HEADER TRANSFERASE 29-JUL-16 5LM3 TITLE PLASMODIUM FALCIPARUM NICOTINIC ACID MONONUCLEOTIDE TITLE 2 ADENYLYLTRANSFERASE COMPLEXED WITH APC COMPND MOL_ID: 1; COMPND 2 MOLECULE: NICOTINATE-NUCLEOTIDE ADENYLYLTRANSFERASE; COMPND 3 CHAIN: A; COMPND 4 EC: 2.7.7.18; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PLASMODIUM FALCIPARUM (ISOLATE 3D7); SOURCE 3 ORGANISM_TAXID: 36329; SOURCE 4 STRAIN: ISOLATE 3D7; SOURCE 5 GENE: PF3D7_1327600; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: KRX KEYWDS NICOTINIC ACID MONONUCLEOTIDE ADENYLYLTRANSFERASE, NAMNAT, PROTEIN KEYWDS 2 CRYSTALLOGRAPHY, PLASMODIUM FALCIPARUM, DRUG TARGET, MALARIA, NAD KEYWDS 3 METABOLISM, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR J.BATHKE,K.FRITZ-WOLF,S.RAHLFS,C.BRANDSTAETHER,A.BURKHARDT,K.BECKER REVDAT 5 10-JAN-24 5LM3 1 REMARK REVDAT 4 29-MAR-17 5LM3 1 JRNL REVDAT 3 08-FEB-17 5LM3 1 REMARK REVDAT 2 28-DEC-16 5LM3 1 JRNL REVDAT 1 30-NOV-16 5LM3 0 JRNL AUTH J.BATHKE,K.FRITZ-WOLF,C.BRANDSTADTER,A.BURKHARDT,E.JORTZIK, JRNL AUTH 2 S.RAHLFS,K.BECKER JRNL TITL STRUCTURAL AND FUNCTIONAL CHARACTERIZATION OF PLASMODIUM JRNL TITL 2 FALCIPARUM NICOTINIC ACID MONONUCLEOTIDE JRNL TITL 3 ADENYLYLTRANSFERASE. JRNL REF J. MOL. BIOL. V. 428 4946 2016 JRNL REFN ESSN 1089-8638 JRNL PMID 27984041 JRNL DOI 10.1016/J.JMB.2016.10.023 REMARK 2 REMARK 2 RESOLUTION. 2.50 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.23 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 8522 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.215 REMARK 3 R VALUE (WORKING SET) : 0.211 REMARK 3 FREE R VALUE : 0.263 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.050 REMARK 3 FREE R VALUE TEST SET COUNT : 516 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 32.2322 - 3.9664 0.98 2057 129 0.1792 0.2119 REMARK 3 2 3.9664 - 3.1491 0.98 2001 131 0.1990 0.2534 REMARK 3 3 3.1491 - 2.7513 0.99 1989 129 0.2445 0.3264 REMARK 3 4 2.7513 - 2.4998 0.98 1959 127 0.3419 0.4283 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) : 0.320 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 34.060 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 : 0.001 1769 REMARK 3 ANGLE : 0.388 2394 REMARK 3 CHIRALITY : 0.042 261 REMARK 3 PLANARITY : 0.004 289 REMARK 3 DIHEDRAL : 10.355 1043 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 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5LM3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 29-JUL-16. REMARK 100 THE DEPOSITION ID IS D_1200000971. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-FEB-14 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 : PETRA III, DESY REMARK 200 BEAMLINE : P11 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.033208 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS 20151231 REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8537 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 32.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.12300 REMARK 200 R SYM (I) : 0.10400 REMARK 200 FOR THE DATA SET : 8.1600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.56 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 0.81500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.050 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX 1.10.1_2155 REMARK 200 STARTING MODEL: 5LLT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.36 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.43 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 14 MG/ML, 0.15 M BICINE, PH 8.5 AND REMARK 280 19% PEG 6000, 5MM APC, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 300K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 19.46000 REMARK 290 SMTRY3 2 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1750 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10490 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 8.0 KCAL/MOL 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 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 GLY A 2 REMARK 465 ARG A 44 REMARK 465 ASN A 45 REMARK 465 ASP A 46 REMARK 465 LYS A 47 REMARK 465 HIS A 208 REMARK 465 HIS A 209 REMARK 465 HIS A 210 REMARK 465 HIS A 211 REMARK 465 HIS A 212 REMARK 465 HIS A 213 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 HIS A 138 -12.15 70.11 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 APC A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 502 DBREF 5LM3 A 3 205 UNP Q8IE38 Q8IE38_PLAF7 2 204 SEQADV 5LM3 MET A 1 UNP Q8IE38 INITIATING METHIONINE SEQADV 5LM3 GLY A 2 UNP Q8IE38 EXPRESSION TAG SEQADV 5LM3 LEU A 206 UNP Q8IE38 EXPRESSION TAG SEQADV 5LM3 GLU A 207 UNP Q8IE38 EXPRESSION TAG SEQADV 5LM3 HIS A 208 UNP Q8IE38 EXPRESSION TAG SEQADV 5LM3 HIS A 209 UNP Q8IE38 EXPRESSION TAG SEQADV 5LM3 HIS A 210 UNP Q8IE38 EXPRESSION TAG SEQADV 5LM3 HIS A 211 UNP Q8IE38 EXPRESSION TAG SEQADV 5LM3 HIS A 212 UNP Q8IE38 EXPRESSION TAG SEQADV 5LM3 HIS A 213 UNP Q8IE38 EXPRESSION TAG SEQRES 1 A 213 MET GLY HIS LYS ASN ILE CYS ILE TYR GLY GLY SER PHE SEQRES 2 A 213 ASP PRO ILE THR TYR ALA HIS GLU MET VAL LEU ASP LYS SEQRES 3 A 213 ILE SER ASN LEU ASN TRP ILE HIS GLU ILE TRP VAL VAL SEQRES 4 A 213 ILE CYS ARG CYS ARG ASN ASP LYS SER LEU THR GLU PHE SEQRES 5 A 213 HIS HIS ARG HIS ASN MET PHE THR ILE ILE ILE ASN ASN SEQRES 6 A 213 SER SER LYS ILE ILE LYS SER LYS ILE PHE LEU LYS ASP SEQRES 7 A 213 LEU GLU SER HIS SER GLU MET THR PRO THR TYR ASP LEU SEQRES 8 A 213 LEU LYS THR GLN LYS GLU LEU HIS PRO ASN TYR THR PHE SEQRES 9 A 213 TYR PHE GLY LEU GLY SER ASP LEU ILE CYS ASP ILE PHE SEQRES 10 A 213 SER TRP ASP GLU GLY GLU LYS LEU VAL LEU GLU ASN ALA SEQRES 11 A 213 PHE ILE ILE ILE GLU ARG GLY HIS PHE LYS ILE ASP GLU SEQRES 12 A 213 SER ILE LEU LYS LYS PHE PRO LYS TYR TYR LEU ILE ASN SEQRES 13 A 213 ILE PRO LYS LEU SER PHE ILE ASN PHE ILE SER SER SER SEQRES 14 A 213 GLU ALA ARG LYS PHE LEU THR LYS GLU ASN ASP ILE ASN SEQRES 15 A 213 ASP ILE LYS LYS TYR ILE HIS PRO LEU THR ILE ASP TYR SEQRES 16 A 213 ILE ILE LYS TYR ASN LEU TYR ASP PHE ASN LEU GLU HIS SEQRES 17 A 213 HIS HIS HIS HIS HIS HET APC A 501 31 HET EDO A 502 4 HETNAM APC DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER HETNAM EDO 1,2-ETHANEDIOL HETSYN APC ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE HETSYN EDO ETHYLENE GLYCOL FORMUL 2 APC C11 H18 N5 O12 P3 FORMUL 3 EDO C2 H6 O2 FORMUL 4 HOH *33(H2 O) HELIX 1 AA1 THR A 17 ASN A 29 1 13 HELIX 2 AA2 GLU A 51 ASN A 65 1 15 HELIX 3 AA3 ILE A 70 SER A 72 5 3 HELIX 4 AA4 PRO A 87 HIS A 99 1 13 HELIX 5 AA5 CYS A 114 TRP A 119 5 6 HELIX 6 AA6 GLU A 121 GLU A 128 1 8 HELIX 7 AA7 ASP A 142 LYS A 147 1 6 HELIX 8 AA8 SER A 161 ILE A 166 5 6 HELIX 9 AA9 SER A 167 PHE A 174 1 8 HELIX 10 AB1 ASP A 180 LYS A 185 1 6 HELIX 11 AB2 HIS A 189 ASN A 200 1 12 HELIX 12 AB3 LEU A 201 PHE A 204 5 4 SHEET 1 AA1 6 ILE A 74 LEU A 76 0 SHEET 2 AA1 6 GLU A 35 ILE A 40 1 N VAL A 38 O PHE A 75 SHEET 3 AA1 6 LYS A 4 GLY A 11 1 N CYS A 7 O TRP A 37 SHEET 4 AA1 6 TYR A 102 GLY A 109 1 O TYR A 105 N ILE A 8 SHEET 5 AA1 6 ALA A 130 ILE A 134 1 O ILE A 132 N PHE A 106 SHEET 6 AA1 6 LYS A 151 ILE A 155 1 O ILE A 155 N ILE A 133 CISPEP 1 ASP A 14 PRO A 15 0 -3.47 SITE 1 AC1 22 TYR A 9 GLY A 11 SER A 12 PHE A 13 SITE 2 AC1 22 ALA A 19 HIS A 20 LEU A 108 GLY A 109 SITE 3 AC1 22 ASP A 111 LEU A 112 ARG A 136 ILE A 163 SITE 4 AC1 22 ASN A 164 ILE A 166 SER A 167 SER A 168 SITE 5 AC1 22 SER A 169 HOH A 601 HOH A 604 HOH A 605 SITE 6 AC1 22 HOH A 608 HOH A 609 SITE 1 AC2 6 MET A 85 PRO A 87 THR A 88 TRP A 119 SITE 2 AC2 6 ASP A 120 HOH A 603 CRYST1 55.240 38.920 62.710 90.00 113.54 90.00 P 1 21 1 2 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 0.018103 0.000000 0.007885 0.00000 SCALE2 0.000000 0.025694 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017394 0.00000