HEADER TRANSFERASE 07-APR-14 4CXM TITLE CRYSTAL STRUCTURE OF PLASMODIUM FALCIPARUM SPERMIDINE SYNTHASE IN TITLE 2 COMPLEX WITH METHYLTHIOADENOSIN AND SPERMIDINE AFTER CATALYSIS IN TITLE 3 CRYSTAL COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPERMIDINE SYNTHASE; COMPND 3 CHAIN: A, B, C; COMPND 4 FRAGMENT: RESIDUES 41-321 (ACCORDING TO UNIPROT SEQUENCE Q8II73); COMPND 5 EC: 2.5.1.16; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PLASMODIUM FALCIPARUM; SOURCE 3 ORGANISM_TAXID: 36329; SOURCE 4 STRAIN: 3D7; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: P15-TEV-LIC KEYWDS TRANSFERASE, ANINOPROPYL TRANSFERASE, POLYAMINE PATHWAY. ROSSMANN- KEYWDS 2 LIKE FOLD EXPDTA X-RAY DIFFRACTION AUTHOR J.SPRENGER,B.SVENSSON,S.AL-KARADAGHI,L.PERSSON REVDAT 6 20-DEC-23 4CXM 1 REMARK REVDAT 5 17-JAN-18 4CXM 1 REMARK REVDAT 4 25-MAR-15 4CXM 1 JRNL REVDAT 3 11-MAR-15 4CXM 1 JRNL REVDAT 2 14-JAN-15 4CXM 1 JRNL REVDAT 1 08-OCT-14 4CXM 0 JRNL AUTH J.SPRENGER,B.SVENSSON,J.HALANDER,J.CAREY,L.PERSSON, JRNL AUTH 2 S.AL-KARADAGHI JRNL TITL THREE-DIMENSIONAL STRUCTURES OF PLASMODIUM FALCIPARUM JRNL TITL 2 SPERMIDINE SYNTHASE WITH BOUND INHIBITORS SUGGEST NEW JRNL TITL 3 STRATEGIES FOR DRUG DESIGN. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 71 484 2015 JRNL REFN ISSN 0907-4449 JRNL PMID 25760598 JRNL DOI 10.1107/S1399004714027011 REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0029 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.94 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 118415 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 + TEST SET) : 0.181 REMARK 3 R VALUE (WORKING SET) : 0.179 REMARK 3 FREE R VALUE : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 6255 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.75 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.79 REMARK 3 REFLECTION IN BIN (WORKING SET) : 8683 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.15 REMARK 3 BIN R VALUE (WORKING SET) : 0.3140 REMARK 3 BIN FREE R VALUE SET COUNT : 441 REMARK 3 BIN FREE R VALUE : 0.3580 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6750 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 90 REMARK 3 SOLVENT ATOMS : 496 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.32 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.092 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.096 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.071 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.300 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.964 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.948 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6993 ; 0.023 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 6722 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9443 ; 2.180 ; 1.980 REMARK 3 BOND ANGLES OTHERS (DEGREES): 15585 ; 1.078 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 839 ; 6.607 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 294 ;39.620 ;25.714 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1279 ;14.258 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 6 ;19.121 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1051 ; 0.149 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 7693 ; 0.012 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1514 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. REMARK 4 REMARK 4 4CXM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 07-APR-14. REMARK 100 THE DEPOSITION ID IS D_1290059843. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-DEC-13 REMARK 200 TEMPERATURE (KELVIN) : 110 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : MAX II REMARK 200 BEAMLINE : I911-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.04122 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MULTILAYER MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH 65 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 124715 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 200 DATA REDUNDANCY : 2.700 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.9800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.04 REMARK 200 R MERGE FOR SHELL (I) : 0.53000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.290 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 2I7C REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.66 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.38 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 27 % PEG 3350, 0.1 M MES PH 5.5, 0.1 M REMARK 280 AMMONIUM SULPHATE 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 98.95000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 67.20000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 98.95000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 67.20000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: 5080 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21520 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -6.8 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, C 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 350 REMARK 350 BIOMOLECULE: 2 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: 5080 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21860 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -6.1 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 A2019 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 GLY A 39 REMARK 465 SER A 40 REMARK 465 GLY B 39 REMARK 465 SER B 40 REMARK 465 ILE B 321 REMARK 465 GLY C 39 REMARK 465 SER C 40 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 B 70 CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH B 2101 O HOH C 2171 4444 1.47 REMARK 500 O HOH A 2006 O HOH A 2009 2555 1.80 REMARK 500 O HOH A 2009 O HOH A 2009 2555 1.90 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 ASP A 295 CB - CG - OD1 ANGL. DEV. = 7.9 DEGREES REMARK 500 ASP B 178 CB - CG - OD1 ANGL. DEV. = 6.5 DEGREES REMARK 500 TYR B 299 CZ - CE2 - CD2 ANGL. DEV. = -6.6 DEGREES REMARK 500 MET C 50 CG - SD - CE ANGL. DEV. = 13.2 DEGREES REMARK 500 MET C 243 CG - SD - CE ANGL. DEV. = -10.2 DEGREES REMARK 500 ASP C 295 CB - CG - OD1 ANGL. DEV. = 7.1 DEGREES REMARK 500 ASP C 295 CB - CG - OD2 ANGL. DEV. = -6.1 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 SER A 198 -177.51 -63.80 REMARK 500 ILE A 235 -108.13 -112.08 REMARK 500 LEU A 250 -43.61 -131.61 REMARK 500 TYR A 298 -58.55 -128.84 REMARK 500 ASP B 196 65.84 -105.79 REMARK 500 ILE B 235 -87.28 -114.49 REMARK 500 TYR B 298 -62.26 -133.38 REMARK 500 TYR C 65 138.07 -171.50 REMARK 500 PHE C 208 54.26 -113.07 REMARK 500 CYS C 230 47.72 -146.65 REMARK 500 GLU C 231 -171.78 64.04 REMARK 500 ILE C 235 -7.39 -142.65 REMARK 500 TYR C 298 -64.88 -127.18 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 MTA A 540 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SPD A 640 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MTA B 540 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SPD B 640 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MTA C 540 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SPD C 640 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4CWA RELATED DB: PDB REMARK 900 STRUCTURE OF PLASMODIUM FALCIPARUM SPERMIDINE SYNTHASE IN COMPLEX REMARK 900 WITH 1H-BENZIMIDAZOLE-2-PENTANAMINE REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE CONSTRUCT USED FOR CRYSTALLIZATION IS MISSES 40 REMARK 999 RESIDUES FROM NATIVE SEQUENCE. RESIDUE LYS 41 FROM UNIPROT REMARK 999 SEQUENCE IS N-TERMINAL RESIDUE IN THIS STRUCTURE DBREF 4CXM A 40 321 UNP Q8II73 Q8II73_PLAF7 40 321 DBREF 4CXM B 40 321 UNP Q8II73 Q8II73_PLAF7 40 321 DBREF 4CXM C 40 321 UNP Q8II73 Q8II73_PLAF7 40 321 SEQADV 4CXM GLY A 39 UNP Q8II73 EXPRESSION TAG SEQADV 4CXM GLY B 39 UNP Q8II73 EXPRESSION TAG SEQADV 4CXM GLY C 39 UNP Q8II73 EXPRESSION TAG SEQRES 1 A 283 GLY SER LYS LYS TRP PHE SER GLU PHE SER ILE MET TRP SEQRES 2 A 283 PRO GLY GLN ALA PHE SER LEU LYS ILE LYS LYS ILE LEU SEQRES 3 A 283 TYR GLU THR LYS SER LYS TYR GLN ASN VAL LEU VAL PHE SEQRES 4 A 283 GLU SER THR THR TYR GLY LYS VAL LEU VAL LEU ASP GLY SEQRES 5 A 283 VAL ILE GLN LEU THR GLU LYS ASP GLU PHE ALA TYR HIS SEQRES 6 A 283 GLU MET MET THR HIS VAL PRO MET THR VAL SER LYS GLU SEQRES 7 A 283 PRO LYS ASN VAL LEU VAL VAL GLY GLY GLY ASP GLY GLY SEQRES 8 A 283 ILE ILE ARG GLU LEU CYS LYS TYR LYS SER VAL GLU ASN SEQRES 9 A 283 ILE ASP ILE CYS GLU ILE ASP GLU THR VAL ILE GLU VAL SEQRES 10 A 283 SER LYS ILE TYR PHE LYS ASN ILE SER CYS GLY TYR GLU SEQRES 11 A 283 ASP LYS ARG VAL ASN VAL PHE ILE GLU ASP ALA SER LYS SEQRES 12 A 283 PHE LEU GLU ASN VAL THR ASN THR TYR ASP VAL ILE ILE SEQRES 13 A 283 VAL ASP SER SER ASP PRO ILE GLY PRO ALA GLU THR LEU SEQRES 14 A 283 PHE ASN GLN ASN PHE TYR GLU LYS ILE TYR ASN ALA LEU SEQRES 15 A 283 LYS PRO ASN GLY TYR CYS VAL ALA GLN CYS GLU SER LEU SEQRES 16 A 283 TRP ILE HIS VAL GLY THR ILE LYS ASN MET ILE GLY TYR SEQRES 17 A 283 ALA LYS LYS LEU PHE LYS LYS VAL GLU TYR ALA ASN ILE SEQRES 18 A 283 SER ILE PRO THR TYR PRO CYS GLY CYS ILE GLY ILE LEU SEQRES 19 A 283 CYS CYS SER LYS THR ASP THR GLY LEU THR LYS PRO ASN SEQRES 20 A 283 LYS LYS LEU GLU SER LYS GLU PHE ALA ASP LEU LYS TYR SEQRES 21 A 283 TYR ASN TYR GLU ASN HIS SER ALA ALA PHE LYS LEU PRO SEQRES 22 A 283 ALA PHE LEU LEU LYS GLU ILE GLU ASN ILE SEQRES 1 B 283 GLY SER LYS LYS TRP PHE SER GLU PHE SER ILE MET TRP SEQRES 2 B 283 PRO GLY GLN ALA PHE SER LEU LYS ILE LYS LYS ILE LEU SEQRES 3 B 283 TYR GLU THR LYS SER LYS TYR GLN ASN VAL LEU VAL PHE SEQRES 4 B 283 GLU SER THR THR TYR GLY LYS VAL LEU VAL LEU ASP GLY SEQRES 5 B 283 VAL ILE GLN LEU THR GLU LYS ASP GLU PHE ALA TYR HIS SEQRES 6 B 283 GLU MET MET THR HIS VAL PRO MET THR VAL SER LYS GLU SEQRES 7 B 283 PRO LYS ASN VAL LEU VAL VAL GLY GLY GLY ASP GLY GLY SEQRES 8 B 283 ILE ILE ARG GLU LEU CYS LYS TYR LYS SER VAL GLU ASN SEQRES 9 B 283 ILE ASP ILE CYS GLU ILE ASP GLU THR VAL ILE GLU VAL SEQRES 10 B 283 SER LYS ILE TYR PHE LYS ASN ILE SER CYS GLY TYR GLU SEQRES 11 B 283 ASP LYS ARG VAL ASN VAL PHE ILE GLU ASP ALA SER LYS SEQRES 12 B 283 PHE LEU GLU ASN VAL THR ASN THR TYR ASP VAL ILE ILE SEQRES 13 B 283 VAL ASP SER SER ASP PRO ILE GLY PRO ALA GLU THR LEU SEQRES 14 B 283 PHE ASN GLN ASN PHE TYR GLU LYS ILE TYR ASN ALA LEU SEQRES 15 B 283 LYS PRO ASN GLY TYR CYS VAL ALA GLN CYS GLU SER LEU SEQRES 16 B 283 TRP ILE HIS VAL GLY THR ILE LYS ASN MET ILE GLY TYR SEQRES 17 B 283 ALA LYS LYS LEU PHE LYS LYS VAL GLU TYR ALA ASN ILE SEQRES 18 B 283 SER ILE PRO THR TYR PRO CYS GLY CYS ILE GLY ILE LEU SEQRES 19 B 283 CYS CYS SER LYS THR ASP THR GLY LEU THR LYS PRO ASN SEQRES 20 B 283 LYS LYS LEU GLU SER LYS GLU PHE ALA ASP LEU LYS TYR SEQRES 21 B 283 TYR ASN TYR GLU ASN HIS SER ALA ALA PHE LYS LEU PRO SEQRES 22 B 283 ALA PHE LEU LEU LYS GLU ILE GLU ASN ILE SEQRES 1 C 283 GLY SER LYS LYS TRP PHE SER GLU PHE SER ILE MET TRP SEQRES 2 C 283 PRO GLY GLN ALA PHE SER LEU LYS ILE LYS LYS ILE LEU SEQRES 3 C 283 TYR GLU THR LYS SER LYS TYR GLN ASN VAL LEU VAL PHE SEQRES 4 C 283 GLU SER THR THR TYR GLY LYS VAL LEU VAL LEU ASP GLY SEQRES 5 C 283 VAL ILE GLN LEU THR GLU LYS ASP GLU PHE ALA TYR HIS SEQRES 6 C 283 GLU MET MET THR HIS VAL PRO MET THR VAL SER LYS GLU SEQRES 7 C 283 PRO LYS ASN VAL LEU VAL VAL GLY GLY GLY ASP GLY GLY SEQRES 8 C 283 ILE ILE ARG GLU LEU CYS LYS TYR LYS SER VAL GLU ASN SEQRES 9 C 283 ILE ASP ILE CYS GLU ILE ASP GLU THR VAL ILE GLU VAL SEQRES 10 C 283 SER LYS ILE TYR PHE LYS ASN ILE SER CYS GLY TYR GLU SEQRES 11 C 283 ASP LYS ARG VAL ASN VAL PHE ILE GLU ASP ALA SER LYS SEQRES 12 C 283 PHE LEU GLU ASN VAL THR ASN THR TYR ASP VAL ILE ILE SEQRES 13 C 283 VAL ASP SER SER ASP PRO ILE GLY PRO ALA GLU THR LEU SEQRES 14 C 283 PHE ASN GLN ASN PHE TYR GLU LYS ILE TYR ASN ALA LEU SEQRES 15 C 283 LYS PRO ASN GLY TYR CYS VAL ALA GLN CYS GLU SER LEU SEQRES 16 C 283 TRP ILE HIS VAL GLY THR ILE LYS ASN MET ILE GLY TYR SEQRES 17 C 283 ALA LYS LYS LEU PHE LYS LYS VAL GLU TYR ALA ASN ILE SEQRES 18 C 283 SER ILE PRO THR TYR PRO CYS GLY CYS ILE GLY ILE LEU SEQRES 19 C 283 CYS CYS SER LYS THR ASP THR GLY LEU THR LYS PRO ASN SEQRES 20 C 283 LYS LYS LEU GLU SER LYS GLU PHE ALA ASP LEU LYS TYR SEQRES 21 C 283 TYR ASN TYR GLU ASN HIS SER ALA ALA PHE LYS LEU PRO SEQRES 22 C 283 ALA PHE LEU LEU LYS GLU ILE GLU ASN ILE HET MTA A 540 20 HET SPD A 640 10 HET MTA B 540 20 HET SPD B 640 10 HET MTA C 540 20 HET SPD C 640 10 HETNAM MTA 5'-DEOXY-5'-METHYLTHIOADENOSINE HETNAM SPD SPERMIDINE HETSYN SPD N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE; PA(34) FORMUL 4 MTA 3(C11 H15 N5 O3 S) FORMUL 5 SPD 3(C7 H19 N3) FORMUL 10 HOH *496(H2 O) HELIX 1 1 ASP A 98 SER A 114 1 17 HELIX 2 2 GLY A 128 CYS A 135 1 8 HELIX 3 3 ASP A 149 PHE A 160 1 12 HELIX 4 4 PHE A 160 CYS A 165 1 6 HELIX 5 5 GLY A 166 ASP A 169 5 4 HELIX 6 6 ASP A 178 VAL A 186 1 9 HELIX 7 7 GLY A 202 PHE A 208 5 7 HELIX 8 8 ASN A 209 ALA A 219 1 11 HELIX 9 9 HIS A 236 LYS A 249 1 14 HELIX 10 10 TYR A 264 CYS A 266 5 3 HELIX 11 11 SER A 290 ALA A 294 5 5 HELIX 12 12 ASN A 300 ALA A 307 1 8 HELIX 13 13 PRO A 311 GLU A 319 1 9 HELIX 14 14 ASP B 98 THR B 112 1 15 HELIX 15 15 GLY B 128 LYS B 136 1 9 HELIX 16 16 ASP B 149 PHE B 160 1 12 HELIX 17 17 PHE B 160 CYS B 165 1 6 HELIX 18 18 GLY B 166 ASP B 169 5 4 HELIX 19 19 ASP B 178 LEU B 183 1 6 HELIX 20 20 GLU B 184 VAL B 186 5 3 HELIX 21 21 GLY B 202 PHE B 208 5 7 HELIX 22 22 ASN B 209 ALA B 219 1 11 HELIX 23 23 HIS B 236 LYS B 249 1 14 HELIX 24 24 TYR B 264 CYS B 266 5 3 HELIX 25 25 SER B 290 ALA B 294 5 5 HELIX 26 26 ASN B 300 ALA B 307 1 8 HELIX 27 27 PRO B 311 ASN B 320 1 10 HELIX 28 28 ASP C 98 SER C 114 1 17 HELIX 29 29 GLY C 128 LYS C 136 1 9 HELIX 30 30 ASP C 149 PHE C 160 1 12 HELIX 31 31 SER C 164 ASP C 169 5 6 HELIX 32 32 ASP C 178 LEU C 183 1 6 HELIX 33 33 GLY C 202 PHE C 208 5 7 HELIX 34 34 ASN C 209 ALA C 219 1 11 HELIX 35 35 HIS C 236 LYS C 249 1 14 HELIX 36 36 TYR C 264 CYS C 266 5 3 HELIX 37 37 SER C 290 ALA C 294 5 5 HELIX 38 38 ASN C 300 ALA C 307 1 8 HELIX 39 39 PRO C 311 ASN C 320 1 10 SHEET 1 AA 5 TRP A 43 GLU A 46 0 SHEET 2 AA 5 PHE A 56 LYS A 68 -1 O PHE A 56 N GLU A 46 SHEET 3 AA 5 ASN A 73 SER A 79 -1 O VAL A 74 N THR A 67 SHEET 4 AA 5 LYS A 84 LEU A 88 -1 O VAL A 85 N PHE A 77 SHEET 5 AA 5 VAL A 91 THR A 95 -1 O VAL A 91 N LEU A 88 SHEET 1 AB 7 VAL A 172 ILE A 176 0 SHEET 2 AB 7 ASN A 142 GLU A 147 1 O ILE A 143 N ASN A 173 SHEET 3 AB 7 ASN A 119 GLY A 124 1 O VAL A 120 N ASP A 144 SHEET 4 AB 7 TYR A 190 ASP A 196 1 N ASP A 191 O ASN A 119 SHEET 5 AB 7 LEU A 220 CYS A 230 1 N LYS A 221 O TYR A 190 SHEET 6 AB 7 CYS A 268 SER A 275 -1 O GLY A 270 N CYS A 230 SHEET 7 AB 7 LYS A 253 SER A 260 -1 O LYS A 253 N SER A 275 SHEET 1 BA 2 TRP B 43 GLU B 46 0 SHEET 2 BA 2 GLN B 54 LYS B 68 -1 O PHE B 56 N GLU B 46 SHEET 1 BB 8 VAL B 91 THR B 95 0 SHEET 2 BB 8 LYS B 84 LEU B 88 -1 O LEU B 86 N GLN B 93 SHEET 3 BB 8 ASN B 73 SER B 79 -1 O LEU B 75 N VAL B 87 SHEET 4 BB 8 GLN B 54 LYS B 68 -1 N LYS B 61 O GLU B 78 SHEET 5 BB 8 GLN C 54 LYS C 68 -1 O ALA C 55 N SER B 57 SHEET 6 BB 8 ASN C 73 SER C 79 -1 O VAL C 74 N THR C 67 SHEET 7 BB 8 LYS C 84 LEU C 88 -1 O VAL C 85 N PHE C 77 SHEET 8 BB 8 VAL C 91 THR C 95 -1 O VAL C 91 N LEU C 88 SHEET 1 BC 5 VAL B 91 THR B 95 0 SHEET 2 BC 5 LYS B 84 LEU B 88 -1 O LEU B 86 N GLN B 93 SHEET 3 BC 5 ASN B 73 SER B 79 -1 O LEU B 75 N VAL B 87 SHEET 4 BC 5 GLN B 54 LYS B 68 -1 N LYS B 61 O GLU B 78 SHEET 5 BC 5 TRP B 43 GLU B 46 -1 O PHE B 44 N LEU B 58 SHEET 1 CA 2 TRP C 43 GLU C 46 0 SHEET 2 CA 2 GLN C 54 LYS C 68 1 O PHE C 56 N GLU C 46 SHEET 1 BD 6 VAL B 91 THR B 95 0 SHEET 2 BD 6 LYS B 84 LEU B 88 -1 O LEU B 86 N GLN B 93 SHEET 3 BD 6 ASN B 73 SER B 79 -1 O LEU B 75 N VAL B 87 SHEET 4 BD 6 GLN B 54 LYS B 68 -1 N LYS B 61 O GLU B 78 SHEET 5 BD 6 GLN C 54 LYS C 68 -1 O ALA C 55 N SER B 57 SHEET 6 BD 6 TRP C 43 GLU C 46 1 O PHE C 44 N LEU C 58 SHEET 1 BE 7 VAL B 172 ILE B 176 0 SHEET 2 BE 7 ASN B 142 GLU B 147 1 O ILE B 143 N ASN B 173 SHEET 3 BE 7 ASN B 119 GLY B 124 1 O VAL B 120 N ASP B 144 SHEET 4 BE 7 TYR B 190 ASP B 196 1 N ASP B 191 O ASN B 119 SHEET 5 BE 7 LEU B 220 CYS B 230 1 N LYS B 221 O TYR B 190 SHEET 6 BE 7 CYS B 268 SER B 275 -1 O GLY B 270 N CYS B 230 SHEET 7 BE 7 LYS B 253 SER B 260 -1 O LYS B 253 N SER B 275 SHEET 1 CB 7 VAL C 172 ILE C 176 0 SHEET 2 CB 7 ASN C 142 GLU C 147 1 O ILE C 143 N ASN C 173 SHEET 3 CB 7 ASN C 119 GLY C 124 1 O VAL C 120 N ASP C 144 SHEET 4 CB 7 TYR C 190 ASP C 196 1 N ASP C 191 O ASN C 119 SHEET 5 CB 7 LEU C 220 GLN C 229 1 N LYS C 221 O TYR C 190 SHEET 6 CB 7 CYS C 268 SER C 275 -1 O LEU C 272 N ALA C 228 SHEET 7 CB 7 LYS C 253 SER C 260 -1 O LYS C 253 N SER C 275 SITE 1 AC1 20 GLN A 72 LEU A 88 GLN A 93 GLY A 124 SITE 2 AC1 20 GLY A 125 ASP A 127 CYS A 146 GLU A 147 SITE 3 AC1 20 ILE A 148 ASP A 149 VAL A 152 ASP A 178 SITE 4 AC1 20 ALA A 179 ASP A 196 SER A 197 SER A 198 SITE 5 AC1 20 PRO A 203 ALA A 204 THR A 206 SPD A 640 SITE 1 AC2 11 VAL A 91 ILE A 92 GLN A 93 HIS A 103 SITE 2 AC2 11 ASP A 127 ASP A 196 SER A 197 ASP A 199 SITE 3 AC2 11 TYR A 264 MTA A 540 HOH A2012 SITE 1 AC3 18 GLN B 72 GLY B 124 GLY B 125 ASP B 127 SITE 2 AC3 18 CYS B 146 GLU B 147 ILE B 148 ASP B 149 SITE 3 AC3 18 VAL B 152 ASP B 178 ALA B 179 ASP B 196 SITE 4 AC3 18 SER B 197 SER B 198 PRO B 203 ALA B 204 SITE 5 AC3 18 THR B 206 SPD B 640 SITE 1 AC4 11 ILE B 92 GLN B 93 TYR B 102 HIS B 103 SITE 2 AC4 11 ASP B 127 ASP B 196 SER B 197 ASP B 199 SITE 3 AC4 11 TYR B 264 MTA B 540 HOH B2009 SITE 1 AC5 21 GLN C 72 LEU C 88 GLN C 93 GLY C 124 SITE 2 AC5 21 GLY C 125 ASP C 127 CYS C 146 GLU C 147 SITE 3 AC5 21 ILE C 148 ASP C 149 VAL C 152 ASP C 178 SITE 4 AC5 21 ALA C 179 ASP C 196 SER C 197 SER C 198 SITE 5 AC5 21 PRO C 203 ALA C 204 THR C 206 LEU C 207 SITE 6 AC5 21 SPD C 640 SITE 1 AC6 14 TRP C 51 VAL C 91 ILE C 92 GLN C 93 SITE 2 AC6 14 TYR C 102 HIS C 103 ASP C 127 ASP C 196 SITE 3 AC6 14 SER C 197 ASP C 199 TYR C 264 MTA C 540 SITE 4 AC6 14 HOH C2008 HOH C2140 CRYST1 197.900 134.400 48.300 90.00 95.50 90.00 C 1 2 1 12 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 0.005053 0.000000 0.000487 0.00000 SCALE2 0.000000 0.007440 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020800 0.00000