HEADER LYASE 01-MAY-18 6DA9 TITLE CRYSTAL STRUCTURE OF THE TTND DECARBOXYLASE FROM THE TAUTOMYCETIN TITLE 2 BIOSYNTHESIS PATHWAY OF STREPTOMYCES GRISEOCHROMOGENES WITH FMN BOUND TITLE 3 AT 2.05 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBID-LIKE DECARBOXYLASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: TTND DECARBOXYLASE FROM THE TAUTOMYCETIN BIOSYNTHESIS COMPND 5 PATHWAY OF STREPTOMYCES GRISEOCHROMOGENES; COMPND 6 EC: 4.1.1.-; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES GRISEOCHROMOGENES; SOURCE 3 ORGANISM_TAXID: 68214; SOURCE 4 GENE: TTND; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); 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: PBS13033 KEYWDS TTND, DECARBOXYLASE, TAUTOMYCETIN BIOSYNTHESIS, PRFMN BINDING, LYASE, KEYWDS 2 STRUCTURAL GENOMICS, PSI-BIOLOGY, ENZYME DISCOVERY FOR NATURAL KEYWDS 3 PRODUCT BIOSYNTHESIS, NATPRO EXPDTA X-RAY DIFFRACTION AUTHOR L.HAN,J.D.RUDOLF,C.-Y.CHANG,M.D.MILLER,J.SOMAN,W.XU,G.N.PHILLIPS JR., AUTHOR 2 B.SHEN,ENZYME DISCOVERY FOR NATURAL PRODUCT BIOSYNTHESIS (NATPRO) REVDAT 3 04-OCT-23 6DA9 1 REMARK REVDAT 2 01-JAN-20 6DA9 1 REMARK REVDAT 1 03-OCT-18 6DA9 0 JRNL AUTH T.ANNAVAL,L.HAN,J.D.RUDOLF,G.XIE,D.YANG,C.Y.CHANG,M.MA, JRNL AUTH 2 I.CRNOVCIC,M.D.MILLER,J.SOMAN,W.XU,G.N.PHILLIPS JR.,B.SHEN JRNL TITL BIOCHEMICAL AND STRUCTURAL CHARACTERIZATION OF TTND, A JRNL TITL 2 PRENYLATED FMN-DEPENDENT DECARBOXYLASE FROM THE TAUTOMYCETIN JRNL TITL 3 BIOSYNTHETIC PATHWAY. JRNL REF ACS CHEM. BIOL. V. 13 2728 2018 JRNL REFN ESSN 1554-8937 JRNL PMID 30152678 JRNL DOI 10.1021/ACSCHEMBIO.8B00673 REMARK 2 REMARK 2 RESOLUTION. 2.05 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.10.3 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.98 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 37267 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) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.860 REMARK 3 FREE R VALUE TEST SET COUNT : 1437 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 19 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 2.05 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.11 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.35 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2754 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2780 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2641 REMARK 3 BIN R VALUE (WORKING SET) : 0.2776 REMARK 3 BIN FREE R VALUE : 0.2875 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.10 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 113 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.000 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3553 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 107 REMARK 3 SOLVENT ATOMS : 187 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 40.59 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 54.85 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.43270 REMARK 3 B22 (A**2) : -7.76160 REMARK 3 B33 (A**2) : 5.32890 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.270 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.170 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.143 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.299 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.143 REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.947 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.930 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 7513 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 13612 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 1642 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : NULL ; NULL ; NULL REMARK 3 GENERAL PLANES : 1189 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 7513 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : 1 ; 5.000 ; SEMIHARMONIC REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 489 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 8028 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.03 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 3.71 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 14.13 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: { A|0 - A|44 } REMARK 3 ORIGIN FOR THE GROUP (A): 7.7561 18.4957 41.0712 REMARK 3 T TENSOR REMARK 3 T11: -0.0339 T22: 0.0775 REMARK 3 T33: -0.1355 T12: -0.0013 REMARK 3 T13: -0.0117 T23: -0.1147 REMARK 3 L TENSOR REMARK 3 L11: 1.4639 L22: 0.0000 REMARK 3 L33: 1.6074 L12: 0.4095 REMARK 3 L13: 0.5940 L23: 0.3463 REMARK 3 S TENSOR REMARK 3 S11: 0.0333 S12: -0.4102 S13: -0.0456 REMARK 3 S21: 0.1804 S22: -0.0272 S23: -0.0225 REMARK 3 S31: 0.1219 S32: 0.0216 S33: -0.0061 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: { A|45 - A|309 } REMARK 3 ORIGIN FOR THE GROUP (A): 8.4294 30.7065 29.5001 REMARK 3 T TENSOR REMARK 3 T11: -0.0130 T22: 0.0424 REMARK 3 T33: -0.0553 T12: -0.0080 REMARK 3 T13: -0.0007 T23: -0.1200 REMARK 3 L TENSOR REMARK 3 L11: 0.4376 L22: 0.3349 REMARK 3 L33: 0.4732 L12: 0.0927 REMARK 3 L13: 0.1921 L23: 0.4943 REMARK 3 S TENSOR REMARK 3 S11: -0.0245 S12: -0.0657 S13: 0.0793 REMARK 3 S21: 0.0287 S22: 0.0848 S23: 0.0072 REMARK 3 S31: -0.1640 S32: -0.0010 S33: -0.0603 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: { A|310 - A|460 } REMARK 3 ORIGIN FOR THE GROUP (A): -4.9326 10.4314 13.6824 REMARK 3 T TENSOR REMARK 3 T11: -0.0602 T22: 0.0664 REMARK 3 T33: -0.0236 T12: 0.0118 REMARK 3 T13: 0.0050 T23: -0.0172 REMARK 3 L TENSOR REMARK 3 L11: 0.3080 L22: 0.2644 REMARK 3 L33: 0.5663 L12: 0.0164 REMARK 3 L13: 0.0653 L23: -0.0555 REMARK 3 S TENSOR REMARK 3 S11: -0.0256 S12: -0.0876 S13: 0.0161 REMARK 3 S21: 0.0002 S22: 0.0161 S23: 0.0249 REMARK 3 S31: -0.0629 S32: -0.0266 S33: 0.0094 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: { A|461 - A|485 } REMARK 3 ORIGIN FOR THE GROUP (A): -20.9109 -6.4294 34.0330 REMARK 3 T TENSOR REMARK 3 T11: -0.0985 T22: 0.1344 REMARK 3 T33: -0.0606 T12: 0.0820 REMARK 3 T13: 0.0914 T23: 0.0505 REMARK 3 L TENSOR REMARK 3 L11: 1.6707 L22: 1.9056 REMARK 3 L33: 0.3361 L12: -2.3347 REMARK 3 L13: -0.9057 L23: -1.1078 REMARK 3 S TENSOR REMARK 3 S11: -0.0669 S12: 0.1275 S13: 0.1211 REMARK 3 S21: 0.1882 S22: 0.0797 S23: 0.1630 REMARK 3 S31: -0.0570 S32: 0.0627 S33: -0.0128 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: 1. TLS GROUPS WERE ASSIGNED WITH THE REMARK 3 AID OF TLSMD. 2. ZERO OCCUPANCY HYDROGENS IN THEIR RIDING REMARK 3 POSITION WERE USED AS ANTI-BUMPING RESTRAINTS. 3. LSSR TARGET REMARK 3 RESTRAINTS TO THE APO TTND STRUCTURE (PDBID 6DA7) WERE INCLUDED. REMARK 3 4. CRYSTAL WAS SOAKED WITH FMN AS A MIMIC OF THE REQUIRED CO- REMARK 3 FACTOR, PRENYLATED-FMN (PRFMN). 4. AN UNKNOWN LIGAND (UNL) IS REMARK 3 MODELED. THERE ARE 2 UNL'S BOUND IN THE TETRAMER. THE SHAPE REMARK 3 LOOKS LIKE BENZOATE OR NIACIN. THE SITE IS ON A CRYSTALLOGRPAHIC REMARK 3 TWO-FOLD AXIS. REMARK 4 REMARK 4 6DA9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-MAY-18. REMARK 100 THE DEPOSITION ID IS D_1000234249. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-DEC-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 31-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9793 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-225 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 37316 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.050 REMARK 200 RESOLUTION RANGE LOW (A) : 48.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 200 DATA REDUNDANCY : 7.240 REMARK 200 R MERGE (I) : 0.13400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.10 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.4 REMARK 200 DATA REDUNDANCY IN SHELL : 6.00 REMARK 200 R MERGE FOR SHELL (I) : 1.39200 REMARK 200 R SYM FOR SHELL (I) : 1.39200 REMARK 200 FOR SHELL : 0.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: PHENIX 1.10_2155 REMARK 200 STARTING MODEL: 6DA7 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.03 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.68 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 3 MM TTND1, 3 MM MNCL2, 0.5 MM FMN, REMARK 280 20% (V/V) GLYCEROL IN PRECIPITANT SOLUTION, PH 7.0, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 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,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+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 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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 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 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 26.03500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 58.05450 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 96.98450 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 26.03500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 58.05450 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 96.98450 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 26.03500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 58.05450 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 96.98450 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 26.03500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 58.05450 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 96.98450 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 31840 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 62750 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -140.0 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 -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 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 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 4 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 O1 UNL A 514 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 728 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 767 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 MET A -15 REMARK 465 GLY A -14 REMARK 465 SER 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 GLN A -4 REMARK 465 ASP A -3 REMARK 465 PRO A -2 REMARK 465 ASN A -1 REMARK 465 GLY A 267 REMARK 465 ARG A 268 REMARK 465 THR A 269 REMARK 465 ALA A 270 REMARK 465 VAL A 271 REMARK 465 GLU A 272 REMARK 465 GLY A 273 REMARK 465 PRO A 274 REMARK 465 MET A 275 REMARK 465 GLY A 276 REMARK 465 GLU A 277 REMARK 465 TYR A 278 REMARK 465 ALA A 279 REMARK 465 GLY A 280 REMARK 465 TYR A 281 REMARK 465 GLN A 282 REMARK 465 PRO A 283 REMARK 465 ARG A 284 REMARK 465 HIS A 285 REMARK 465 THR A 286 REMARK 465 SER A 287 REMARK 465 MET A 288 REMARK 465 GLN A 289 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 31 -34.46 68.21 REMARK 500 ALA A 420 -50.14 -120.93 REMARK 500 CYS A 436 35.28 -82.38 REMARK 500 SER A 466 83.08 -154.84 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 502 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 164 OD1 REMARK 620 2 HIS A 187 ND1 91.7 REMARK 620 3 GLU A 228 OE2 98.6 169.7 REMARK 620 4 FMN A 501 O1P 92.7 88.2 90.7 REMARK 620 5 HOH A 602 O 98.7 84.5 94.4 166.6 REMARK 620 6 HOH A 625 O 173.5 93.6 76.1 83.6 85.6 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FMN A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 507 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 508 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 509 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 510 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 511 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 512 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: NATPRO-GO.121069 RELATED DB: TARGETTRACK REMARK 900 RELATED ID: MCSG-APC109476 RELATED DB: TARGETTRACK REMARK 900 RELATED ID: 6DA6 RELATED DB: PDB REMARK 900 APO TTND DECARBOXYLASE FROM THE TAUTOMYCETIN BIOSYNTHESIS PATHWAY REMARK 900 OF STREPTOMYCES GRISEOCHROMOGENES, P212121 FORM AT 2.59 A REMARK 900 RELATED ID: 6DA7 RELATED DB: PDB REMARK 900 APO TTND DECARBOXYLASE FROM THE TAUTOMYCETIN BIOSYNTHESIS PATHWAY REMARK 900 OF STREPTOMYCES GRISEOCHROMOGENES, I222 FORM AT 1.83 A DBREF 6DA9 A 1 485 UNP C6ZCR8 C6ZCR8_9ACTN 1 485 SEQADV 6DA9 MET A -15 UNP C6ZCR8 INITIATING METHIONINE SEQADV 6DA9 GLY A -14 UNP C6ZCR8 EXPRESSION TAG SEQADV 6DA9 SER A -13 UNP C6ZCR8 EXPRESSION TAG SEQADV 6DA9 SER A -12 UNP C6ZCR8 EXPRESSION TAG SEQADV 6DA9 HIS A -11 UNP C6ZCR8 EXPRESSION TAG SEQADV 6DA9 HIS A -10 UNP C6ZCR8 EXPRESSION TAG SEQADV 6DA9 HIS A -9 UNP C6ZCR8 EXPRESSION TAG SEQADV 6DA9 HIS A -8 UNP C6ZCR8 EXPRESSION TAG SEQADV 6DA9 HIS A -7 UNP C6ZCR8 EXPRESSION TAG SEQADV 6DA9 HIS A -6 UNP C6ZCR8 EXPRESSION TAG SEQADV 6DA9 SER A -5 UNP C6ZCR8 EXPRESSION TAG SEQADV 6DA9 GLN A -4 UNP C6ZCR8 EXPRESSION TAG SEQADV 6DA9 ASP A -3 UNP C6ZCR8 EXPRESSION TAG SEQADV 6DA9 PRO A -2 UNP C6ZCR8 EXPRESSION TAG SEQADV 6DA9 ASN A -1 UNP C6ZCR8 EXPRESSION TAG SEQADV 6DA9 SER A 0 UNP C6ZCR8 EXPRESSION TAG SEQRES 1 A 501 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER GLN ASP SEQRES 2 A 501 PRO ASN SER MET LYS ARG LEU LYS ASP LEU ARG GLU TYR SEQRES 3 A 501 LEU ALA VAL LEU GLU ALA HIS GLN ASP VAL ARG GLU ILE SEQRES 4 A 501 ASP GLU PRO VAL ASP PRO HIS LEU GLU ALA GLY ALA ALA SEQRES 5 A 501 ALA ARG TRP THR TYR GLU ASN ARG GLY PRO ALA LEU MET SEQRES 6 A 501 LEU ASN ASP LEU THR GLY THR GLY ARG PHE CYS ARG ILE SEQRES 7 A 501 LEU ALA ALA PRO ALA GLY LEU SER THR ILE PRO GLY SER SEQRES 8 A 501 PRO LEU ALA ARG VAL ALA LEU SER LEU GLY LEU ASP VAL SEQRES 9 A 501 SER ALA THR ALA HIS GLU ILE VAL ASP SER LEU ALA ALA SEQRES 10 A 501 ALA ARG THR ARG GLU PRO VAL ALA PRO VAL VAL VAL ASP SEQRES 11 A 501 SER ALA PRO CYS GLN ASP ASN VAL LEU LEU GLY ASP ASP SEQRES 12 A 501 ALA ASN LEU ASP ARG PHE PRO ALA PRO LEU LEU HIS GLU SEQRES 13 A 501 GLY ASP GLY GLY PRO TYR LEU ASN THR TRP GLY THR ILE SEQRES 14 A 501 ILE VAL SER THR PRO ASP GLY SER PHE THR ASN TRP ALA SEQRES 15 A 501 ILE ALA ARG VAL MET LYS ILE ASP GLY LYS ARG MET THR SEQRES 16 A 501 GLY THR PHE ILE PRO THR GLN HIS LEU GLY GLN ILE ARG SEQRES 17 A 501 LYS LEU TRP ASP ASN LEU GLY GLN PRO MET PRO PHE ALA SEQRES 18 A 501 ILE VAL GLN GLY THR GLU PRO GLY ILE PRO PHE VAL ALA SEQRES 19 A 501 SER MET PRO LEU PRO ASP GLY ILE GLU GLU VAL GLY PHE SEQRES 20 A 501 LEU GLY ALA TYR PHE GLY GLU PRO LEU GLU LEU VAL ARG SEQRES 21 A 501 ALA LYS THR VAL ASP LEU LEU VAL PRO ALA SER ALA GLU SEQRES 22 A 501 ILE VAL ILE GLU GLY HIS VAL MET PRO GLY ARG THR ALA SEQRES 23 A 501 VAL GLU GLY PRO MET GLY GLU TYR ALA GLY TYR GLN PRO SEQRES 24 A 501 ARG HIS THR SER MET GLN PRO GLU TYR VAL VAL ASP ALA SEQRES 25 A 501 ILE THR TYR ARG ASP ASP PRO ILE TRP PRO ILE SER VAL SEQRES 26 A 501 ALA GLY GLU PRO VAL ASP GLU THR HIS THR ALA TRP GLY SEQRES 27 A 501 LEU VAL THR ALA ALA GLU ALA LEU ALA LEU LEU ARG ALA SEQRES 28 A 501 ALA LYS LEU PRO VAL ALA THR ALA TRP MET PRO PHE GLU SEQRES 29 A 501 ALA ALA ALA HIS TRP LEU ILE VAL CYS LEU THR GLU ASP SEQRES 30 A 501 TRP ARG GLU ARG MET PRO GLY LEU SER ARG ASP GLY ILE SEQRES 31 A 501 CYS LEU ARG ILE SER GLN VAL LEU ALA ALA THR ARG ILE SEQRES 32 A 501 GLU ALA MET MET THR ARG VAL PHE VAL LEU ASP ASP ASP SEQRES 33 A 501 VAL ASP PRO SER ASP GLN THR GLU LEU ALA TRP ALA ILE SEQRES 34 A 501 ALA THR ARG VAL SER PRO ALA HIS GLY ARG LEU VAL ARG SEQRES 35 A 501 HIS GLY MET ILE ASN PRO LEU ALA GLY CYS TYR SER ALA SEQRES 36 A 501 GLU GLU ARG ARG LEU GLY TYR GLY PRO LYS ALA VAL LEU SEQRES 37 A 501 ASN GLY LEU LEU PRO PRO MET ALA GLU ARG SER ARG ARG SEQRES 38 A 501 SER SER PHE ARG HIS THR TYR PRO GLU PRO VAL ARG GLN SEQRES 39 A 501 ARG VAL ILE GLU LEU LEU ALA HET FMN A 501 31 HET MN A 502 1 HET GOL A 503 6 HET GOL A 504 6 HET GOL A 505 6 HET GOL A 506 6 HET GOL A 507 6 HET GOL A 508 6 HET GOL A 509 6 HET GOL A 510 6 HET GOL A 511 6 HET GOL A 512 6 HET GOL A 513 6 HET UNL A 514 9 HETNAM FMN FLAVIN MONONUCLEOTIDE HETNAM MN MANGANESE (II) ION HETNAM GOL GLYCEROL HETNAM UNL UNKNOWN LIGAND HETSYN FMN RIBOFLAVIN MONOPHOSPHATE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 FMN C17 H21 N4 O9 P FORMUL 3 MN MN 2+ FORMUL 4 GOL 11(C3 H8 O3) FORMUL 16 HOH *187(H2 O) HELIX 1 AA1 ASP A 6 HIS A 17 1 12 HELIX 2 AA2 LEU A 31 ARG A 44 1 14 HELIX 3 AA3 LEU A 77 LEU A 84 1 8 HELIX 4 AA4 THR A 91 ARG A 103 1 13 HELIX 5 AA5 ALA A 116 ASP A 120 5 5 HELIX 6 AA6 ASP A 126 ALA A 128 5 3 HELIX 7 AA7 ASN A 129 PHE A 133 5 5 HELIX 8 AA8 GLN A 186 LEU A 198 1 13 HELIX 9 AA9 PRO A 212 SER A 219 1 8 HELIX 10 AB1 GLU A 227 GLY A 237 1 11 HELIX 11 AB2 ASP A 315 ALA A 320 1 6 HELIX 12 AB3 ALA A 320 ALA A 336 1 17 HELIX 13 AB4 PRO A 346 ALA A 350 5 5 HELIX 14 AB5 ASP A 361 MET A 366 1 6 HELIX 15 AB6 SER A 370 ALA A 384 1 15 HELIX 16 AB7 ILE A 387 MET A 391 5 5 HELIX 17 AB8 ASP A 405 VAL A 417 1 13 HELIX 18 AB9 SER A 438 GLY A 445 1 8 HELIX 19 AC1 ALA A 460 ARG A 465 1 6 HELIX 20 AC2 SER A 467 TYR A 472 1 6 HELIX 21 AC3 PRO A 473 ALA A 485 1 13 SHEET 1 AA1 4 VAL A 20 ILE A 23 0 SHEET 2 AA1 4 ALA A 47 LEU A 50 1 O MET A 49 N ILE A 23 SHEET 3 AA1 4 ARG A 61 ALA A 64 -1 O ILE A 62 N LEU A 50 SHEET 4 AA1 4 ILE A 304 ILE A 307 1 O ILE A 307 N LEU A 63 SHEET 1 AA2 3 VAL A 111 VAL A 113 0 SHEET 2 AA2 3 GLU A 241 ARG A 244 1 O LEU A 242 N VAL A 111 SHEET 3 AA2 3 LEU A 251 PRO A 253 -1 O VAL A 252 N VAL A 243 SHEET 1 AA3 5 ASN A 121 LEU A 124 0 SHEET 2 AA3 5 GLU A 291 TYR A 299 -1 O ILE A 297 N LEU A 123 SHEET 3 AA3 5 ARG A 177 THR A 179 -1 N MET A 178 O TYR A 292 SHEET 4 AA3 5 VAL A 170 LYS A 172 -1 N MET A 171 O THR A 179 SHEET 5 AA3 5 TYR A 146 ASN A 148 -1 N ASN A 148 O VAL A 170 SHEET 1 AA4 6 ASN A 121 LEU A 124 0 SHEET 2 AA4 6 GLU A 291 TYR A 299 -1 O ILE A 297 N LEU A 123 SHEET 3 AA4 6 ILE A 258 MET A 265 -1 N GLU A 261 O ALA A 296 SHEET 4 AA4 6 MET A 202 GLN A 208 -1 N ILE A 206 O ILE A 260 SHEET 5 AA4 6 THR A 152 SER A 156 -1 N ILE A 154 O ALA A 205 SHEET 6 AA4 6 THR A 163 ALA A 166 -1 O ALA A 166 N ILE A 153 SHEET 1 AA5 5 VAL A 340 TRP A 344 0 SHEET 2 AA5 5 TRP A 353 LEU A 358 -1 O CYS A 357 N THR A 342 SHEET 3 AA5 5 ARG A 393 ASP A 398 1 O PHE A 395 N VAL A 356 SHEET 4 AA5 5 GLY A 447 ASN A 453 1 O LEU A 452 N VAL A 394 SHEET 5 AA5 5 ARG A 423 GLY A 428 -1 N ARG A 426 O LYS A 449 LINK OD1 ASN A 164 MN MN A 502 1555 1555 1.98 LINK ND1 HIS A 187 MN MN A 502 1555 1555 2.23 LINK OE2 GLU A 228 MN MN A 502 1555 1555 2.34 LINK O1P FMN A 501 MN MN A 502 1555 1555 2.09 LINK MN MN A 502 O HOH A 602 1555 1555 2.29 LINK MN MN A 502 O HOH A 625 1555 1555 2.01 CISPEP 1 PRO A 313 VAL A 314 0 6.21 SITE 1 AC1 24 THR A 149 ASN A 164 ALA A 166 ILE A 167 SITE 2 AC1 24 ALA A 168 ARG A 169 ILE A 183 GLN A 186 SITE 3 AC1 24 HIS A 187 ALA A 218 SER A 219 MET A 220 SITE 4 AC1 24 PRO A 221 GLU A 228 SER A 308 GLU A 316 SITE 5 AC1 24 TRP A 321 ARG A 386 MN A 502 GOL A 512 SITE 6 AC1 24 HOH A 617 HOH A 625 HOH A 659 HOH A 691 SITE 1 AC2 6 ASN A 164 HIS A 187 GLU A 228 FMN A 501 SITE 2 AC2 6 HOH A 602 HOH A 625 SITE 1 AC3 7 GLY A 74 SER A 75 PRO A 76 LEU A 77 SITE 2 AC3 7 SER A 89 HOH A 603 HOH A 680 SITE 1 AC4 4 ASP A 402 SER A 404 ASP A 405 HOH A 680 SITE 1 AC5 6 LEU A 130 ASP A 131 PHE A 133 ALA A 135 SITE 2 AC5 6 LYS A 172 HOH A 630 SITE 1 AC6 3 VAL A 122 LEU A 124 ASP A 127 SITE 1 AC7 4 THR A 163 GLU A 227 LEU A 242 HOH A 639 SITE 1 AC8 1 ARG A 377 SITE 1 AC9 5 TRP A 411 THR A 415 ARG A 416 LEU A 456 SITE 2 AC9 5 ARG A 464 SITE 1 AD1 6 TYR A 41 GLU A 42 ARG A 44 PRO A 313 SITE 2 AD1 6 VAL A 314 HOH A 715 SITE 1 AD2 5 ARG A 363 SER A 370 ARG A 371 HOH A 646 SITE 2 AD2 5 HOH A 673 SITE 1 AD3 5 GLN A 186 PRO A 221 ARG A 386 MET A 390 SITE 2 AD3 5 FMN A 501 CRYST1 52.070 116.109 193.969 90.00 90.00 90.00 I 2 2 2 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 0.019205 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008613 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005155 0.00000