HEADER TRANSFERASE 17-JAN-08 3BZ0 TITLE LACTOBACILLUS CASEI THYMIDYLATE SYNTHASE TERNARY COMPLEX WITH DUMP AND TITLE 2 THE PHTALIMIDIC DERIVATIVE C00 COMPND MOL_ID: 1; COMPND 2 MOLECULE: THYMIDYLATE SYNTHASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: TS, TSASE; COMPND 5 EC: 2.1.1.45; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LACTOBACILLUS CASEI; SOURCE 3 ORGANISM_TAXID: 1582; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: CHI 2913; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PKPTSD KEYWDS NUCLEOTIDE SYNTHASE, STRUCTURE BASED DRUG DESIGN, METHYLTRANSFERASE, KEYWDS 2 NUCLEOTIDE BIOSYNTHESIS, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR R.LEONE,L.CANCIAN,M.P.COSTI,S.FERRARI,R.LUCIANI,S.MANGANI REVDAT 3 01-NOV-23 3BZ0 1 REMARK REVDAT 2 24-JUL-13 3BZ0 1 JRNL VERSN REVDAT 1 20-JAN-09 3BZ0 0 JRNL AUTH S.MANGANI,L.CANCIAN,R.LEONE,C.POZZI,S.LAZZARI,R.LUCIANI, JRNL AUTH 2 S.FERRARI,M.P.COSTI JRNL TITL IDENTIFICATION OF THE BINDING MODES OF N-PHENYLPHTHALIMIDES JRNL TITL 2 INHIBITING BACTERIAL THYMIDYLATE SYNTHASE THROUGH X-RAY JRNL TITL 3 CRYSTALLOGRAPHY SCREENING JRNL REF J.MED.CHEM. V. 54 5454 2011 JRNL REFN ISSN 0022-2623 JRNL PMID 21696158 JRNL DOI 10.1021/JM2005018 REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.37 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 88.6 REMARK 3 NUMBER OF REFLECTIONS : 9511 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) : 0.235 REMARK 3 R VALUE (WORKING SET) : 0.226 REMARK 3 FREE R VALUE : 0.326 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.900 REMARK 3 FREE R VALUE TEST SET COUNT : 932 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) : 2.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.77 REMARK 3 REFLECTION IN BIN (WORKING SET) : 700 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 85.47 REMARK 3 BIN R VALUE (WORKING SET) : 0.3550 REMARK 3 BIN FREE R VALUE SET COUNT : 58 REMARK 3 BIN FREE R VALUE : 0.4630 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2521 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 45 REMARK 3 SOLVENT ATOMS : 36 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 56.53 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.42 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.02000 REMARK 3 B22 (A**2) : 0.02000 REMARK 3 B33 (A**2) : -0.02000 REMARK 3 B12 (A**2) : 0.01000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.475 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.320 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 15.150 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.907 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.801 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2648 ; 0.019 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3598 ; 2.151 ; 1.959 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 303 ; 8.060 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 133 ;38.425 ;23.835 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 427 ;24.324 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ;23.758 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 372 ; 0.154 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2049 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1250 ; 0.284 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1700 ; 0.331 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 126 ; 0.166 ; 0.200 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): 58 ; 0.329 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 9 ; 0.216 ; 0.200 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): 1572 ; 0.860 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2462 ; 1.518 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1265 ; 1.933 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1136 ; 2.955 ; 4.500 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: NULL REMARK 4 REMARK 4 3BZ0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 21-JAN-08. REMARK 100 THE DEPOSITION ID IS D_1000046133. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JAN-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : BW7B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.078 REMARK 200 MONOCHROMATOR : SI [111] REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10443 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 33.370 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.700 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 88.6 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.13900 REMARK 200 R SYM (I) : 0.13900 REMARK 200 FOR THE DATA SET : 4.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.3 REMARK 200 DATA REDUNDANCY IN SHELL : 4.10 REMARK 200 R MERGE FOR SHELL (I) : 0.43900 REMARK 200 R SYM FOR SHELL (I) : 0.43900 REMARK 200 FOR SHELL : 1.700 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 1LCA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.13 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.68 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1MM EDTA, 20 MM TRIS-HCL, DUMP, 100MM REMARK 280 AMMONIUM PHOPSHATE, 5% (V/V) PEG 400, PH 7.4, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+5/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/6 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 74.72767 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 149.45533 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 112.09150 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 186.81917 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 37.36383 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 74.72767 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 149.45533 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 186.81917 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 112.09150 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 37.36383 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: 5900 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25490 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -17.0 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 350 BIOMT1 2 0.500000 0.866025 0.000000 -38.95800 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 67.47724 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 37.36383 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 335 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 HIS A 97 REMARK 465 GLY A 98 REMARK 465 PRO A 99 REMARK 465 ASP A 111 REMARK 465 PRO A 112 REMARK 465 GLU A 113 REMARK 465 PRO A 313 REMARK 465 VAL A 314 REMARK 465 ALA A 315 REMARK 465 VAL A 316 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 LEU A 14 CA - CB - CG ANGL. DEV. = 14.9 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 15 -70.63 -61.81 REMARK 500 TRP A 63 -72.74 -48.77 REMARK 500 GLN A 76 8.74 -62.63 REMARK 500 ARG A 78 40.08 78.32 REMARK 500 LYS A 89 33.92 -83.29 REMARK 500 ASP A 94 -9.66 -45.82 REMARK 500 MET A 101 17.70 -64.01 REMARK 500 ASP A 103 68.16 38.89 REMARK 500 ARG A 107 56.07 -140.16 REMARK 500 HIS A 119 3.87 -56.32 REMARK 500 HIS A 131 -32.16 -139.76 REMARK 500 ALA A 152 70.54 -150.19 REMARK 500 THR A 155 -158.59 -95.69 REMARK 500 SER A 156 -63.53 -93.14 REMARK 500 LYS A 157 46.92 -73.78 REMARK 500 ALA A 194 -76.11 -62.26 REMARK 500 TYR A 205 136.50 -172.41 REMARK 500 ASP A 208 59.81 36.88 REMARK 500 PRO A 276 154.92 -46.53 REMARK 500 PRO A 280 -165.89 -75.98 REMARK 500 PRO A 286 32.28 -87.73 REMARK 500 ASP A 287 -10.59 -146.80 REMARK 500 HIS A 289 52.90 -148.59 REMARK 500 ASN A 303 39.03 73.61 REMARK 500 ASP A 305 68.44 -119.94 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 UMP A 317 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE C00 A 318 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1LCE RELATED DB: PDB REMARK 900 RELATED ID: 1TSL RELATED DB: PDB REMARK 900 RELATED ID: 3BYX RELATED DB: PDB REMARK 900 RELATED ID: 3BNZ RELATED DB: PDB REMARK 900 RELATED ID: 3C06 RELATED DB: PDB REMARK 900 RELATED ID: 3C0A RELATED DB: PDB DBREF 3BZ0 A 1 316 UNP P00469 TYSY_LACCA 1 316 SEQRES 1 A 316 MET LEU GLU GLN PRO TYR LEU ASP LEU ALA LYS LYS VAL SEQRES 2 A 316 LEU ASP GLU GLY HIS PHE LYS PRO ASP ARG THR HIS THR SEQRES 3 A 316 GLY THR TYR SER ILE PHE GLY HIS GLN MET ARG PHE ASP SEQRES 4 A 316 LEU SER LYS GLY PHE PRO LEU LEU THR THR LYS LYS VAL SEQRES 5 A 316 PRO PHE GLY LEU ILE LYS SER GLU LEU LEU TRP PHE LEU SEQRES 6 A 316 HIS GLY ASP THR ASN ILE ARG PHE LEU LEU GLN HIS ARG SEQRES 7 A 316 ASN HIS ILE TRP ASP GLU TRP ALA PHE GLU LYS TRP VAL SEQRES 8 A 316 LYS SER ASP GLU TYR HIS GLY PRO ASP MET THR ASP PHE SEQRES 9 A 316 GLY HIS ARG SER GLN LYS ASP PRO GLU PHE ALA ALA VAL SEQRES 10 A 316 TYR HIS GLU GLU MET ALA LYS PHE ASP ASP ARG VAL LEU SEQRES 11 A 316 HIS ASP ASP ALA PHE ALA ALA LYS TYR GLY ASP LEU GLY SEQRES 12 A 316 LEU VAL TYR GLY SER GLN TRP ARG ALA TRP HIS THR SER SEQRES 13 A 316 LYS GLY ASP THR ILE ASP GLN LEU GLY ASP VAL ILE GLU SEQRES 14 A 316 GLN ILE LYS THR HIS PRO TYR SER ARG ARG LEU ILE VAL SEQRES 15 A 316 SER ALA TRP ASN PRO GLU ASP VAL PRO THR MET ALA LEU SEQRES 16 A 316 PRO PRO CYS HIS THR LEU TYR GLN PHE TYR VAL ASN ASP SEQRES 17 A 316 GLY LYS LEU SER LEU GLN LEU TYR GLN ARG SER ALA ASP SEQRES 18 A 316 ILE PHE LEU GLY VAL PRO PHE ASN ILE ALA SER TYR ALA SEQRES 19 A 316 LEU LEU THR HIS LEU VAL ALA HIS GLU CYS GLY LEU GLU SEQRES 20 A 316 VAL GLY GLU PHE ILE HIS THR PHE GLY ASP ALA HIS LEU SEQRES 21 A 316 TYR VAL ASN HIS LEU ASP GLN ILE LYS GLU GLN LEU SER SEQRES 22 A 316 ARG THR PRO ARG PRO ALA PRO THR LEU GLN LEU ASN PRO SEQRES 23 A 316 ASP LYS HIS ASP ILE PHE ASP PHE ASP MET LYS ASP ILE SEQRES 24 A 316 LYS LEU LEU ASN TYR ASP PRO TYR PRO ALA ILE LYS ALA SEQRES 25 A 316 PRO VAL ALA VAL HET UMP A 317 20 HET C00 A 318 25 HETNAM UMP 2'-DEOXYURIDINE 5'-MONOPHOSPHATE HETNAM C00 2-(4-HYDROXYBIPHENYL-3-YL)-4-METHYL-1H-ISOINDOLE-1, HETNAM 2 C00 3(2H)-DIONE HETSYN UMP DUMP FORMUL 2 UMP C9 H13 N2 O8 P FORMUL 3 C00 C21 H15 N O3 FORMUL 4 HOH *36(H2 O) HELIX 1 1 GLU A 3 GLY A 17 1 15 HELIX 2 2 SER A 41 GLY A 43 5 3 HELIX 3 3 PRO A 53 HIS A 66 1 14 HELIX 4 4 ILE A 71 GLN A 76 1 6 HELIX 5 5 TRP A 82 LYS A 92 1 11 HELIX 6 6 PHE A 114 ASP A 132 1 19 HELIX 7 7 ASP A 132 GLY A 140 1 9 HELIX 8 8 VAL A 145 ALA A 152 1 8 HELIX 9 9 ASP A 162 HIS A 174 1 13 HELIX 10 10 GLY A 225 GLY A 245 1 21 HELIX 11 11 HIS A 264 SER A 273 1 10 HELIX 12 12 ASP A 290 PHE A 294 5 5 HELIX 13 13 ASP A 295 LYS A 297 5 3 SHEET 1 A 4 HIS A 18 LYS A 20 0 SHEET 2 A 4 THR A 28 PHE A 32 -1 O THR A 28 N LYS A 20 SHEET 3 A 4 GLU A 247 TYR A 261 -1 O LEU A 260 N TYR A 29 SHEET 4 A 4 GLN A 35 ASP A 39 -1 N MET A 36 O HIS A 253 SHEET 1 B 6 HIS A 18 LYS A 20 0 SHEET 2 B 6 THR A 28 PHE A 32 -1 O THR A 28 N LYS A 20 SHEET 3 B 6 GLU A 247 TYR A 261 -1 O LEU A 260 N TYR A 29 SHEET 4 B 6 LYS A 210 ASP A 221 1 N ALA A 220 O HIS A 259 SHEET 5 B 6 LEU A 201 ASN A 207 -1 N LEU A 201 O TYR A 216 SHEET 6 B 6 ILE A 181 SER A 183 -1 N VAL A 182 O TYR A 202 SHEET 1 C 2 TRP A 153 HIS A 154 0 SHEET 2 C 2 THR A 160 ILE A 161 -1 O ILE A 161 N TRP A 153 SHEET 1 D 2 THR A 281 LEU A 284 0 SHEET 2 D 2 ILE A 299 LEU A 302 -1 O LYS A 300 N GLN A 283 SITE 1 AC1 13 ARG A 23 ARG A 178 ARG A 179 CYS A 198 SITE 2 AC1 13 HIS A 199 GLN A 217 ARG A 218 SER A 219 SITE 3 AC1 13 ALA A 220 ASP A 221 ASN A 229 HIS A 259 SITE 4 AC1 13 TYR A 261 SITE 1 AC2 5 TRP A 82 GLU A 84 TRP A 85 LEU A 195 SITE 2 AC2 5 PHE A 228 CRYST1 77.916 77.916 224.183 90.00 90.00 120.00 P 61 2 2 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 0.012834 0.007410 0.000000 0.00000 SCALE2 0.000000 0.014820 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004461 0.00000