HEADER TRANSFERASE 07-NOV-11 3UJD TITLE PHOSPHOETHANOLAMINE METHYLTRANSFERASE MUTANT (Y19F) FROM PLASMODIUM TITLE 2 FALCIPARUM IN COMPLEX WITH PHOSPHOCHOLINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHOETHANOLAMINE N-METHYLTRANSFERASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PLASMODIUM FALCIPARUM; SOURCE 3 ORGANISM_TAXID: 5833; SOURCE 4 GENE: PMT; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PLASMODIUM, PARASITE, METHYLTRANSFERASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR S.G.LEE,Y.KIM,T.D.ALPERT,A.NAGATA,J.M.JEZ REVDAT 4 28-FEB-24 3UJD 1 REMARK SEQADV REVDAT 3 21-MAR-12 3UJD 1 JRNL REVDAT 2 07-DEC-11 3UJD 1 ATOM REVDAT 1 30-NOV-11 3UJD 0 JRNL AUTH S.G.LEE,Y.KIM,T.D.ALPERT,A.NAGATA,J.M.JEZ JRNL TITL STRUCTURE AND REACTION MECHANISM OF PHOSPHOETHANOLAMINE JRNL TITL 2 METHYLTRANSFERASE FROM THE MALARIA PARASITE PLASMODIUM JRNL TITL 3 FALCIPARUM: AN ANTIPARASITIC DRUG TARGET. JRNL REF J.BIOL.CHEM. V. 287 1426 2012 JRNL REFN ISSN 0021-9258 JRNL PMID 22117061 JRNL DOI 10.1074/JBC.M111.315267 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.6.2_432) 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.99 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 45391 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.163 REMARK 3 R VALUE (WORKING SET) : 0.162 REMARK 3 FREE R VALUE : 0.183 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.080 REMARK 3 FREE R VALUE TEST SET COUNT : 2304 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 43.0034 - 3.2230 0.99 4424 248 0.1543 0.1655 REMARK 3 2 3.2230 - 2.5583 0.99 4374 221 0.1560 0.1725 REMARK 3 3 2.5583 - 2.2349 0.99 4370 213 0.1521 0.1760 REMARK 3 4 2.2349 - 2.0306 0.99 4317 249 0.1529 0.1690 REMARK 3 5 2.0306 - 1.8851 1.00 4327 233 0.1522 0.1958 REMARK 3 6 1.8851 - 1.7739 1.00 4338 215 0.1604 0.1924 REMARK 3 7 1.7739 - 1.6851 1.00 4374 223 0.1752 0.2264 REMARK 3 8 1.6851 - 1.6117 1.00 4304 241 0.1941 0.2174 REMARK 3 9 1.6117 - 1.5497 1.00 4317 232 0.2191 0.2737 REMARK 3 10 1.5497 - 1.4962 0.91 3942 229 0.2647 0.2699 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.20 REMARK 3 SHRINKAGE RADIUS : 0.95 REMARK 3 K_SOL : 0.38 REMARK 3 B_SOL : 42.20 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.780 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) : 0.00240 REMARK 3 B22 (A**2) : -0.94430 REMARK 3 B33 (A**2) : 0.94190 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 1.43270 REMARK 3 B23 (A**2) : 0.00000 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 : 0.006 2239 REMARK 3 ANGLE : 0.975 3036 REMARK 3 CHIRALITY : 0.071 327 REMARK 3 PLANARITY : 0.004 385 REMARK 3 DIHEDRAL : 11.404 858 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A REMARK 3 ORIGIN FOR THE GROUP (A): 19.3901 19.9533 19.8604 REMARK 3 T TENSOR REMARK 3 T11: 0.1086 T22: 0.1080 REMARK 3 T33: 0.0744 T12: 0.0089 REMARK 3 T13: -0.0170 T23: 0.0021 REMARK 3 L TENSOR REMARK 3 L11: 0.4617 L22: 0.7781 REMARK 3 L33: 0.2321 L12: 0.2496 REMARK 3 L13: -0.0980 L23: 0.1384 REMARK 3 S TENSOR REMARK 3 S11: -0.0123 S12: 0.0203 S13: -0.0043 REMARK 3 S21: -0.0403 S22: 0.0020 S23: -0.0013 REMARK 3 S31: -0.0070 S32: -0.0245 S33: 0.0090 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 3UJD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-NOV-11. REMARK 100 THE DEPOSITION ID IS D_1000068828. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-AUG-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : ROSENBAUM-ROCK HIGH-RESOLUTION REMARK 200 DOUBLE-CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 45420 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.496 REMARK 200 RESOLUTION RANGE LOW (A) : 43.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 26.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.6 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.50400 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.76 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.31 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG-8000, 0.1 M SODIUM CACODYLATE, REMARK 280 PH 6.5, 0.2 M SODIUM ACETATE, 5 MM 2-MERCAPTOETHANOL, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 44.61350 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.03200 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 44.61350 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 22.03200 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 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 332 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 333 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 379 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 THR A 2 REMARK 465 LEU A 3 REMARK 465 ILE A 4 REMARK 465 GLU A 5 REMARK 465 ASN A 6 REMARK 465 LEU A 7 REMARK 465 ASN A 8 REMARK 465 SER A 9 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 17 -95.25 -132.10 REMARK 500 ASN A 197 10.62 81.89 REMARK 500 PHE A 232 -118.12 -123.61 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 PC A 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3UJ6 RELATED DB: PDB REMARK 900 RELATED ID: 3UJ7 RELATED DB: PDB REMARK 900 RELATED ID: 3UJ8 RELATED DB: PDB REMARK 900 RELATED ID: 3UJ9 RELATED DB: PDB REMARK 900 RELATED ID: 3UJA RELATED DB: PDB REMARK 900 RELATED ID: 3UJB RELATED DB: PDB REMARK 900 RELATED ID: 3UJC RELATED DB: PDB DBREF 3UJD A 1 266 UNP Q6T755 Q6T755_PLAFA 1 266 SEQADV 3UJD PHE A 19 UNP Q6T755 TYR 19 ENGINEERED MUTATION SEQRES 1 A 266 MET THR LEU ILE GLU ASN LEU ASN SER ASP LYS THR PHE SEQRES 2 A 266 LEU GLU ASN ASN GLN PHE THR ASP GLU GLY VAL LYS VAL SEQRES 3 A 266 TYR GLU PHE ILE PHE GLY GLU ASN TYR ILE SER SER GLY SEQRES 4 A 266 GLY LEU GLU ALA THR LYS LYS ILE LEU SER ASP ILE GLU SEQRES 5 A 266 LEU ASN GLU ASN SER LYS VAL LEU ASP ILE GLY SER GLY SEQRES 6 A 266 LEU GLY GLY GLY CYS MET TYR ILE ASN GLU LYS TYR GLY SEQRES 7 A 266 ALA HIS THR HIS GLY ILE ASP ILE CYS SER ASN ILE VAL SEQRES 8 A 266 ASN MET ALA ASN GLU ARG VAL SER GLY ASN ASN LYS ILE SEQRES 9 A 266 ILE PHE GLU ALA ASN ASP ILE LEU THR LYS GLU PHE PRO SEQRES 10 A 266 GLU ASN ASN PHE ASP LEU ILE TYR SER ARG ASP ALA ILE SEQRES 11 A 266 LEU HIS LEU SER LEU GLU ASN LYS ASN LYS LEU PHE GLN SEQRES 12 A 266 LYS CYS TYR LYS TRP LEU LYS PRO THR GLY THR LEU LEU SEQRES 13 A 266 ILE THR ASP TYR CYS ALA THR GLU LYS GLU ASN TRP ASP SEQRES 14 A 266 ASP GLU PHE LYS GLU TYR VAL LYS GLN ARG LYS TYR THR SEQRES 15 A 266 LEU ILE THR VAL GLU GLU TYR ALA ASP ILE LEU THR ALA SEQRES 16 A 266 CYS ASN PHE LYS ASN VAL VAL SER LYS ASP LEU SER ASP SEQRES 17 A 266 TYR TRP ASN GLN LEU LEU GLU VAL GLU HIS LYS TYR LEU SEQRES 18 A 266 HIS GLU ASN LYS GLU GLU PHE LEU LYS LEU PHE SER GLU SEQRES 19 A 266 LYS LYS PHE ILE SER LEU ASP ASP GLY TRP SER ARG LYS SEQRES 20 A 266 ILE LYS ASP SER LYS ARG LYS MET GLN ARG TRP GLY TYR SEQRES 21 A 266 PHE LYS ALA THR LYS ASN HET PC A 301 11 HETNAM PC PHOSPHOCHOLINE FORMUL 2 PC C5 H15 N O4 P 1+ FORMUL 3 HOH *365(H2 O) HELIX 1 1 ASP A 10 ASN A 17 1 8 HELIX 2 2 THR A 20 GLY A 32 1 13 HELIX 3 3 GLY A 39 LEU A 48 1 10 HELIX 4 4 GLY A 67 GLY A 78 1 12 HELIX 5 5 CYS A 87 ARG A 97 1 11 HELIX 6 6 ALA A 129 LEU A 133 5 5 HELIX 7 7 SER A 134 TRP A 148 1 15 HELIX 8 8 GLU A 164 TRP A 168 5 5 HELIX 9 9 ASP A 169 LYS A 180 1 12 HELIX 10 10 THR A 185 CYS A 196 1 12 HELIX 11 11 LEU A 206 ASN A 224 1 19 HELIX 12 12 ASN A 224 PHE A 232 1 9 HELIX 13 13 SER A 233 ARG A 253 1 21 SHEET 1 A 7 ILE A 104 ALA A 108 0 SHEET 2 A 7 HIS A 80 ASP A 85 1 N GLY A 83 O ILE A 105 SHEET 3 A 7 LYS A 58 ILE A 62 1 N VAL A 59 O HIS A 80 SHEET 4 A 7 PHE A 121 ARG A 127 1 O TYR A 125 N LEU A 60 SHEET 5 A 7 LEU A 149 ALA A 162 1 O LYS A 150 N PHE A 121 SHEET 6 A 7 GLN A 256 THR A 264 -1 O ALA A 263 N LEU A 155 SHEET 7 A 7 LYS A 199 ASP A 205 -1 N LYS A 199 O THR A 264 SITE 1 AC1 10 GLN A 18 TYR A 27 ILE A 36 ASP A 128 SITE 2 AC1 10 TYR A 160 TYR A 175 ARG A 179 TYR A 181 SITE 3 AC1 10 LYS A 247 HOH A 388 CRYST1 89.227 44.064 76.974 90.00 108.42 90.00 C 1 2 1 4 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 0.011207 0.000000 0.003733 0.00000 SCALE2 0.000000 0.022694 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013693 0.00000