HEADER BIOSYNTHETIC PROTEIN 26-SEP-07 2RES TITLE TETRACENOMYCIN ARO/CYC MUTANT R69A COMPND MOL_ID: 1; COMPND 2 MOLECULE: MULTIFUNCTIONAL CYCLASE-DEHYDRATASE-3-O-METHYL TRANSFERASE COMPND 3 TCMN; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: N-TERMINAL DOMAIN; COMPND 6 SYNONYM: TETRACENOMYCIN C AROMATASE/CYCLASE; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES GLAUCESCENS; SOURCE 3 ORGANISM_TAXID: 1907; SOURCE 4 GENE: TCMN; 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: PET28A KEYWDS TETRACENOMYCIN, POLYKETIDE, AROMATASE, CYCLASE, DEHYDRATASE, HELIX- KEYWDS 2 GRIP, ANTIBIOTIC BIOSYNTHESIS, METHYLTRANSFERASE, MULTIFUNCTIONAL KEYWDS 3 ENZYME, TRANSFERASE, LYASE, BIOSYNTHETIC PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR B.D.AMES,S.C.TSAI REVDAT 4 21-FEB-24 2RES 1 REMARK REVDAT 3 20-OCT-21 2RES 1 SEQADV REVDAT 2 24-FEB-09 2RES 1 VERSN REVDAT 1 22-APR-08 2RES 0 JRNL AUTH B.D.AMES,T.P.KORMAN,W.ZHANG,P.SMITH,T.VU,Y.TANG,S.C.TSAI JRNL TITL CRYSTAL STRUCTURE AND FUNCTIONAL ANALYSIS OF TETRACENOMYCIN JRNL TITL 2 ARO/CYC: IMPLICATIONS FOR CYCLIZATION SPECIFICITY OF JRNL TITL 3 AROMATIC POLYKETIDES. JRNL REF PROC.NATL.ACAD.SCI.USA V. 105 5349 2008 JRNL REFN ISSN 0027-8424 JRNL PMID 18388203 JRNL DOI 10.1073/PNAS.0709223105 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.91 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 93.6 REMARK 3 NUMBER OF REFLECTIONS : 9673 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 SET) : 0.210 REMARK 3 FREE R VALUE : 0.255 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1519 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 : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.34 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 81.50 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2680 REMARK 3 BIN FREE R VALUE : 0.3170 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 188 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.023 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1239 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 75 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.23000 REMARK 3 B22 (A**2) : 7.23000 REMARK 3 B33 (A**2) : -4.00000 REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.25 REMARK 3 ESD FROM SIGMAA (A) : 0.25 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.31 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.32 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.20 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.810 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2RES COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-OCT-07. REMARK 100 THE DEPOSITION ID IS D_1000044769. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-NOV-05 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 4.60 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : SI(220) REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9992 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07200 REMARK 200 FOR THE DATA SET : 24.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.24 REMARK 200 COMPLETENESS FOR SHELL (%) : 83.2 REMARK 200 DATA REDUNDANCY IN SHELL : 4.30 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.43800 REMARK 200 FOR SHELL : 3.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.52 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 21% PEG 8000, 0.1M SODIUM ACETATE, PH REMARK 280 4.60, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z 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 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 25.55500 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 25.55500 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 36.54000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 52.54000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 36.54000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 52.54000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 25.55500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 36.54000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 52.54000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 25.55500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 36.54000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 52.54000 REMARK 290 SMTRY3 8 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 ARG A 153 REMARK 465 THR A 154 REMARK 465 PRO A 155 REMARK 465 ALA A 156 REMARK 465 SER A 157 REMARK 465 VAL A 158 REMARK 465 LEU A 159 REMARK 465 PRO A 160 REMARK 465 THR A 161 REMARK 465 GLU A 162 REMARK 465 LEU A 163 REMARK 465 HIS A 164 REMARK 465 ALA A 165 REMARK 465 GLN A 166 REMARK 465 GLN A 167 REMARK 465 LEU A 168 REMARK 465 LEU A 169 REMARK 465 LEU A 170 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 CD ARG A 147 CD ARG A 147 3755 2.17 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 57 -166.83 -79.98 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2RER RELATED DB: PDB REMARK 900 WILD-TYPE PROTEIN REMARK 900 RELATED ID: 2RES RELATED DB: PDB DBREF 2RES A 1 170 UNP P16559 TCMN_STRGA 1 170 SEQADV 2RES GLY A -2 UNP P16559 EXPRESSION TAG SEQADV 2RES SER A -1 UNP P16559 EXPRESSION TAG SEQADV 2RES HIS A 0 UNP P16559 EXPRESSION TAG SEQADV 2RES ALA A 69 UNP P16559 ARG 69 ENGINEERED MUTATION SEQRES 1 A 173 GLY SER HIS MET ALA ALA ARG THR ASP ASN SER ILE VAL SEQRES 2 A 173 VAL ASN ALA PRO PHE GLU LEU VAL TRP ASP VAL THR ASN SEQRES 3 A 173 ASP ILE GLU ALA TRP PRO GLU LEU PHE SER GLU TYR ALA SEQRES 4 A 173 GLU ALA GLU ILE LEU ARG GLN ASP GLY ASP GLY PHE ASP SEQRES 5 A 173 PHE ARG LEU LYS THR ARG PRO ASP ALA ASN GLY ARG VAL SEQRES 6 A 173 TRP GLU TRP VAL SER HIS ALA VAL PRO ASP LYS GLY SER SEQRES 7 A 173 ARG THR VAL ARG ALA HIS ARG VAL GLU THR GLY PRO PHE SEQRES 8 A 173 ALA TYR MET ASN LEU HIS TRP THR TYR ARG ALA VAL ALA SEQRES 9 A 173 GLY GLY THR GLU MET ARG TRP VAL GLN GLU PHE ASP MET SEQRES 10 A 173 LYS PRO GLY ALA PRO PHE ASP ASN ALA HIS MET THR ALA SEQRES 11 A 173 HIS LEU ASN THR THR THR ARG ALA ASN MET GLU ARG ILE SEQRES 12 A 173 LYS LYS ILE ILE GLU ASP ARG HIS ARG GLU GLY GLN ARG SEQRES 13 A 173 THR PRO ALA SER VAL LEU PRO THR GLU LEU HIS ALA GLN SEQRES 14 A 173 GLN LEU LEU LEU FORMUL 2 HOH *75(H2 O) HELIX 1 1 PRO A 14 ASN A 23 1 10 HELIX 2 2 ASP A 24 GLU A 26 5 3 HELIX 3 3 ALA A 27 PHE A 32 1 6 HELIX 4 4 LYS A 73 SER A 75 5 3 HELIX 5 5 ASP A 121 GLN A 152 1 32 SHEET 1 A 7 ALA A 3 VAL A 11 0 SHEET 2 A 7 GLY A 103 MET A 114 -1 O THR A 104 N VAL A 11 SHEET 3 A 7 PHE A 88 VAL A 100 -1 N ALA A 89 O ASP A 113 SHEET 4 A 7 THR A 77 ARG A 82 -1 N ALA A 80 O LEU A 93 SHEET 5 A 7 GLU A 64 ASP A 72 -1 N VAL A 70 O ARG A 79 SHEET 6 A 7 PHE A 48 THR A 54 -1 N PHE A 48 O ALA A 69 SHEET 7 A 7 TYR A 35 GLN A 43 -1 N ALA A 36 O LYS A 53 CRYST1 73.080 105.080 51.110 90.00 90.00 90.00 C 2 2 21 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 0.013684 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009517 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019566 0.00000