HEADER TRANSFERASE 11-JAN-13 4IQB TITLE HIGH RESOLUTION CRYSTAL STRUCTURE OF C.ELEGANS THYMIDYLATE SYNTHASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: THYMIDYLATE SYNTHASE; COMPND 3 CHAIN: A, B; COMPND 4 EC: 2.1.1.45; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CAENORHABDITIS ELEGANS; SOURCE 3 ORGANISM_COMMON: NEMATODE; SOURCE 4 ORGANISM_TAXID: 6239; 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: PPIGDM4+STOP KEYWDS PROTEIN DIMER, DEOXYNUCLEOTIDE BIOSYNTHESIS, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR P.WILK,A.DOWIERCIAL,K.BANASZAK,A.JARMULA,W.RYPNIEWSKI,W.RODE REVDAT 3 28-FEB-24 4IQB 1 REMARK REVDAT 2 28-NOV-18 4IQB 1 JRNL REVDAT 1 22-JAN-14 4IQB 0 JRNL AUTH A.JARMULA,P.WILK,P.MAJ,J.LUDWICZAK,A.DOWIERCIAL,K.BANASZAK, JRNL AUTH 2 W.RYPNIEWSKI,J.CIESLA,M.DABROWSKA,T.FRACZYK,A.K.BRONOWSKA, JRNL AUTH 3 J.JAKOWIECKI,S.FILIPEK,W.RODE JRNL TITL CRYSTAL STRUCTURES OF NEMATODE (PARASITIC T. SPIRALIS AND JRNL TITL 2 FREE LIVING C. ELEGANS), COMPARED TO MAMMALIAN, THYMIDYLATE JRNL TITL 3 SYNTHASES (TS). MOLECULAR DOCKING AND MOLECULAR DYNAMICS JRNL TITL 4 SIMULATIONS IN SEARCH FOR NEMATODE-SPECIFIC INHIBITORS OF JRNL TITL 5 TS. JRNL REF J. MOL. GRAPH. MODEL. V. 77 33 2017 JRNL REFN ISSN 1873-4243 JRNL PMID 28826032 JRNL DOI 10.1016/J.JMGM.2017.08.008 REMARK 2 REMARK 2 RESOLUTION. 1.13 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 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) : 1.13 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.30 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 228161 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) : 0.115 REMARK 3 R VALUE (WORKING SET) : 0.114 REMARK 3 FREE R VALUE : 0.139 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 11419 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) : 1.13 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.16 REMARK 3 REFLECTION IN BIN (WORKING SET) : 14292 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 89.45 REMARK 3 BIN R VALUE (WORKING SET) : 0.2550 REMARK 3 BIN FREE R VALUE SET COUNT : 710 REMARK 3 BIN FREE R VALUE : 0.2820 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4616 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 10 REMARK 3 SOLVENT ATOMS : 942 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.73 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.02000 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) : -0.02000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.025 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.026 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.016 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.731 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.984 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.978 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5164 ; 0.023 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 3634 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7079 ; 2.194 ; 1.964 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8907 ; 1.210 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 697 ; 6.784 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 252 ;34.120 ;23.611 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 958 ;12.623 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 41 ;16.829 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 762 ; 0.144 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5855 ; 0.014 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1102 ; 0.003 ; 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): 8797 ; 6.804 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 199 ;40.705 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 9362 ;11.661 ; 5.000 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 U VALUES: REFINED INDIVIDUALLY REMARK 4 REMARK 4 4IQB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-JAN-13. REMARK 100 THE DEPOSITION ID IS D_1000077074. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-DEC-11 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BESSY REMARK 200 BEAMLINE : 14.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.918 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 228161 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.130 REMARK 200 RESOLUTION RANGE LOW (A) : 29.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL 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) : 1.13 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.15 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.43900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.010 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.3.0 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.78 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M MES PH 5.6, 0.15M (NH4)2SO4, 18% REMARK 280 PEG 5000MME, VAPOR 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 49.66750 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 49.18350 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 49.66750 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 49.18350 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4390 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23990 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -44.0 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 MET A 1 REMARK 465 GLU A 2 REMARK 465 VAL A 3 REMARK 465 MET A 4 REMARK 465 ASN A 5 REMARK 465 LYS A 6 REMARK 465 GLU A 7 REMARK 465 ASN A 8 REMARK 465 ILE A 9 REMARK 465 ILE A 10 REMARK 465 ALA A 11 REMARK 465 ASP A 12 REMARK 465 ALA A 13 REMARK 465 PRO A 14 REMARK 465 SER A 15 REMARK 465 ASP A 16 REMARK 465 VAL A 17 REMARK 465 VAL A 18 REMARK 465 LYS A 19 REMARK 465 THR A 20 REMARK 465 VAL A 21 REMARK 465 GLN A 22 REMARK 465 GLN A 23 REMARK 465 ASP A 312 REMARK 465 MET A 313 REMARK 465 ALA A 314 REMARK 465 VAL A 315 REMARK 465 MET B 1 REMARK 465 GLU B 2 REMARK 465 VAL B 3 REMARK 465 MET B 4 REMARK 465 ASN B 5 REMARK 465 LYS B 6 REMARK 465 GLU B 7 REMARK 465 ASN B 8 REMARK 465 ILE B 9 REMARK 465 ILE B 10 REMARK 465 ALA B 11 REMARK 465 ASP B 12 REMARK 465 ALA B 13 REMARK 465 PRO B 14 REMARK 465 SER B 15 REMARK 465 ASP B 16 REMARK 465 VAL B 17 REMARK 465 VAL B 18 REMARK 465 LYS B 19 REMARK 465 THR B 20 REMARK 465 VAL B 21 REMARK 465 GLN B 22 REMARK 465 GLN B 23 REMARK 465 ASP B 312 REMARK 465 MET B 313 REMARK 465 ALA B 314 REMARK 465 VAL B 315 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 B 204 O HOH B 974 2.09 REMARK 500 OE1 GLU B 39 O HOH B 947 2.10 REMARK 500 OD1 ASP A 50 OG1 THR A 54 2.12 REMARK 500 O HOH A 520 O HOH A 814 2.17 REMARK 500 O HOH B 777 O HOH B 853 2.17 REMARK 500 O HOH B 611 O HOH B 976 2.18 REMARK 500 O HOH A 697 O HOH A 902 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 OE2 GLU B 172 OE2 GLU B 172 2454 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 ASP A 154 CG ASP A 154 OD2 -0.156 REMARK 500 ARG A 168 CZ ARG A 168 NH2 -0.078 REMARK 500 ARG A 178 CZ ARG A 178 NH2 -0.097 REMARK 500 CYS A 197 CB CYS A 197 SG -0.097 REMARK 500 GLU B 129 CD GLU B 129 OE2 -0.073 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 TYR A 34 CB - CG - CD2 ANGL. DEV. = -5.4 DEGREES REMARK 500 TYR A 34 CB - CG - CD1 ANGL. DEV. = 6.1 DEGREES REMARK 500 TYR A 34 CZ - CE2 - CD2 ANGL. DEV. = -5.5 DEGREES REMARK 500 ARG A 69 CD - NE - CZ ANGL. DEV. = -10.6 DEGREES REMARK 500 ARG A 69 NE - CZ - NH1 ANGL. DEV. = 8.6 DEGREES REMARK 500 ARG A 69 NE - CZ - NH2 ANGL. DEV. = -7.6 DEGREES REMARK 500 ARG A 117 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 ARG A 128 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG A 128 NE - CZ - NH1 ANGL. DEV. = -3.9 DEGREES REMARK 500 ARG A 128 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ASP A 175 CB - CG - OD1 ANGL. DEV. = 14.0 DEGREES REMARK 500 ASP A 175 CB - CG - OD2 ANGL. DEV. = -12.5 DEGREES REMARK 500 ARG A 177 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 ARG A 177 NE - CZ - NH2 ANGL. DEV. = -6.3 DEGREES REMARK 500 ARG A 178 NH1 - CZ - NH2 ANGL. DEV. = 7.1 DEGREES REMARK 500 ARG A 178 NE - CZ - NH2 ANGL. DEV. = -8.1 DEGREES REMARK 500 LEU A 254 CB - CG - CD2 ANGL. DEV. = 13.9 DEGREES REMARK 500 TYR B 34 CB - CG - CD2 ANGL. DEV. = -3.7 DEGREES REMARK 500 ARG B 51 NE - CZ - NH2 ANGL. DEV. = 3.0 DEGREES REMARK 500 ARG B 80 NE - CZ - NH1 ANGL. DEV. = 12.9 DEGREES REMARK 500 ARG B 80 NE - CZ - NH2 ANGL. DEV. = -9.4 DEGREES REMARK 500 GLU B 129 OE1 - CD - OE2 ANGL. DEV. = -8.1 DEGREES REMARK 500 ARG B 177 NE - CZ - NH1 ANGL. DEV. = -4.9 DEGREES REMARK 500 ARG B 178 NE - CZ - NH1 ANGL. DEV. = -3.5 DEGREES REMARK 500 ARG B 178 NE - CZ - NH2 ANGL. DEV. = -5.1 DEGREES REMARK 500 ASP B 206 CB - CG - OD1 ANGL. DEV. = 7.9 DEGREES REMARK 500 ASP B 220 CB - CG - OD2 ANGL. DEV. = -7.0 DEGREES REMARK 500 ARG B 282 NE - CZ - NH1 ANGL. DEV. = -3.9 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 ASP A 50 -156.77 -149.40 REMARK 500 ARG A 51 45.30 -159.42 REMARK 500 TYR A 137 -87.18 3.94 REMARK 500 HIS A 143 38.64 -146.30 REMARK 500 VAL A 149 -75.56 -116.74 REMARK 500 LEU A 223 -75.36 -145.21 REMARK 500 ASP B 50 -168.89 -74.25 REMARK 500 ARG B 51 38.84 -86.41 REMARK 500 TYR B 137 -93.27 14.77 REMARK 500 HIS B 143 34.28 -146.19 REMARK 500 VAL B 149 -71.41 -117.91 REMARK 500 ASN B 207 52.99 37.70 REMARK 500 LEU B 223 -78.03 -147.84 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ARG A 51 THR A 52 144.46 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 SO4 A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 401 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3IHI RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF MOUSE THYMIDYLATE SYNTHASE REMARK 900 RELATED ID: 3IHH RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF MOUSE THYMIDYLATE SYNTHASE IN COMPLEX WITH DUMP REMARK 900 RELATED ID: 4EB4 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF MOUSE THYMIDYLATE SYNTHASE IN TERNARY COMPLEX REMARK 900 WITH DUMP AND TOMUDEX REMARK 900 RELATED ID: 4G9U RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF T.SPIRALIS THYMIDYLATE SYNTHASE IN COMPLEX REMARK 900 WITH DUMP REMARK 900 RELATED ID: 4IQQ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF C.ELEGANS THYMIDYLATE SYNTHASE IN COMPLEX WITH REMARK 900 DUMP AND TOMUDEX REMARK 900 RELATED ID: 4IRR RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF C.ELEGANS THYMIDYLATE SYNTHASE IN COMPLEX WITH REMARK 900 DUMP REMARK 900 RELATED ID: 4ISW RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF PHOSPHORYLATED C.ELEGANS THYMIDYLATE SYNTHASE REMARK 900 IN COMPLEX WITH DUMP DBREF 4IQB A 1 315 UNP Q9Y052 Q9Y052_CAEEL 1 315 DBREF 4IQB B 1 315 UNP Q9Y052 Q9Y052_CAEEL 1 315 SEQRES 1 A 315 MET GLU VAL MET ASN LYS GLU ASN ILE ILE ALA ASP ALA SEQRES 2 A 315 PRO SER ASP VAL VAL LYS THR VAL GLN GLN GLN VAL HIS SEQRES 3 A 315 LEU ASN GLN ASP GLU TYR LYS TYR LEU LYS GLN VAL GLU SEQRES 4 A 315 GLN ILE LEU ARG GLU GLY THR ARG ARG ASP ASP ARG THR SEQRES 5 A 315 GLY THR GLY THR ILE SER ILE PHE GLY MET GLN SER LYS SEQRES 6 A 315 TYR CYS LEU ARG ASN GLY THR ILE PRO LEU LEU THR THR SEQRES 7 A 315 LYS ARG VAL TYR TRP LYS GLY VAL LEU GLU GLU LEU LEU SEQRES 8 A 315 TRP PHE ILE SER GLY SER THR ASP GLY LYS LEU LEU MET SEQRES 9 A 315 GLU LYS ASN VAL LYS ILE TRP GLU LYS ASN GLY ASP ARG SEQRES 10 A 315 ALA PHE LEU ASP ASN LEU GLY PHE THR SER ARG GLU GLU SEQRES 11 A 315 GLY ASP LEU GLY PRO VAL TYR GLY PHE GLN TRP ARG HIS SEQRES 12 A 315 PHE GLY ALA LYS TYR VAL ASP CYS HIS THR ASP TYR SER SEQRES 13 A 315 GLY GLN GLY VAL ASP GLN LEU ALA GLU VAL ILE ARG GLN SEQRES 14 A 315 ILE LYS GLU GLN PRO ASP SER ARG ARG ILE ILE MET SER SEQRES 15 A 315 ALA TRP ASN PRO SER ASP LEU GLY GLN MET VAL LEU PRO SEQRES 16 A 315 PRO CYS HIS THR MET CYS GLN PHE TYR VAL ASP ASN GLY SEQRES 17 A 315 GLU LEU SER CYS GLN LEU TYR GLN ARG SER GLY ASP MET SEQRES 18 A 315 GLY LEU GLY VAL PRO PHE ASN LEU ALA SER TYR GLY LEU SEQRES 19 A 315 LEU THR HIS MET ILE ALA LYS VAL CYS GLY LEU LYS PRO SEQRES 20 A 315 GLY THR LEU VAL HIS THR LEU GLY ASP ALA HIS VAL TYR SEQRES 21 A 315 SER ASN HIS VAL ASP ALA LEU LYS ILE GLN LEU ASP ARG SEQRES 22 A 315 GLU PRO TYR ALA PHE PRO LYS ILE ARG PHE THR ARG ASP SEQRES 23 A 315 VAL ALA SER ILE ASP ASP PHE THR SER ASP MET ILE ALA SEQRES 24 A 315 LEU ASP ASP TYR LYS CYS HIS PRO LYS ILE PRO MET ASP SEQRES 25 A 315 MET ALA VAL SEQRES 1 B 315 MET GLU VAL MET ASN LYS GLU ASN ILE ILE ALA ASP ALA SEQRES 2 B 315 PRO SER ASP VAL VAL LYS THR VAL GLN GLN GLN VAL HIS SEQRES 3 B 315 LEU ASN GLN ASP GLU TYR LYS TYR LEU LYS GLN VAL GLU SEQRES 4 B 315 GLN ILE LEU ARG GLU GLY THR ARG ARG ASP ASP ARG THR SEQRES 5 B 315 GLY THR GLY THR ILE SER ILE PHE GLY MET GLN SER LYS SEQRES 6 B 315 TYR CYS LEU ARG ASN GLY THR ILE PRO LEU LEU THR THR SEQRES 7 B 315 LYS ARG VAL TYR TRP LYS GLY VAL LEU GLU GLU LEU LEU SEQRES 8 B 315 TRP PHE ILE SER GLY SER THR ASP GLY LYS LEU LEU MET SEQRES 9 B 315 GLU LYS ASN VAL LYS ILE TRP GLU LYS ASN GLY ASP ARG SEQRES 10 B 315 ALA PHE LEU ASP ASN LEU GLY PHE THR SER ARG GLU GLU SEQRES 11 B 315 GLY ASP LEU GLY PRO VAL TYR GLY PHE GLN TRP ARG HIS SEQRES 12 B 315 PHE GLY ALA LYS TYR VAL ASP CYS HIS THR ASP TYR SER SEQRES 13 B 315 GLY GLN GLY VAL ASP GLN LEU ALA GLU VAL ILE ARG GLN SEQRES 14 B 315 ILE LYS GLU GLN PRO ASP SER ARG ARG ILE ILE MET SER SEQRES 15 B 315 ALA TRP ASN PRO SER ASP LEU GLY GLN MET VAL LEU PRO SEQRES 16 B 315 PRO CYS HIS THR MET CYS GLN PHE TYR VAL ASP ASN GLY SEQRES 17 B 315 GLU LEU SER CYS GLN LEU TYR GLN ARG SER GLY ASP MET SEQRES 18 B 315 GLY LEU GLY VAL PRO PHE ASN LEU ALA SER TYR GLY LEU SEQRES 19 B 315 LEU THR HIS MET ILE ALA LYS VAL CYS GLY LEU LYS PRO SEQRES 20 B 315 GLY THR LEU VAL HIS THR LEU GLY ASP ALA HIS VAL TYR SEQRES 21 B 315 SER ASN HIS VAL ASP ALA LEU LYS ILE GLN LEU ASP ARG SEQRES 22 B 315 GLU PRO TYR ALA PHE PRO LYS ILE ARG PHE THR ARG ASP SEQRES 23 B 315 VAL ALA SER ILE ASP ASP PHE THR SER ASP MET ILE ALA SEQRES 24 B 315 LEU ASP ASP TYR LYS CYS HIS PRO LYS ILE PRO MET ASP SEQRES 25 B 315 MET ALA VAL HET SO4 A 401 5 HET SO4 B 401 5 HETNAM SO4 SULFATE ION FORMUL 3 SO4 2(O4 S 2-) FORMUL 5 HOH *942(H2 O) HELIX 1 1 ASN A 28 GLY A 45 1 18 HELIX 2 2 ARG A 69 THR A 72 5 4 HELIX 3 3 TYR A 82 SER A 95 1 14 HELIX 4 4 ASP A 99 GLU A 105 1 7 HELIX 5 5 GLU A 112 GLY A 115 5 4 HELIX 6 6 ASP A 116 LEU A 123 1 8 HELIX 7 7 VAL A 136 PHE A 144 1 9 HELIX 8 8 ASP A 161 GLN A 173 1 13 HELIX 9 9 ASP A 188 MET A 192 5 5 HELIX 10 10 LEU A 223 GLY A 244 1 22 HELIX 11 11 HIS A 263 ASP A 272 1 10 HELIX 12 12 THR A 294 ASP A 296 5 3 HELIX 13 13 ASN B 28 GLY B 45 1 18 HELIX 14 14 ARG B 69 THR B 72 5 4 HELIX 15 15 TYR B 82 GLY B 96 1 15 HELIX 16 16 ASP B 99 GLU B 105 1 7 HELIX 17 17 TRP B 111 ASP B 116 1 6 HELIX 18 18 ASP B 116 LEU B 123 1 8 HELIX 19 19 VAL B 136 PHE B 144 1 9 HELIX 20 20 ASP B 161 GLN B 173 1 13 HELIX 21 21 ASP B 188 MET B 192 5 5 HELIX 22 22 LEU B 223 GLY B 244 1 22 HELIX 23 23 HIS B 263 ASP B 272 1 10 HELIX 24 24 THR B 294 ASP B 296 5 3 SHEET 1 A 6 THR A 46 ARG A 48 0 SHEET 2 A 6 THR A 56 CYS A 67 -1 O SER A 58 N THR A 46 SHEET 3 A 6 LYS A 246 TYR A 260 -1 O HIS A 252 N SER A 64 SHEET 4 A 6 GLU A 209 ASP A 220 1 N CYS A 212 O VAL A 251 SHEET 5 A 6 HIS A 198 ASP A 206 -1 N TYR A 204 O SER A 211 SHEET 6 A 6 ILE A 180 SER A 182 -1 N MET A 181 O CYS A 201 SHEET 1 B 2 LYS A 280 PHE A 283 0 SHEET 2 B 2 ILE A 298 ASP A 301 -1 O ALA A 299 N ARG A 282 SHEET 1 C 6 THR B 46 ASP B 49 0 SHEET 2 C 6 GLY B 55 CYS B 67 -1 O THR B 56 N ARG B 48 SHEET 3 C 6 LYS B 246 TYR B 260 -1 O HIS B 252 N SER B 64 SHEET 4 C 6 GLU B 209 ASP B 220 1 N LEU B 210 O GLY B 248 SHEET 5 C 6 HIS B 198 ASP B 206 -1 N TYR B 204 O SER B 211 SHEET 6 C 6 ILE B 180 SER B 182 -1 N MET B 181 O CYS B 201 SHEET 1 D 2 LYS B 280 PHE B 283 0 SHEET 2 D 2 ILE B 298 ASP B 301 -1 O ASP B 301 N LYS B 280 SITE 1 AC1 5 LEU A 194 ARG A 217 ARG B 177 ARG B 178 SITE 2 AC1 5 HOH B 680 SITE 1 AC2 5 ARG A 178 LEU B 194 ARG B 217 HOH B 742 SITE 2 AC2 5 HOH B 975 CRYST1 99.335 98.367 69.159 90.00 111.77 90.00 C 1 2 1 8 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 0.010067 0.000000 0.004020 0.00000 SCALE2 0.000000 0.010166 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015570 0.00000