HEADER TRANSFERASE 09-DEC-10 3PX3 TITLE STRUCTURE OF TYLM1 FROM STREPTOMYCES FRADIAE H123A MUTANT IN COMPLEX TITLE 2 WITH SAH AND DTDP-QUIP3N COMPND MOL_ID: 1; COMPND 2 MOLECULE: N-METHYLTRANSFERASE; COMPND 3 CHAIN: A, D; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES FRADIAE; SOURCE 3 ORGANISM_TAXID: 1906; SOURCE 4 STRAIN: ATCC 19609; SOURCE 5 GENE: TYLM1, TYLMI(ORF3*); SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET31B KEYWDS SAM BINDING, N, N-DIMETHYLTRANSFERASE, DTDP-QUIP3N BINDING, KEYWDS 2 TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR H.M.HOLDEN,A.E.CARNEY REVDAT 4 13-SEP-23 3PX3 1 REMARK SEQADV REVDAT 3 16-FEB-11 3PX3 1 JRNL REVDAT 2 29-DEC-10 3PX3 1 JRNL REVDAT 1 22-DEC-10 3PX3 0 JRNL AUTH A.E.CARNEY,H.M.HOLDEN JRNL TITL MOLECULAR ARCHITECTURE OF TYLM1 FROM STREPTOMYCES FRADIAE: JRNL TITL 2 AN N,N-DIMETHYLTRANSFERASE INVOLVED IN THE PRODUCTION OF JRNL TITL 3 DTDP-D-MYCAMINOSE . JRNL REF BIOCHEMISTRY V. 50 780 2011 JRNL REFN ISSN 0006-2960 JRNL PMID 21142177 JRNL DOI 10.1021/BI101733Y REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0066 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.57 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.4 REMARK 3 NUMBER OF REFLECTIONS : 44824 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) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.245 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2392 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2846 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 81.66 REMARK 3 BIN R VALUE (WORKING SET) : 0.2550 REMARK 3 BIN FREE R VALUE SET COUNT : 190 REMARK 3 BIN FREE R VALUE : 0.3230 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3652 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 126 REMARK 3 SOLVENT ATOMS : 387 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.86 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.03000 REMARK 3 B33 (A**2) : -0.03000 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): 0.132 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.140 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.091 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.968 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.946 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.906 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3884 ; 0.013 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5291 ; 2.263 ; 1.982 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 480 ; 7.108 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 177 ;33.492 ;21.977 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 563 ;15.602 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 39 ;22.394 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 577 ; 0.211 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2983 ; 0.014 ; 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): 2381 ; 1.636 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3778 ; 2.427 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1443 ; 4.032 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1412 ; 5.686 ; 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 : 1.40 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 REMARK 4 REMARK 4 3PX3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-DEC-10. REMARK 100 THE DEPOSITION ID IS D_1000062918. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-AUG-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54178 REMARK 200 MONOCHROMATOR : NICKEL FILTER REMARK 200 OPTICS : MONTELL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : BRUKER PLATINUM 135 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : SAINT REMARK 200 DATA SCALING SOFTWARE : SADABS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 47224 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 43.600 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.4 REMARK 200 DATA REDUNDANCY : 2.800 REMARK 200 R MERGE (I) : 0.07500 REMARK 200 R SYM (I) : 0.07500 REMARK 200 FOR THE DATA SET : 8.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 83.3 REMARK 200 DATA REDUNDANCY IN SHELL : 1.50 REMARK 200 R MERGE FOR SHELL (I) : 0.30500 REMARK 200 R SYM FOR SHELL (I) : 0.30500 REMARK 200 FOR SHELL : 2.000 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: PDB ENTRY 3PFH REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.58 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.39 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 16% PEG 5000 MONOMETHYL-ETHER, 2% 1,4 REMARK 280 -DIOXANE, 100MM HEPES, PH 7.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 20.44500 REMARK 290 SMTRY3 2 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: 1530 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19120 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -18.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, D 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 ALA A 2 REMARK 465 HIS A 3 REMARK 465 SER A 4 REMARK 465 SER A 5 REMARK 465 ALA A 6 REMARK 465 THR A 7 REMARK 465 ALA A 8 REMARK 465 GLY A 9 REMARK 465 ALA A 250 REMARK 465 LYS A 251 REMARK 465 GLY A 252 REMARK 465 GLU A 253 REMARK 465 THR A 254 REMARK 465 ARG A 255 REMARK 465 LEU A 256 REMARK 465 GLU A 257 REMARK 465 HIS A 258 REMARK 465 HIS A 259 REMARK 465 HIS A 260 REMARK 465 HIS A 261 REMARK 465 HIS A 262 REMARK 465 HIS A 263 REMARK 465 MET D 1 REMARK 465 ALA D 2 REMARK 465 HIS D 3 REMARK 465 SER D 4 REMARK 465 SER D 5 REMARK 465 ALA D 6 REMARK 465 THR D 7 REMARK 465 ALA D 8 REMARK 465 GLY D 9 REMARK 465 ALA D 250 REMARK 465 LYS D 251 REMARK 465 GLY D 252 REMARK 465 GLU D 253 REMARK 465 THR D 254 REMARK 465 ARG D 255 REMARK 465 LEU D 256 REMARK 465 GLU D 257 REMARK 465 HIS D 258 REMARK 465 HIS D 259 REMARK 465 HIS D 260 REMARK 465 HIS D 261 REMARK 465 HIS D 262 REMARK 465 HIS D 263 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 NH2 ARG A 183 O HOH A 340 2.08 REMARK 500 NH2 ARG A 35 O HOH A 374 2.10 REMARK 500 O HOH D 424 O HOH D 529 2.12 REMARK 500 NE ARG A 183 O HOH A 370 2.13 REMARK 500 O HOH A 342 O HOH A 531 2.13 REMARK 500 NH1 ARG D 90 O HOH D 534 2.15 REMARK 500 NZ LYS A 50 OD2 ASP A 144 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 OE2 GLU A 76 NH1 ARG D 109 1655 2.15 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 ARG A 35 NE - CZ - NH1 ANGL. DEV. = 6.0 DEGREES REMARK 500 ARG A 35 NE - CZ - NH2 ANGL. DEV. = -4.1 DEGREES REMARK 500 ARG A 136 NE - CZ - NH1 ANGL. DEV. = -3.6 DEGREES REMARK 500 ARG A 136 NE - CZ - NH2 ANGL. DEV. = 5.3 DEGREES REMARK 500 ARG A 183 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 ILE A 203 CG1 - CB - CG2 ANGL. DEV. = -16.9 DEGREES REMARK 500 ARG A 241 NE - CZ - NH2 ANGL. DEV. = -4.0 DEGREES REMARK 500 ASP D 101 CB - CG - OD2 ANGL. DEV. = 5.8 DEGREES REMARK 500 ARG D 109 NE - CZ - NH1 ANGL. DEV. = -3.3 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 104 50.15 -154.06 REMARK 500 GLU A 184 75.23 -114.23 REMARK 500 SER D 48 71.97 -165.26 REMARK 500 ASP D 104 89.79 -165.70 REMARK 500 GLU D 186 33.89 -98.67 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 SAH A 264 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE T3Q A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 265 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SAH D 264 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE T3Q D 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3PFG RELATED DB: PDB REMARK 900 WILD TYPE ENZYME IN COMPLEX WITH SAM AND DTDP-PHENOL REMARK 900 RELATED ID: 3PFH RELATED DB: PDB REMARK 900 WILD TYPE ENZYME IN COMPLEX WITH SAH AND DTDP-QUIP3N DBREF 3PX3 A 1 255 UNP P95748 P95748_STRFR 1 255 DBREF 3PX3 D 1 255 UNP P95748 P95748_STRFR 1 255 SEQADV 3PX3 ALA A 123 UNP P95748 HIS 123 ENGINEERED MUTATION SEQADV 3PX3 LEU A 256 UNP P95748 EXPRESSION TAG SEQADV 3PX3 GLU A 257 UNP P95748 EXPRESSION TAG SEQADV 3PX3 HIS A 258 UNP P95748 EXPRESSION TAG SEQADV 3PX3 HIS A 259 UNP P95748 EXPRESSION TAG SEQADV 3PX3 HIS A 260 UNP P95748 EXPRESSION TAG SEQADV 3PX3 HIS A 261 UNP P95748 EXPRESSION TAG SEQADV 3PX3 HIS A 262 UNP P95748 EXPRESSION TAG SEQADV 3PX3 HIS A 263 UNP P95748 EXPRESSION TAG SEQADV 3PX3 ALA D 123 UNP P95748 HIS 123 ENGINEERED MUTATION SEQADV 3PX3 LEU D 256 UNP P95748 EXPRESSION TAG SEQADV 3PX3 GLU D 257 UNP P95748 EXPRESSION TAG SEQADV 3PX3 HIS D 258 UNP P95748 EXPRESSION TAG SEQADV 3PX3 HIS D 259 UNP P95748 EXPRESSION TAG SEQADV 3PX3 HIS D 260 UNP P95748 EXPRESSION TAG SEQADV 3PX3 HIS D 261 UNP P95748 EXPRESSION TAG SEQADV 3PX3 HIS D 262 UNP P95748 EXPRESSION TAG SEQADV 3PX3 HIS D 263 UNP P95748 EXPRESSION TAG SEQRES 1 A 263 MET ALA HIS SER SER ALA THR ALA GLY PRO GLN ALA ASP SEQRES 2 A 263 TYR SER GLY GLU ILE ALA GLU LEU TYR ASP LEU VAL HIS SEQRES 3 A 263 GLN GLY LYS GLY LYS ASP TYR HIS ARG GLU ALA ALA ASP SEQRES 4 A 263 LEU ALA ALA LEU VAL ARG ARG HIS SER PRO LYS ALA ALA SEQRES 5 A 263 SER LEU LEU ASP VAL ALA CYS GLY THR GLY MET HIS LEU SEQRES 6 A 263 ARG HIS LEU ALA ASP SER PHE GLY THR VAL GLU GLY LEU SEQRES 7 A 263 GLU LEU SER ALA ASP MET LEU ALA ILE ALA ARG ARG ARG SEQRES 8 A 263 ASN PRO ASP ALA VAL LEU HIS HIS GLY ASP MET ARG ASP SEQRES 9 A 263 PHE SER LEU GLY ARG ARG PHE SER ALA VAL THR CYS MET SEQRES 10 A 263 PHE SER SER ILE GLY ALA LEU ALA GLY GLN ALA GLU LEU SEQRES 11 A 263 ASP ALA ALA LEU GLU ARG PHE ALA ALA HIS VAL LEU PRO SEQRES 12 A 263 ASP GLY VAL VAL VAL VAL GLU PRO TRP TRP PHE PRO GLU SEQRES 13 A 263 ASN PHE THR PRO GLY TYR VAL ALA ALA GLY THR VAL GLU SEQRES 14 A 263 ALA GLY GLY THR THR VAL THR ARG VAL SER HIS SER SER SEQRES 15 A 263 ARG GLU GLY GLU ALA THR ARG ILE GLU VAL HIS TYR LEU SEQRES 16 A 263 VAL ALA GLY PRO ASP ARG GLY ILE THR HIS HIS GLU GLU SEQRES 17 A 263 SER HIS ARG ILE THR LEU PHE THR ARG GLU GLN TYR GLU SEQRES 18 A 263 ARG ALA PHE THR ALA ALA GLY LEU SER VAL GLU PHE MET SEQRES 19 A 263 PRO GLY GLY PRO SER GLY ARG GLY LEU PHE THR GLY LEU SEQRES 20 A 263 PRO GLY ALA LYS GLY GLU THR ARG LEU GLU HIS HIS HIS SEQRES 21 A 263 HIS HIS HIS SEQRES 1 D 263 MET ALA HIS SER SER ALA THR ALA GLY PRO GLN ALA ASP SEQRES 2 D 263 TYR SER GLY GLU ILE ALA GLU LEU TYR ASP LEU VAL HIS SEQRES 3 D 263 GLN GLY LYS GLY LYS ASP TYR HIS ARG GLU ALA ALA ASP SEQRES 4 D 263 LEU ALA ALA LEU VAL ARG ARG HIS SER PRO LYS ALA ALA SEQRES 5 D 263 SER LEU LEU ASP VAL ALA CYS GLY THR GLY MET HIS LEU SEQRES 6 D 263 ARG HIS LEU ALA ASP SER PHE GLY THR VAL GLU GLY LEU SEQRES 7 D 263 GLU LEU SER ALA ASP MET LEU ALA ILE ALA ARG ARG ARG SEQRES 8 D 263 ASN PRO ASP ALA VAL LEU HIS HIS GLY ASP MET ARG ASP SEQRES 9 D 263 PHE SER LEU GLY ARG ARG PHE SER ALA VAL THR CYS MET SEQRES 10 D 263 PHE SER SER ILE GLY ALA LEU ALA GLY GLN ALA GLU LEU SEQRES 11 D 263 ASP ALA ALA LEU GLU ARG PHE ALA ALA HIS VAL LEU PRO SEQRES 12 D 263 ASP GLY VAL VAL VAL VAL GLU PRO TRP TRP PHE PRO GLU SEQRES 13 D 263 ASN PHE THR PRO GLY TYR VAL ALA ALA GLY THR VAL GLU SEQRES 14 D 263 ALA GLY GLY THR THR VAL THR ARG VAL SER HIS SER SER SEQRES 15 D 263 ARG GLU GLY GLU ALA THR ARG ILE GLU VAL HIS TYR LEU SEQRES 16 D 263 VAL ALA GLY PRO ASP ARG GLY ILE THR HIS HIS GLU GLU SEQRES 17 D 263 SER HIS ARG ILE THR LEU PHE THR ARG GLU GLN TYR GLU SEQRES 18 D 263 ARG ALA PHE THR ALA ALA GLY LEU SER VAL GLU PHE MET SEQRES 19 D 263 PRO GLY GLY PRO SER GLY ARG GLY LEU PHE THR GLY LEU SEQRES 20 D 263 PRO GLY ALA LYS GLY GLU THR ARG LEU GLU HIS HIS HIS SEQRES 21 D 263 HIS HIS HIS HET SAH A 264 26 HET T3Q A 301 35 HET EDO A 265 4 HET SAH D 264 26 HET T3Q D 301 35 HETNAM SAH S-ADENOSYL-L-HOMOCYSTEINE HETNAM T3Q [(3R,4S,5S,6R)-4-AMINO-3,5-DIHYDROXY-6-METHYLOXAN-2- HETNAM 2 T3Q YL][HYDROXY-[[(2R,3S,5R)-3-HYDROXY-5-(5-METHYL-2,4- HETNAM 3 T3Q DIOXOPYRIMIDIN-1-YL)OXOLAN-2-YL]METHOXY]PHOSPHORYL] HETNAM 4 T3Q HYDROGEN PHOSPHATE HETNAM EDO 1,2-ETHANEDIOL HETSYN T3Q THYMIDINE-5'-DIPHOSPHATE-ALPHA-D-3,6-DIDEOXY-3- HETSYN 2 T3Q AMINOGLUCOSE HETSYN EDO ETHYLENE GLYCOL FORMUL 3 SAH 2(C14 H20 N6 O5 S) FORMUL 4 T3Q 2(C16 H27 N3 O14 P2) FORMUL 5 EDO C2 H6 O2 FORMUL 8 HOH *387(H2 O) HELIX 1 1 SER A 15 LYS A 29 1 15 HELIX 2 2 ASP A 32 SER A 48 1 17 HELIX 3 3 GLY A 62 ALA A 69 1 8 HELIX 4 4 SER A 81 ASN A 92 1 12 HELIX 5 5 SER A 119 LEU A 124 5 6 HELIX 6 6 ALA A 125 ALA A 139 1 15 HELIX 7 7 THR A 216 ALA A 227 1 12 HELIX 8 8 SER D 15 LYS D 29 1 15 HELIX 9 9 ASP D 32 SER D 48 1 17 HELIX 10 10 GLY D 62 ALA D 69 1 8 HELIX 11 11 SER D 81 ASN D 92 1 12 HELIX 12 12 SER D 119 LEU D 124 5 6 HELIX 13 13 GLY D 126 ALA D 139 1 14 HELIX 14 14 PHE D 154 PHE D 158 5 5 HELIX 15 15 THR D 216 ALA D 227 1 12 SHEET 1 A 7 VAL A 96 HIS A 99 0 SHEET 2 A 7 THR A 74 GLU A 79 1 N GLY A 77 O HIS A 98 SHEET 3 A 7 SER A 53 VAL A 57 1 N ASP A 56 O GLU A 76 SHEET 4 A 7 PHE A 111 CYS A 116 1 O THR A 115 N VAL A 57 SHEET 5 A 7 VAL A 141 VAL A 149 1 O LEU A 142 N PHE A 111 SHEET 6 A 7 GLY A 240 PRO A 248 -1 O GLY A 246 N VAL A 147 SHEET 7 A 7 LEU A 229 GLY A 236 -1 N GLY A 236 O GLY A 242 SHEET 1 B 4 VAL A 163 ALA A 170 0 SHEET 2 B 4 THR A 173 GLU A 184 -1 O VAL A 175 N VAL A 168 SHEET 3 B 4 ALA A 187 GLY A 198 -1 O ALA A 197 N THR A 174 SHEET 4 B 4 GLY A 202 THR A 213 -1 O THR A 204 N VAL A 196 SHEET 1 C 7 VAL D 96 HIS D 99 0 SHEET 2 C 7 THR D 74 GLU D 79 1 N GLY D 77 O HIS D 98 SHEET 3 C 7 SER D 53 VAL D 57 1 N ASP D 56 O GLU D 76 SHEET 4 C 7 PHE D 111 CYS D 116 1 O THR D 115 N VAL D 57 SHEET 5 C 7 VAL D 141 VAL D 149 1 O LEU D 142 N PHE D 111 SHEET 6 C 7 GLY D 240 PRO D 248 -1 O PHE D 244 N VAL D 149 SHEET 7 C 7 LEU D 229 GLY D 236 -1 N SER D 230 O LEU D 247 SHEET 1 D 4 VAL D 163 ALA D 170 0 SHEET 2 D 4 THR D 173 GLU D 184 -1 O VAL D 175 N VAL D 168 SHEET 3 D 4 ALA D 187 GLY D 198 -1 O ALA D 197 N THR D 174 SHEET 4 D 4 GLY D 202 THR D 213 -1 O ILE D 212 N THR D 188 SITE 1 AC1 22 TYR A 14 TYR A 22 TYR A 33 ALA A 58 SITE 2 AC1 22 GLY A 60 HIS A 64 GLU A 79 LEU A 80 SITE 3 AC1 22 SER A 81 ASP A 101 MET A 102 MET A 117 SITE 4 AC1 22 PHE A 118 SER A 120 ALA A 123 HOH A 268 SITE 5 AC1 22 HOH A 283 T3Q A 301 HOH A 311 HOH A 350 SITE 6 AC1 22 HOH A 354 HOH A 391 SITE 1 AC2 21 TYR A 14 HIS A 26 LYS A 29 PHE A 118 SITE 2 AC2 21 TRP A 152 TRP A 153 PHE A 158 THR A 159 SITE 3 AC2 21 TYR A 162 ALA A 164 ARG A 177 SER A 179 SITE 4 AC2 21 SER A 181 ILE A 190 ARG A 241 SAH A 264 SITE 5 AC2 21 HOH A 277 HOH A 282 HOH A 289 HOH A 349 SITE 6 AC2 21 HOH A 359 SITE 1 AC3 6 GLY A 126 GLU A 186 THR A 213 PHE A 215 SITE 2 AC3 6 GLN A 219 HOH A 402 SITE 1 AC4 22 TYR D 14 TYR D 22 TYR D 33 ALA D 58 SITE 2 AC4 22 GLY D 60 HIS D 64 GLU D 79 LEU D 80 SITE 3 AC4 22 MET D 84 ASP D 101 MET D 102 MET D 117 SITE 4 AC4 22 PHE D 118 SER D 120 ALA D 123 HOH D 274 SITE 5 AC4 22 HOH D 292 HOH D 293 T3Q D 301 HOH D 324 SITE 6 AC4 22 HOH D 326 HOH D 401 SITE 1 AC5 21 TYR D 14 HIS D 26 LYS D 29 PHE D 118 SITE 2 AC5 21 TRP D 152 TRP D 153 PHE D 158 THR D 159 SITE 3 AC5 21 TYR D 162 ALA D 164 ARG D 177 SER D 179 SITE 4 AC5 21 SER D 181 ILE D 190 ARG D 241 SAH D 264 SITE 5 AC5 21 HOH D 281 HOH D 296 HOH D 319 HOH D 385 SITE 6 AC5 21 HOH D 408 CRYST1 86.557 40.890 87.202 90.00 118.04 90.00 P 1 21 1 4 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 0.011553 0.000000 0.006154 0.00000 SCALE2 0.000000 0.024456 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012993 0.00000