HEADER LYASE 26-SEP-07 2ZA3 TITLE CRYSTAL STRUCTURE OF OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE TITLE 2 COMPLEXED WITH URIDINE 5'-MONOPHOSPHATE FROM P.FALCIPARUM COMPND MOL_ID: 1; COMPND 2 MOLECULE: OROTIDINE 5'-PHOSPHATE 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_COMMON: MALARIA PARASITE P. FALCIPARUM; SOURCE 4 ORGANISM_TAXID: 5833; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PTRCHIS-TOPO KEYWDS OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE, PLASMODIUM FALCIPARUM, KEYWDS 2 URIDINE 5'-MONOPHOSPHATE, LYASE, PYRIMIDINE BIOSYNTHESIS EXPDTA X-RAY DIFFRACTION AUTHOR K.TOKUOKA,T.INOUE REVDAT 4 01-NOV-23 2ZA3 1 REMARK REVDAT 3 24-FEB-09 2ZA3 1 VERSN REVDAT 2 05-FEB-08 2ZA3 1 JRNL REVDAT 1 04-DEC-07 2ZA3 0 JRNL AUTH K.TOKUOKA,Y.KUSAKARI,S.R.KRUNGKRAI,H.MATSUMURA,Y.KAI, JRNL AUTH 2 J.KRUNGKRAI,T.HORII,T.INOUE JRNL TITL STRUCTURAL BASIS FOR THE DECARBOXYLATION OF OROTIDINE JRNL TITL 2 5'-MONOPHOSPHATE (OMP) BY PLASMODIUM FALCIPARUM OMP JRNL TITL 3 DECARBOXYLASE JRNL REF J.BIOCHEM.(TOKYO) V. 143 69 2008 JRNL REFN ISSN 0021-924X JRNL PMID 17981823 JRNL DOI 10.1093/JB/MVM193 REMARK 2 REMARK 2 RESOLUTION. 2.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.27 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 2267742.760 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 19658 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.204 REMARK 3 FREE R VALUE : 0.287 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1939 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.007 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.65 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.82 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.90 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3000 REMARK 3 BIN R VALUE (WORKING SET) : 0.2840 REMARK 3 BIN FREE R VALUE : 0.4000 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.40 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 313 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.023 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5098 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 42 REMARK 3 SOLVENT ATOMS : 47 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 60.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 51.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.33000 REMARK 3 B22 (A**2) : 1.33000 REMARK 3 B33 (A**2) : -2.67000 REMARK 3 B12 (A**2) : 8.58000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.31 REMARK 3 ESD FROM SIGMAA (A) : 0.30 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.47 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.51 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 21.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.820 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.35 REMARK 3 BSOL : 53.66 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : UMP_XPLOR.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : UMP_XPLOR.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2ZA3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 03-OCT-07. REMARK 100 THE DEPOSITION ID IS D_1000027711. 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) : 1.0 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 : 20877 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 (%) : 99.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.08700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL 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) : 2.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.31700 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: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 2ZA2 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.19 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.33 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 101.25000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 58.45671 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 14.90000 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 101.25000 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 58.45671 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 14.90000 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 101.25000 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 58.45671 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 14.90000 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 116.91343 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 29.80000 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 116.91343 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 29.80000 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 116.91343 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 29.80000 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: 6260 ANGSTROM**2 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 ILE A 70 REMARK 465 ILE A 71 REMARK 465 ARG A 72 REMARK 465 GLN A 319 REMARK 465 ASN A 320 REMARK 465 MET A 321 REMARK 465 GLU A 322 REMARK 465 SER A 323 REMARK 465 GLU B 73 REMARK 465 GLU B 74 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 MET A 1 CG SD CE REMARK 470 LYS A 27 CG CD CE NZ REMARK 470 LYS A 34 CG CD CE NZ REMARK 470 ASN A 42 CG OD1 ND2 REMARK 470 LEU A 273 CG CD1 CD2 REMARK 470 TYR A 281 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS A 304 CG CD CE NZ REMARK 470 MET B 1 CG SD CE 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 ARG B 72 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 75 CG CD CE NZ REMARK 470 SER B 76 OG REMARK 470 GLU B 180 CG CD OE1 OE2 REMARK 470 ASN B 210 CG OD1 ND2 REMARK 470 ASN B 270 CG OD1 ND2 REMARK 470 LYS B 275 CG CD CE NZ REMARK 470 LEU B 277 CG CD1 CD2 REMARK 470 TYR B 281 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 TYR B 301 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS B 304 CG CD CE NZ REMARK 470 LEU B 317 CG CD1 CD2 REMARK 470 LYS B 318 CG CD CE NZ 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 THR A 276 N - CA - C ANGL. DEV. = -17.6 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 ASN A 15 82.26 27.08 REMARK 500 LYS A 34 -20.79 176.81 REMARK 500 ASN A 39 33.03 -152.27 REMARK 500 ASN A 40 26.87 42.79 REMARK 500 TYR A 41 -119.38 72.59 REMARK 500 ASN A 42 -43.04 97.26 REMARK 500 PRO A 67 -164.46 -46.04 REMARK 500 ASP A 68 84.72 81.01 REMARK 500 LYS A 138 45.06 37.03 REMARK 500 ASN A 140 135.20 -174.35 REMARK 500 ASP A 141 -164.76 178.76 REMARK 500 VAL A 146 -32.95 -37.33 REMARK 500 TYR A 167 -32.23 -37.25 REMARK 500 ILE A 176 -56.73 -123.01 REMARK 500 LEU A 191 109.40 -59.79 REMARK 500 ASP A 198 40.24 -87.91 REMARK 500 ILE A 201 -39.69 -37.86 REMARK 500 PHE A 256 56.15 -149.96 REMARK 500 ASN A 270 -4.10 53.50 REMARK 500 ASP A 272 124.15 -28.68 REMARK 500 HIS A 274 37.14 136.38 REMARK 500 LYS A 275 60.10 37.48 REMARK 500 TYR A 281 12.82 -141.94 REMARK 500 HIS A 282 165.75 -44.39 REMARK 500 LYS A 283 -160.80 171.49 REMARK 500 TYR A 285 134.74 -22.71 REMARK 500 GLU A 286 -27.15 130.37 REMARK 500 ALA A 315 -71.62 -53.86 REMARK 500 LEU A 317 27.67 -63.74 REMARK 500 ASN B 15 74.00 44.12 REMARK 500 LYS B 34 -77.59 -53.28 REMARK 500 GLU B 38 39.77 -93.13 REMARK 500 ASN B 39 12.15 -154.48 REMARK 500 ASN B 42 -79.53 -56.76 REMARK 500 LEU B 48 -14.13 -48.99 REMARK 500 LYS B 59 55.67 34.27 REMARK 500 PRO B 67 -80.95 -48.89 REMARK 500 ASP B 68 -66.50 -25.36 REMARK 500 ASN B 69 68.26 -65.61 REMARK 500 ILE B 70 1.42 -156.30 REMARK 500 ASN B 95 -35.49 -39.96 REMARK 500 SER B 113 -59.42 -24.02 REMARK 500 LYS B 138 56.51 28.79 REMARK 500 ASN B 140 136.06 179.55 REMARK 500 ASP B 141 -166.92 175.28 REMARK 500 GLU B 155 -61.12 -93.14 REMARK 500 GLU B 181 -22.38 -35.29 REMARK 500 ASN B 183 -84.27 72.93 REMARK 500 LYS B 184 126.14 30.86 REMARK 500 SER B 199 39.17 -75.06 REMARK 500 REMARK 500 THIS ENTRY HAS 71 RAMACHANDRAN OUTLIERS. 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 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE U5P B 600 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2F84 RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH PO4 ION REMARK 900 RELATED ID: 2ZA1 RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH OROTIDINE 5'-MONOPHOSPHATE REMARK 900 RELATED ID: 2ZA2 RELATED DB: PDB REMARK 900 THE SAME PROTEIN, APO-FORM DBREF 2ZA3 A 1 323 UNP Q8T6J6 Q8T6J6_PLAFA 1 323 DBREF 2ZA3 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 500 21 HET U5P B 600 21 HETNAM U5P URIDINE-5'-MONOPHOSPHATE FORMUL 3 U5P 2(C9 H13 N2 O9 P) FORMUL 5 HOH *47(H2 O) HELIX 1 1 GLY A 2 ASN A 15 1 14 HELIX 2 2 LYS A 27 MET A 33 1 7 HELIX 3 3 ASN A 42 GLU A 50 1 9 HELIX 4 4 TYR A 52 VAL A 56 5 5 HELIX 5 5 LYS A 59 LEU A 64 1 6 HELIX 6 6 GLU A 77 ASN A 95 1 19 HELIX 7 7 LYS A 96 ALA A 98 5 3 HELIX 8 8 ALA A 106 ILE A 109 5 4 HELIX 9 9 GLY A 112 LEU A 129 1 18 HELIX 10 10 ILE A 142 GLU A 155 1 14 HELIX 11 11 ILE A 166 ILE A 176 5 11 HELIX 12 12 GLU A 180 ASN A 183 5 4 HELIX 13 13 ASN A 196 ASP A 198 5 3 HELIX 14 14 SER A 199 LYS A 204 1 6 HELIX 15 15 ALA A 213 LEU A 228 1 16 HELIX 16 16 LEU A 230 ASN A 234 5 5 HELIX 17 17 SER A 245 PHE A 256 1 12 HELIX 18 18 GLY A 293 LYS A 298 1 6 HELIX 19 19 TYR A 301 LEU A 317 1 17 HELIX 20 20 GLY B 2 ASN B 15 1 14 HELIX 21 21 ASP B 25 GLU B 38 1 14 HELIX 22 22 TYR B 41 LEU B 48 1 8 HELIX 23 23 LYS B 49 GLU B 50 5 2 HELIX 24 24 LYS B 51 VAL B 56 5 6 HELIX 25 25 LYS B 59 LEU B 64 1 6 HELIX 26 26 GLU B 77 ASN B 95 1 19 HELIX 27 27 LYS B 96 ALA B 98 5 3 HELIX 28 28 ALA B 106 ILE B 109 5 4 HELIX 29 29 GLY B 112 LEU B 129 1 18 HELIX 30 30 ILE B 142 GLU B 155 1 14 HELIX 31 31 THR B 170 ILE B 176 5 7 HELIX 32 32 GLU B 180 LYS B 182 5 3 HELIX 33 33 ALA B 213 TYR B 227 1 15 HELIX 34 34 LEU B 228 ASN B 234 5 7 HELIX 35 35 SER B 245 PHE B 256 1 12 HELIX 36 36 GLY B 293 LYS B 298 1 6 HELIX 37 37 TYR B 301 ALA B 315 1 15 SHEET 1 A 9 LEU A 18 GLY A 21 0 SHEET 2 A 9 THR A 100 ASN A 104 1 O LYS A 102 N ILE A 20 SHEET 3 A 9 THR A 133 ILE A 139 1 O ILE A 134 N MET A 103 SHEET 4 A 9 SER A 161 VAL A 164 1 N THR A 163 O LEU A 135 SHEET 5 A 9 SER A 187 LYS A 193 1 O PHE A 189 N VAL A 164 SHEET 6 A 9 ILE A 237 VAL A 241 1 O VAL A 240 N VAL A 190 SHEET 7 A 9 ILE A 261 SER A 263 1 O LEU A 262 N PHE A 239 SHEET 8 A 9 ILE A 288 ILE A 292 1 O LEU A 289 N ILE A 261 SHEET 9 A 9 LEU A 18 GLY A 21 1 N CYS A 19 O ILE A 290 SHEET 1 B 2 TYR A 178 ASP A 179 0 SHEET 2 B 2 LYS A 184 TYR A 185 -1 O LYS A 184 N ASP A 179 SHEET 1 C 2 SER A 207 LEU A 208 0 SHEET 2 C 2 LYS A 211 GLN A 212 -1 O LYS A 211 N LEU A 208 SHEET 1 D 9 LEU B 18 LEU B 22 0 SHEET 2 D 9 THR B 100 ASN B 104 1 O LYS B 102 N LEU B 22 SHEET 3 D 9 THR B 133 ILE B 139 1 O ASP B 136 N MET B 103 SHEET 4 D 9 SER B 161 VAL B 164 1 O SER B 161 N LEU B 135 SHEET 5 D 9 SER B 187 LYS B 193 1 O PHE B 189 N VAL B 164 SHEET 6 D 9 ILE B 237 VAL B 241 1 O VAL B 240 N VAL B 190 SHEET 7 D 9 ILE B 261 SER B 263 1 O LEU B 262 N PHE B 239 SHEET 8 D 9 ILE B 288 ILE B 292 1 O LEU B 289 N ILE B 261 SHEET 9 D 9 LEU B 18 LEU B 22 1 N CYS B 19 O ILE B 290 SHEET 1 E 2 TYR B 178 ASP B 179 0 SHEET 2 E 2 ASN B 183 TYR B 185 -1 O ASN B 183 N ASP B 179 SHEET 1 F 2 SER B 207 LEU B 208 0 SHEET 2 F 2 LYS B 211 GLN B 212 -1 O LYS B 211 N LEU B 208 SITE 1 AC1 17 ASP A 23 ASN A 104 ASP A 136 LYS A 138 SITE 2 AC1 17 THR A 194 THR A 195 PRO A 264 GLN A 269 SITE 3 AC1 17 ASN A 291 GLY A 293 ARG A 294 HOH A 511 SITE 4 AC1 17 HOH A 512 HOH A 514 HOH A 515 ASP B 141 SITE 5 AC1 17 MET B 168 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 THR B 194 SITE 3 AC2 18 THR B 195 PRO B 264 GLN B 269 ASN B 291 SITE 4 AC2 18 GLY B 293 ARG B 294 HOH B 601 HOH B 609 SITE 5 AC2 18 HOH B 624 HOH B 625 CRYST1 202.500 202.500 44.700 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 0.004938 0.002851 0.000000 0.00000 SCALE2 0.000000 0.005702 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022371 0.00000