TYR A 111 O HOH A 502 2.01 REMARK 500 O3P U5P B 401 O HOH B 501 2.04 REMARK 500 OG SER A 225 O HOH A 503 2.13 REMARK 500 ND2 ASN A 183 O HOH A 504 2.19 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 ASP A 141 -177.68 -179.08 REMARK 500 ASN A 270 56.42 76.50 REMARK 500 ASP B 141 -177.52 -179.58 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 U5P A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue U5P B 401 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2ZA1 RELATED DB: PDB REMARK 900 THIS ENTRY 6DSR REFLECTS AN ALTERNATIVE MODELING OF X-RAY DATA IN REMARK 900 ENTRY 2ZA1 DBREF 6DSR A 1 323 UNP Q8T6J6 Q8T6J6_PLAFA 1 323 DBREF 6DSR B 1 323 UNP Q8T6J6 Q8T6J6_PLAFA 1 323 SEQRES 1 A 323 MET GLY PHE LYS VAL LYS LEU GLU LYS ARG ARG ASN ALA SEQRES 2 A 323 ILE ASN THR CYS LEU CYS ILE GLY LEU ASP PRO ASP GLU SEQRES 3 A 323 LYS ASP ILE GLU ASN PHE MET LYS ASN GLU LYS GLU ASN SEQRES 4 A 323 ASN TYR ASN ASN ILE LYS LYS ASN LEU LYS GLU LYS TYR SEQRES 5 A 323 ILE ASN ASN VAL SER ILE LYS LYS ASP ILE LEU LEU LYS SEQRES 6 A 323 ALA PRO ASP ASN ILE ILE ARG GLU GLU LYS SER GLU GLU SEQRES 7 A 323 PHE PHE TYR PHE PHE ASN HIS PHE CYS PHE TYR ILE ILE SEQRES 8 A 323 ASN GLU THR ASN LYS TYR ALA LEU THR PHE LYS MET ASN SEQRES 9 A 323 PHE ALA PHE TYR ILE PRO TYR GLY SER VAL GLY ILE ASP SEQRES 10 A 323 VAL LEU LYS ASN VAL PHE ASP TYR LEU TYR GLU LEU ASN SEQRES 11 A 323 ILE PRO THR ILE LEU ASP MET LYS ILE ASN ASP ILE GLY SEQRES 12 A 323 ASN THR VAL LYS ASN TYR ARG LYS PHE ILE PHE GLU TYR SEQRES 13 A 323 LEU LYS SER ASP SER CYS THR VAL ASN ILE TYR MET GLY SEQRES 14 A 323 THR ASN MET LEU LYS ASP ILE CYS TYR ASP GLU GLU LYS SEQRES 15 A 323 ASN LYS TYR TYR SER ALA PHE VAL LEU VAL LYS THR THR SEQRES 16 A 323 ASN PRO ASP SER ALA ILE PHE GLN LYS ASN LEU SER LEU SEQRES 17 A 323 ASP ASN LYS GLN ALA TYR VAL ILE MET ALA GLN GLU ALA SEQRES 18 A 323 LEU ASN MET SER SER TYR LEU ASN LEU GLU GLN ASN ASN SEQRES 19 A 323 GLU PHE ILE GLY PHE VAL VAL GLY ALA ASN SER TYR ASP SEQRES 20 A 323 GLU MET ASN TYR ILE ARG THR TYR PHE PRO ASN CYS TYR SEQRES 21 A 323 ILE LEU SER PRO GLY ILE GLY ALA GLN ASN GLY ASP LEU SEQRES 22 A 323 HIS LYS THR LEU THR ASN GLY TYR HIS LYS SER TYR GLU SEQRES 23 A 323 LYS ILE LEU ILE ASN ILE GLY ARG ALA ILE THR LYS ASN SEQRES 24 A 323 PRO TYR PRO GLN LYS ALA ALA GLN MET TYR TYR ASP GLN SEQRES 25 A 323 ILE ASN ALA ILE LEU LYS GLN ASN MET GLU SER SEQRES 1 B 323 MET GLY PHE LYS VAL LYS LEU GLU LYS ARG ARG ASN ALA SEQRES 2 B 323 ILE ASN THR CYS LEU CYS ILE GLY LEU ASP PRO ASP GLU SEQRES 3 B 323 LYS ASP ILE GLU ASN PHE MET LYS ASN GLU LYS GLU ASN SEQRES 4 B 323 ASN TYR ASN ASN ILE LYS LYS ASN LEU LYS GLU LYS TYR SEQRES 5 B 323 ILE ASN ASN VAL SER ILE LYS LYS ASP ILE LEU LEU LYS SEQRES 6 B 323 ALA PRO ASP ASN ILE ILE ARG GLU GLU LYS SER GLU GLU SEQRES 7 B 323 PHE PHE TYR PHE PHE ASN HIS PHE CYS PHE TYR ILE ILE SEQRES 8 B 323 ASN GLU THR ASN LYS TYR ALA LEU THR PHE LYS MET ASN SEQRES 9 B 323 PHE ALA PHE TYR ILE PRO TYR GLY SER VAL GLY ILE ASP SEQRES 10 B 323 VAL LEU LYS ASN VAL PHE ASP TYR LEU TYR GLU LEU ASN SEQRES 11 B 323 ILE PRO THR ILE LEU ASP MET LYS ILE ASN ASP ILE GLY SEQRES 12 B 323 ASN THR VAL LYS ASN TYR ARG LYS PHE ILE PHE GLU TYR SEQRES 13 B 323 LEU LYS SER ASP SER CYS THR VAL ASN ILE TYR MET GLY SEQRES 14 B 323 THR ASN MET LEU LYS ASP ILE CYS TYR ASP GLU GLU LYS SEQRES 15 B 323 ASN LYS TYR TYR SER ALA PHE VAL LEU VAL LYS THR THR SEQRES 16 B 323 ASN PRO ASP SER ALA ILE PHE GLN LYS ASN LEU SER LEU SEQRES 17 B 323 ASP ASN LYS GLN ALA TYR VAL ILE MET ALA GLN GLU ALA SEQRES 18 B 323 LEU ASN MET SER SER TYR LEU ASN LEU GLU GLN ASN ASN SEQRES 19 B 323 GLU PHE ILE GLY PHE VAL VAL GLY ALA ASN SER TYR ASP SEQRES 20 B 323 GLU MET ASN TYR ILE ARG THR TYR PHE PRO ASN CYS TYR SEQRES 21 B 323 ILE LEU SER PRO GLY ILE GLY ALA GLN ASN GLY ASP LEU SEQRES 22 B 323 HIS LYS THR LEU THR ASN GLY TYR HIS LYS SER TYR GLU SEQRES 23 B 323 LYS ILE LEU ILE ASN ILE GLY ARG ALA ILE THR LYS ASN SEQRES 24 B 323 PRO TYR PRO GLN LYS ALA ALA GLN MET TYR TYR ASP GLN SEQRES 25 B 323 ILE ASN ALA ILE LEU LYS GLN ASN MET GLU SER HET U5P A 401 21 HET U5P B 401 21 HETNAM U5P URIDINE-5'-MONOPHOSPHATE FORMUL 3 U5P 2(C9 H13 N2 O9 P) FORMUL 5 HOH *54(H2 O) HELIX 1 AA1 GLY A 2 ASN A 15 1 14 HELIX 2 AA2 ASP A 25 ASN A 39 1 15 HELIX 3 AA3 TYR A 41 GLU A 50 1 10 HELIX 4 AA4 LYS A 51 VAL A 56 5 6 HELIX 5 AA5 LYS A 59 LYS A 65 1 7 HELIX 6 AA6 GLU A 77 ASN A 95 1 19 HELIX 7 AA7 LYS A 96 ALA A 98 5 3 HELIX 8 AA8 ALA A 106 ILE A 109 5 4 HELIX 9 AA9 GLY A 112 LEU A 129 1 18 HELIX 10 AB1 ILE A 142 GLU A 155 1 14 HELIX 11 AB2 ILE A 166 ILE A 176 5 11 HELIX 12 AB3 SER A 199 LYS A 204 1 6 HELIX 13 AB4 ALA A 213 LEU A 228 1 16 HELIX 14 AB5 LEU A 230 ASN A 234 5 5 HELIX 15 AB6 SER A 245 PHE A 256 1 12 HELIX 16 AB7 ASP A 272 GLY A 280 1 9 HELIX 17 AB8 SER A 284 GLU A 286 5 3 HELIX 18 AB9 GLY A 293 LYS A 298 1 6 HELIX 19 AC1 TYR A 301 GLN A 319 1 19 HELIX 20 AC2 GLY B 2 ASN B 15 1 14 HELIX 21 AC3 ASP B 25 ASN B 39 1 15 HELIX 22 AC4 TYR B 41 GLU B 50 1 10 HELIX 23 AC5 LYS B 51 VAL B 56 5 6 HELIX 24 AC6 LYS B 59 LEU B 64 1 6 HELIX 25 AC7 GLU B 77 ASN B 95 1 19 HELIX 26 AC8 LYS B 96 ALA B 98 5 3 HELIX 27 AC9 ALA B 106 ILE B 109 5 4 HELIX 28 AD1 GLY B 112 LEU B 129 1 18 HELIX 29 AD2 ILE B 142 GLU B 155 1 14 HELIX 30 AD3 ILE B 166 ILE B 176 5 11 HELIX 31 AD4 SER B 199 LYS B 204 1 6 HELIX 32 AD5 ALA B 213 LEU B 228 1 16 HELIX 33 AD6 LEU B 230 ASN B 234 5 5 HELIX 34 AD7 SER B 245 PHE B 256 1 12 HELIX 35 AD8 ASP B 272 GLY B 280 1 9 HELIX 36 AD9 SER B 284 GLU B 286 5 3 HELIX 37 AE1 GLY B 293 LYS B 298 1 6 HELIX 38 AE2 TYR B 301 ILE B 316 1 16 SHEET 1 AA1 9 LEU A 18 GLY A 21 0 SHEET 2 AA1 9 THR A 100 ASN A 104 1 O THR A 100 N ILE A 20 SHEET 3 AA1 9 THR A 133 ILE A 139 1 O ILE A 134 N MET A 103 SHEET 4 AA1 9 SER A 161 VAL A 164 1 O SER A 161 N LEU A 135 SHEET 5 AA1 9 SER A 187 LYS A 193 1 O PHE A 189 N VAL A 164 SHEET 6 AA1 9 ILE A 237 VAL A 241 1 O GLY A 238 N ALA A 188 SHEET 7 AA1 9 ILE A 261 SER A 263 1 O LEU A 262 N PHE A 239 SHEET 8 AA1 9 ILE A 288 ILE A 292 1 O LEU A 289 N SER A 263 SHEET 9 AA1 9 LEU A 18 GLY A 21 1 N CYS A 19 O ILE A 290 SHEET 1 AA2 2 TYR A 178 ASP A 179 0 SHEET 2 AA2 2 LYS A 184 TYR A 185 -1 O LYS A 184 N ASP A 179 SHEET 1 AA3 2 SER A 207 LEU A 208 0 SHEET 2 AA3 2 LYS A 211 GLN A 212 -1 O LYS A 211 N LEU A 208 SHEET 1 AA4 9 LEU B 18 GLY B 21 0 SHEET 2 AA4 9 THR B 100 ASN B 104 1 O THR B 100 N ILE B 20 SHEET 3 AA4 9 THR B 133 ILE B 139 1 O ILE B 134 N MET B 103 SHEET 4 AA4 9 SER B 161 VAL B 164 1 O SER B 161 N LEU B 135 SHEET 5 AA4 9 SER B 187 LYS B 193 1 O LEU B 191 N VAL B 164 SHEET 6 AA4 9 ILE B 237 VAL B 241 1 O GLY B 238 N VAL B 190 SHEET 7 AA4 9 ILE B 261 SER B 263 1 O LEU B 262 N PHE B 239 SHEET 8 AA4 9 ILE B 288 ILE B 292 1 O LEU B 289 N SER B 263 SHEET 9 AA4 9 LEU B 18 GLY B 21 1 N CYS B 19 O ILE B 290 SHEET 1 AA5 2 TYR B 178 ASP B 179 0 SHEET 2 AA5 2 LYS B 184 TYR B 185 -1 O LYS B 184 N ASP B 179 SHEET 1 AA6 2 SER B 207 LEU B 208 0 SHEET 2 AA6 2 LYS B 211 GLN B 212 -1 O LYS B 211 N LEU B 208 SITE 1 AC1 15 ASP A 23 LYS A 102 ASN A 104 ASP A 136 SITE 2 AC1 15 LYS A 138 THR A 194 THR A 195 PRO A 264 SITE 3 AC1 15 GLN A 269 GLY A 293 ARG A 294 HOH A 509 SITE 4 AC1 15 ASP B 141 ILE B 142 THR B 145 SITE 1 AC2 18 ASP A 141 ILE A 142 THR A 145 ASP B 23 SITE 2 AC2 18 LYS B 102 ASN B 104 ASP B 136 LYS B 138 SITE 3 AC2 18 THR B 194 THR B 195 PRO B 264 GLN B 269 SITE 4 AC2 18 ASN B 291 GLY B 293 ARG B 294 HOH B 501 SITE 5 AC2 18 HOH B 513 HOH B 514 CRYST1 201.879 201.879 44.191 90.00 90.00 120.00 H 3 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 0.004953 0.002860 0.000000 0.00000 SCALE2 0.000000 0.005720 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022629 0.00000