HEADER HYDROLASE 10-JUL-15 5CHP TITLE T. MARITIMA THYX IN COMPLEX WITH TYC5-03 COMPND MOL_ID: 1; COMPND 2 MOLECULE: THYMIDYLATE SYNTHASE THYX; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: TSASE; COMPND 5 EC: 2.1.1.148; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOTOGA MARITIMA; SOURCE 3 ORGANISM_TAXID: 2336; SOURCE 4 GENE: THYX, THY1, TM_0449; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS THYX IN COMPLEX WITH INHIBITOR, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR S.SURADE,R.LUCIANI,P.SAXENA,M.SANTUCCI,S.FERRARI,A.VENTURELLI, AUTHOR 2 G.MARVERTI,G.PONTERINI,C.A.ABELL,T.L.BLUNDELL,M.P.COSTI REVDAT 2 10-JAN-24 5CHP 1 REMARK REVDAT 1 19-OCT-16 5CHP 0 JRNL AUTH S.SURADE JRNL TITL IDENTIFICATION OF INHIBITORS TARGETING SUBSTRATE-BINDING JRNL TITL 2 SITE IN MYCOBACTERIUM TUBERCULOSIS FAD-DEPENDENT THYMIDYLATE JRNL TITL 3 SYNTHASE (THYX) THROUGH VIRTUAL SCREENING: A NEW STUDY JRNL TITL 4 DE-FINING THE BINDING MECHANISM OF INHIBITORS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.74 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 39622 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) : 0.171 REMARK 3 R VALUE (WORKING SET) : 0.170 REMARK 3 FREE R VALUE : 0.201 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2104 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) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.75 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2639 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.14 REMARK 3 BIN R VALUE (WORKING SET) : 0.2690 REMARK 3 BIN FREE R VALUE SET COUNT : 143 REMARK 3 BIN FREE R VALUE : 0.2810 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1817 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 67 REMARK 3 SOLVENT ATOMS : 225 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.69 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.05000 REMARK 3 B22 (A**2) : -0.05000 REMARK 3 B33 (A**2) : 0.10000 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): 0.077 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.080 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.046 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.371 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.966 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.957 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1953 ; 0.027 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2650 ; 2.576 ; 1.990 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 218 ; 6.363 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 95 ;32.445 ;22.421 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 331 ;15.062 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 17 ;22.003 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 277 ; 0.217 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1478 ; 0.016 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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 USED IF PRESENT IN REMARK 3 THE INPUT REMARK 4 REMARK 4 5CHP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-JUL-15. REMARK 100 THE DEPOSITION ID IS D_1000211467. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-DEC-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0-7.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97630 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39623 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 31.560 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 6.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 20.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL 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: 1KQ4 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.64 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.38 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: HANGING DROP, SOAKING REGROWN CRYSTAL REMARK 280 WITH THE ORGANIC COMPOUND, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 41 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 3555 -Y,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X,Z+3/4 REMARK 290 5555 -X+1/2,Y,-Z+3/4 REMARK 290 6555 X,-Y+1/2,-Z+1/4 REMARK 290 7555 Y+1/2,X+1/2,-Z+1/2 REMARK 290 8555 -Y,-X,-Z REMARK 290 9555 X+1/2,Y+1/2,Z+1/2 REMARK 290 10555 -X,-Y,Z REMARK 290 11555 -Y+1/2,X,Z+3/4 REMARK 290 12555 Y,-X+1/2,Z+1/4 REMARK 290 13555 -X,Y+1/2,-Z+1/4 REMARK 290 14555 X+1/2,-Y,-Z+3/4 REMARK 290 15555 Y,X,-Z REMARK 290 16555 -Y+1/2,-X+1/2,-Z+1/2 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 55.29000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 55.29000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 61.48000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 55.29000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 30.74000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 55.29000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 92.22000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 55.29000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 92.22000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 55.29000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 30.74000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 55.29000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 55.29000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 61.48000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 1.000000 0.000000 0.000000 55.29000 REMARK 290 SMTRY2 9 0.000000 1.000000 0.000000 55.29000 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 61.48000 REMARK 290 SMTRY1 10 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 11 0.000000 -1.000000 0.000000 55.29000 REMARK 290 SMTRY2 11 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 1.000000 92.22000 REMARK 290 SMTRY1 12 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 12 -1.000000 0.000000 0.000000 55.29000 REMARK 290 SMTRY3 12 0.000000 0.000000 1.000000 30.74000 REMARK 290 SMTRY1 13 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 55.29000 REMARK 290 SMTRY3 13 0.000000 0.000000 -1.000000 30.74000 REMARK 290 SMTRY1 14 1.000000 0.000000 0.000000 55.29000 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 14 0.000000 0.000000 -1.000000 92.22000 REMARK 290 SMTRY1 15 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 15 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 16 0.000000 -1.000000 0.000000 55.29000 REMARK 290 SMTRY2 16 -1.000000 0.000000 0.000000 55.29000 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 61.48000 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 300 THE ASSEMBLY REPRESENTED IN THIS ENTRY HAS REGULAR REMARK 300 DIHEDRAL POINT SYMMETRY (SCHOENFLIES SYMBOL = D2). 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 21480 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 32910 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -70.0 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 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 4 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 -13 REMARK 465 SER A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 HIS A -9 REMARK 465 HIS A -8 REMARK 465 HIS A -7 REMARK 465 HIS A -6 REMARK 465 SER A -5 REMARK 465 MET A -4 REMARK 465 ASP A -3 REMARK 465 ILE A -2 REMARK 465 GLU A -1 REMARK 465 LEU A 0 REMARK 465 VAL A 218 REMARK 465 GLN A 219 REMARK 465 VAL A 220 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 CB SER A 166 O HOH A 401 1.33 REMARK 500 CB ILE A 214 O HOH A 493 1.61 REMARK 500 CB SER A 139 O HOH A 428 1.62 REMARK 500 CB ARG A 157 O HOH A 408 1.68 REMARK 500 CB ARG A 28 O HOH A 405 1.78 REMARK 500 CA ALA A 26 O HOH A 440 1.81 REMARK 500 O HOH A 448 O HOH A 488 1.82 REMARK 500 O HOH A 448 O HOH A 576 1.84 REMARK 500 CG2 VAL A 126 O HOH A 574 1.86 REMARK 500 CB ALA A 146 O HOH A 438 1.86 REMARK 500 O HOH A 432 O HOH A 441 1.90 REMARK 500 CB SER A 102 O HOH A 404 1.91 REMARK 500 CG2 VAL A 14 O HOH A 543 1.93 REMARK 500 CD2 PHE A 205 O HOH A 568 1.99 REMARK 500 CG LYS A 67 O HOH A 491 2.00 REMARK 500 O HOH A 496 O HOH A 556 2.01 REMARK 500 OG SER A 166 O HOH A 401 2.03 REMARK 500 CG1 ILE A 214 O HOH A 493 2.05 REMARK 500 CG2 VAL A 16 O HOH A 490 2.06 REMARK 500 O LYS A 216 O HOH A 402 2.06 REMARK 500 CG LYS A 8 O HOH A 597 2.08 REMARK 500 CE3 TRP A 76 O HOH A 418 2.10 REMARK 500 CD2 HIS A 53 O HOH A 552 2.13 REMARK 500 C8M FAD A 301 O HOH A 555 2.18 REMARK 500 CD ARG A 157 O HOH A 417 2.18 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 CG1 ILE A 81 O HOH A 544 8555 1.94 REMARK 500 O HOH A 492 O HOH A 509 10555 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 HIS A 43 CG HIS A 43 CD2 0.058 REMARK 500 TRP A 181 CE2 TRP A 181 CD2 0.074 REMARK 500 TRP A 200 CE2 TRP A 200 CD2 0.072 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 VAL A 14 CB - CA - C ANGL. DEV. = -11.9 DEGREES REMARK 500 PHE A 57 CB - CG - CD2 ANGL. DEV. = -4.7 DEGREES REMARK 500 ARG A 74 NE - CZ - NH2 ANGL. DEV. = -5.0 DEGREES REMARK 500 PHE A 77 CB - CG - CD2 ANGL. DEV. = -4.8 DEGREES REMARK 500 PHE A 77 CB - CG - CD1 ANGL. DEV. = 4.8 DEGREES REMARK 500 ARG A 78 NE - CZ - NH1 ANGL. DEV. = -4.8 DEGREES REMARK 500 ARG A 80 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 ARG A 147 NE - CZ - NH1 ANGL. DEV. = -4.0 DEGREES REMARK 500 LEU A 167 CB - CG - CD2 ANGL. DEV. = -11.8 DEGREES REMARK 500 PHE A 194 CB - CG - CD2 ANGL. DEV. = -4.9 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 LEU A 6 -147.63 61.42 REMARK 500 LYS A 36 135.90 -24.46 REMARK 500 LYS A 216 -77.67 -57.76 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 624 DISTANCE = 6.04 ANGSTROMS REMARK 525 HOH A 625 DISTANCE = 6.44 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FAD A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 51Q A 302 DBREF 5CHP A 1 220 UNP Q9WYT0 THYX_THEMA 1 220 SEQADV 5CHP MET A -13 UNP Q9WYT0 INITIATING METHIONINE SEQADV 5CHP SER A -12 UNP Q9WYT0 EXPRESSION TAG SEQADV 5CHP HIS A -11 UNP Q9WYT0 EXPRESSION TAG SEQADV 5CHP HIS A -10 UNP Q9WYT0 EXPRESSION TAG SEQADV 5CHP HIS A -9 UNP Q9WYT0 EXPRESSION TAG SEQADV 5CHP HIS A -8 UNP Q9WYT0 EXPRESSION TAG SEQADV 5CHP HIS A -7 UNP Q9WYT0 EXPRESSION TAG SEQADV 5CHP HIS A -6 UNP Q9WYT0 EXPRESSION TAG SEQADV 5CHP SER A -5 UNP Q9WYT0 EXPRESSION TAG SEQADV 5CHP MET A -4 UNP Q9WYT0 EXPRESSION TAG SEQADV 5CHP ASP A -3 UNP Q9WYT0 EXPRESSION TAG SEQADV 5CHP ILE A -2 UNP Q9WYT0 EXPRESSION TAG SEQADV 5CHP GLU A -1 UNP Q9WYT0 EXPRESSION TAG SEQADV 5CHP LEU A 0 UNP Q9WYT0 EXPRESSION TAG SEQRES 1 A 234 MET SER HIS HIS HIS HIS HIS HIS SER MET ASP ILE GLU SEQRES 2 A 234 LEU MET LYS ILE ASP ILE LEU ASP LYS GLY PHE VAL GLU SEQRES 3 A 234 LEU VAL ASP VAL MET GLY ASN ASP LEU SER ALA VAL ARG SEQRES 4 A 234 ALA ALA ARG VAL SER PHE ASP MET GLY LEU LYS ASP GLU SEQRES 5 A 234 GLU ARG ASP ARG HIS LEU ILE GLU TYR LEU MET LYS HIS SEQRES 6 A 234 GLY HIS GLU THR PRO PHE GLU HIS ILE VAL PHE THR PHE SEQRES 7 A 234 HIS VAL LYS ALA PRO ILE PHE VAL ALA ARG GLN TRP PHE SEQRES 8 A 234 ARG HIS ARG ILE ALA SER TYR ASN GLU LEU SER GLY ARG SEQRES 9 A 234 TYR SER LYS LEU SER TYR GLU PHE TYR ILE PRO SER PRO SEQRES 10 A 234 GLU ARG LEU GLU GLY TYR LYS THR THR ILE PRO PRO GLU SEQRES 11 A 234 ARG VAL THR GLU LYS ILE SER GLU ILE VAL ASP LYS ALA SEQRES 12 A 234 TYR ARG THR TYR LEU GLU LEU ILE GLU SER GLY VAL PRO SEQRES 13 A 234 ARG GLU VAL ALA ARG ILE VAL LEU PRO LEU ASN LEU TYR SEQRES 14 A 234 THR ARG PHE PHE TRP THR VAL ASN ALA ARG SER LEU MET SEQRES 15 A 234 ASN PHE LEU ASN LEU ARG ALA ASP SER HIS ALA GLN TRP SEQRES 16 A 234 GLU ILE GLN GLN TYR ALA LEU ALA ILE ALA ARG ILE PHE SEQRES 17 A 234 LYS GLU LYS CYS PRO TRP THR PHE GLU ALA PHE LEU LYS SEQRES 18 A 234 TYR ALA TYR LYS GLY ASP ILE LEU LYS GLU VAL GLN VAL HET FAD A 301 53 HET 51Q A 302 14 HETNAM FAD FLAVIN-ADENINE DINUCLEOTIDE HETNAM 51Q (2S)-2-[(3-HYDROXY-5-OXO-4,5-DIHYDRO-1,2,4-TRIAZIN-6- HETNAM 2 51Q YL)SULFANYL]PROPANOIC ACID HETSYN 51Q TYC5-03 FORMUL 2 FAD C27 H33 N9 O15 P2 FORMUL 3 51Q C6 H7 N3 O4 S FORMUL 4 HOH *225(H2 O) HELIX 1 AA1 ASN A 19 VAL A 29 1 11 HELIX 2 AA2 ASP A 37 GLY A 52 1 16 HELIX 3 AA3 GLU A 54 HIS A 59 5 6 HELIX 4 AA4 ILE A 70 PHE A 77 1 8 HELIX 5 AA5 SER A 102 GLU A 107 5 6 HELIX 6 AA6 PRO A 114 SER A 139 1 26 HELIX 7 AA7 PRO A 142 ARG A 147 1 6 HELIX 8 AA8 ILE A 148 LEU A 150 5 3 HELIX 9 AA9 ALA A 164 ALA A 175 1 12 HELIX 10 AB1 GLN A 180 CYS A 198 1 19 HELIX 11 AB2 CYS A 198 ALA A 209 1 12 SHEET 1 AA1 5 LYS A 2 ILE A 5 0 SHEET 2 AA1 5 GLY A 9 MET A 17 -1 O VAL A 11 N ILE A 3 SHEET 3 AA1 5 VAL A 61 PRO A 69 -1 O HIS A 65 N GLU A 12 SHEET 4 AA1 5 TYR A 155 ASN A 163 -1 O VAL A 162 N PHE A 62 SHEET 5 AA1 5 SER A 83 GLU A 86 -1 N SER A 83 O THR A 161 SITE 1 AC1 30 THR A 55 GLU A 58 ARG A 78 HIS A 79 SITE 2 AC1 30 ARG A 80 ILE A 81 ASN A 85 GLU A 86 SITE 3 AC1 30 SER A 88 TYR A 91 ASN A 163 ARG A 165 SITE 4 AC1 30 ASN A 169 LEU A 173 ARG A 174 HIS A 178 SITE 5 AC1 30 51Q A 302 HOH A 406 HOH A 432 HOH A 435 SITE 6 AC1 30 HOH A 441 HOH A 454 HOH A 471 HOH A 477 SITE 7 AC1 30 HOH A 514 HOH A 539 HOH A 544 HOH A 547 SITE 8 AC1 30 HOH A 555 HOH A 557 SITE 1 AC2 10 GLN A 75 GLU A 86 SER A 88 GLY A 89 SITE 2 AC2 10 ARG A 90 ARG A 147 ARG A 174 FAD A 301 SITE 3 AC2 10 HOH A 425 HOH A 456 CRYST1 110.580 110.580 122.960 90.00 90.00 90.00 I 41 2 2 16 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 0.009043 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009043 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008133 0.00000