HEADER TRANSFERASE 09-MAR-12 4E2X TITLE X-RAY STRUCTURE OF THE Y222F MUTANT OF TCAB9, A C-3'- TITLE 2 METHYLTRANSFERASE, IN COMPLEX WITH S-ADENOSYL-L-HOMOCYSTEINE AND DTDP COMPND MOL_ID: 1; COMPND 2 MOLECULE: TCAB9; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: C-3'-METHYLTRANSFERASE; COMPND 5 EC: 2.1.1.-; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MICROMONOSPORA CHALCEA; SOURCE 3 ORGANISM_TAXID: 1874; SOURCE 4 GENE: TCAB9; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: ROSETTA2 DE3; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28 KEYWDS KIJANOSE, TETRONITROSE, TETRADEOXY SUGAR, SUGAR METHYLATION, KEYWDS 2 TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR N.A.BRUENDER,H.M.HOLDEN REVDAT 3 13-SEP-23 4E2X 1 REMARK SEQADV LINK REVDAT 2 30-MAY-12 4E2X 1 JRNL REVDAT 1 25-APR-12 4E2X 0 JRNL AUTH N.A.BRUENDER,H.M.HOLDEN JRNL TITL PROBING THE CATALYTIC MECHANISM OF A C-3'-METHYLTRANSFERASE JRNL TITL 2 INVOLVED IN THE BIOSYNTHESIS OF D-TETRONITROSE. JRNL REF PROTEIN SCI. V. 21 876 2012 JRNL REFN ISSN 0961-8368 JRNL PMID 22495991 JRNL DOI 10.1002/PRO.2074 REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 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) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 94.7 REMARK 3 NUMBER OF REFLECTIONS : 77644 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) : 0.206 REMARK 3 R VALUE (WORKING SET) : 0.204 REMARK 3 FREE R VALUE : 0.236 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4112 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) : 1.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.44 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4890 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 81.92 REMARK 3 BIN R VALUE (WORKING SET) : 0.4060 REMARK 3 BIN FREE R VALUE SET COUNT : 263 REMARK 3 BIN FREE R VALUE : 0.4240 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3161 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 68 REMARK 3 SOLVENT ATOMS : 473 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.96 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.36000 REMARK 3 B22 (A**2) : 0.19000 REMARK 3 B33 (A**2) : 0.17000 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): 0.072 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.075 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.058 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.540 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.953 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.938 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3324 ; 0.010 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4516 ; 2.267 ; 1.974 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 412 ; 6.652 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 161 ;36.554 ;23.043 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 518 ;13.295 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 31 ;20.144 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 494 ; 0.168 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2575 ; 0.009 ; 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): 2033 ; 1.962 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3275 ; 2.853 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1291 ; 4.375 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1237 ; 6.875 ; 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: REMARK 3 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS REMARK 3 U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 4E2X COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-MAR-12. REMARK 100 THE DEPOSITION ID IS D_1000071101. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-MAY-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 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 : MONTEL 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 : 81798 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 38.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.7 REMARK 200 DATA REDUNDANCY : 4.300 REMARK 200 R MERGE (I) : 0.07200 REMARK 200 R SYM (I) : 0.07200 REMARK 200 FOR THE DATA SET : 10.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.50 REMARK 200 COMPLETENESS FOR SHELL (%) : 85.2 REMARK 200 DATA REDUNDANCY IN SHELL : 1.74 REMARK 200 R MERGE FOR SHELL (I) : 0.34000 REMARK 200 R SYM FOR SHELL (I) : 0.34000 REMARK 200 FOR SHELL : 1.830 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 3NDJ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.52 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.34 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.2-1.6 M SODIUM/POTASSIUM PHOSPHATE, REMARK 280 10 MM DTMP, 5 MM S-ADENOSYL-L-HOMOCYSTEINE, PH 8.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 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+1/2,Y+1/2,-Z REMARK 290 4555 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 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 50.27100 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 57.08700 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 50.27100 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 57.08700 REMARK 290 SMTRY3 4 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: MONOMERIC 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 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 825 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 GLY A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 SER A 2 REMARK 465 HIS A 3 REMARK 465 LEU A 4 REMARK 465 ALA A 5 REMARK 465 ASP A 6 REMARK 465 VAL A 7 REMARK 465 SER A 8 REMARK 465 PRO A 9 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 O HOH A 1052 O HOH A 1053 2.03 REMARK 500 O HOH A 725 O HOH A 880 2.09 REMARK 500 O HOH A 942 O HOH A 943 2.10 REMARK 500 NH2 ARG A 34 O HOH A 873 2.10 REMARK 500 O HOH A 649 O HOH A 650 2.15 REMARK 500 O HOH A 1037 O HOH A 1038 2.17 REMARK 500 O HOH A 877 O HOH A 878 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 O HOH A 664 O HOH A 918 1556 1.96 REMARK 500 OE2 GLU A 410 O HOH A 881 1556 2.06 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 ASP A 206 CB - CG - OD1 ANGL. DEV. = 6.7 DEGREES REMARK 500 TYR A 260 CB - CG - CD2 ANGL. DEV. = -3.6 DEGREES REMARK 500 ARG A 264 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 LEU A 278 CB - CG - CD1 ANGL. DEV. = -11.5 DEGREES REMARK 500 ARG A 293 NE - CZ - NH1 ANGL. DEV. = -3.5 DEGREES REMARK 500 ARG A 314 NE - CZ - NH2 ANGL. DEV. = 3.8 DEGREES REMARK 500 ARG A 356 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 ARG A 356 NE - CZ - NH2 ANGL. DEV. = -3.4 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 HIS A 73 -165.86 -176.89 REMARK 500 THR A 100 -71.26 -128.03 REMARK 500 ASN A 115 -130.47 52.72 REMARK 500 THR A 178 -42.61 -133.90 REMARK 500 TYR A 184 42.20 -87.31 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 ZN A 501 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 13 SG REMARK 620 2 CYS A 16 SG 119.0 REMARK 620 3 CYS A 54 SG 104.9 97.4 REMARK 620 4 CYS A 57 SG 105.7 118.4 110.2 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SAH A 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TYD A 507 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4E2W RELATED DB: PDB REMARK 900 H181N MUTANT C-3'-METHYLTRANSFERASE TCAB9 REMARK 900 RELATED ID: 4E2Y RELATED DB: PDB REMARK 900 E224Q MUTANT C-3'-METHYLTRANSFERASE TCAB9 REMARK 900 RELATED ID: 4E2Z RELATED DB: PDB REMARK 900 H225N MUTANT C-3'-METHYLTRANSFERASE TCAB9 REMARK 900 RELATED ID: 4E30 RELATED DB: PDB REMARK 900 H181N/E224Q DOUBLE MUTANT C-3'-METHYLTRANSFERASE TCAB9 REMARK 900 RELATED ID: 4E31 RELATED DB: PDB REMARK 900 Y76F MUTANT C-3'-METHYLTRANSFERASE TCAB9 REMARK 900 RELATED ID: 4E32 RELATED DB: PDB REMARK 900 WILD-TYPE C-3'-METHYLTRANSFERASE TCAB9 COMPLEXED WITH SAH AND DTDP- REMARK 900 SUGAR SUBSTRATE REMARK 900 RELATED ID: 4E33 RELATED DB: PDB REMARK 900 WILD-TYPE C-3'-METHYLTRANSFERASE TCAB9 COMPLEXED WITH SAH AND REMARK 900 REDUCED DTDP-SUGAR SUBSTRATE DBREF 4E2X A 1 414 UNP B5L6K6 B5L6K6_MICCH 1 414 SEQADV 4E2X GLY A -1 UNP B5L6K6 EXPRESSION TAG SEQADV 4E2X HIS A 0 UNP B5L6K6 EXPRESSION TAG SEQADV 4E2X PHE A 222 UNP B5L6K6 TYR 222 ENGINEERED MUTATION SEQRES 1 A 416 GLY HIS MET SER HIS LEU ALA ASP VAL SER PRO PRO THR SEQRES 2 A 416 ALA CYS ARG VAL CYS GLY GLY GLY VAL GLN GLU PHE LEU SEQRES 3 A 416 ASP LEU GLY ARG GLN PRO LEU SER ASP ARG PHE ARG LYS SEQRES 4 A 416 PRO ASP GLU LEU ASP ASP GLU PHE THR TYR ARG LEU ALA SEQRES 5 A 416 VAL GLY ARG CYS ASP SER CYS GLU MET VAL GLN LEU THR SEQRES 6 A 416 GLU GLU VAL PRO ARG ASP LEU MET PHE HIS GLU VAL TYR SEQRES 7 A 416 PRO TYR HIS SER SER GLY SER SER VAL MET ARG GLU HIS SEQRES 8 A 416 PHE ALA MET LEU ALA ARG ASP PHE LEU ALA THR GLU LEU SEQRES 9 A 416 THR GLY PRO ASP PRO PHE ILE VAL GLU ILE GLY CYS ASN SEQRES 10 A 416 ASP GLY ILE MET LEU ARG THR ILE GLN GLU ALA GLY VAL SEQRES 11 A 416 ARG HIS LEU GLY PHE GLU PRO SER SER GLY VAL ALA ALA SEQRES 12 A 416 LYS ALA ARG GLU LYS GLY ILE ARG VAL ARG THR ASP PHE SEQRES 13 A 416 PHE GLU LYS ALA THR ALA ASP ASP VAL ARG ARG THR GLU SEQRES 14 A 416 GLY PRO ALA ASN VAL ILE TYR ALA ALA ASN THR LEU CYS SEQRES 15 A 416 HIS ILE PRO TYR VAL GLN SER VAL LEU GLU GLY VAL ASP SEQRES 16 A 416 ALA LEU LEU ALA PRO ASP GLY VAL PHE VAL PHE GLU ASP SEQRES 17 A 416 PRO TYR LEU GLY ASP ILE VAL ALA LYS THR SER PHE ASP SEQRES 18 A 416 GLN ILE PHE ASP GLU HIS PHE PHE LEU PHE SER ALA THR SEQRES 19 A 416 SER VAL GLN GLY MET ALA GLN ARG CYS GLY PHE GLU LEU SEQRES 20 A 416 VAL ASP VAL GLN ARG LEU PRO VAL HIS GLY GLY GLU VAL SEQRES 21 A 416 ARG TYR THR LEU ALA ARG GLN GLY SER ARG THR PRO SER SEQRES 22 A 416 ALA ALA VAL ALA GLN LEU LEU ALA ALA GLU ARG GLU GLN SEQRES 23 A 416 GLU LEU SER ASP MET ALA THR LEU ARG ALA PHE ALA GLY SEQRES 24 A 416 ASN VAL VAL LYS ILE ARG ASP GLU LEU THR ALA LEU LEU SEQRES 25 A 416 HIS ARG LEU ARG ALA GLU GLY ARG SER VAL VAL GLY TYR SEQRES 26 A 416 GLY ALA THR ALA LYS SER ALA THR VAL THR ASN PHE CYS SEQRES 27 A 416 GLY ILE GLY PRO ASP LEU VAL HIS SER VAL TYR ASP THR SEQRES 28 A 416 THR PRO ASP LYS GLN ASN ARG LEU THR PRO GLY ALA HIS SEQRES 29 A 416 ILE PRO VAL ARG PRO ALA SER ALA PHE SER ASP PRO TYR SEQRES 30 A 416 PRO ASP TYR ALA LEU LEU PHE ALA TRP ASN HIS ALA GLU SEQRES 31 A 416 GLU ILE MET ALA LYS GLU GLN GLU PHE HIS GLN ALA GLY SEQRES 32 A 416 GLY ARG TRP ILE LEU TYR VAL PRO GLU VAL HIS ILE ARG HET ZN A 501 1 HET EDO A 502 4 HET EDO A 503 4 HET EDO A 504 4 HET EDO A 505 4 HET SAH A 506 26 HET TYD A 507 25 HETNAM ZN ZINC ION HETNAM EDO 1,2-ETHANEDIOL HETNAM SAH S-ADENOSYL-L-HOMOCYSTEINE HETNAM TYD THYMIDINE-5'-DIPHOSPHATE HETSYN EDO ETHYLENE GLYCOL FORMUL 2 ZN ZN 2+ FORMUL 3 EDO 4(C2 H6 O2) FORMUL 7 SAH C14 H20 N6 O5 S FORMUL 8 TYD C10 H16 N2 O11 P2 FORMUL 9 HOH *473(H2 O) HELIX 1 1 PRO A 67 PHE A 72 1 6 HELIX 2 2 HIS A 79 GLY A 82 5 4 HELIX 3 3 SER A 83 THR A 100 1 18 HELIX 4 4 MET A 119 ALA A 126 1 8 HELIX 5 5 SER A 136 GLU A 145 1 10 HELIX 6 6 GLU A 156 GLY A 168 1 13 HELIX 7 7 THR A 178 ILE A 182 5 5 HELIX 8 8 TYR A 184 LEU A 195 1 12 HELIX 9 9 TYR A 208 THR A 216 1 9 HELIX 10 10 SER A 217 ILE A 221 5 5 HELIX 11 11 SER A 230 CYS A 241 1 12 HELIX 12 12 PRO A 252 GLY A 255 5 4 HELIX 13 13 SER A 271 GLN A 284 1 14 HELIX 14 14 ASP A 288 GLU A 316 1 29 HELIX 15 15 LYS A 328 GLY A 337 1 10 HELIX 16 16 THR A 350 GLN A 354 5 5 HELIX 17 17 SER A 369 PHE A 371 5 3 HELIX 18 18 ALA A 383 ASN A 385 5 3 HELIX 19 19 HIS A 386 GLU A 394 1 9 HELIX 20 20 GLU A 394 ALA A 400 1 7 SHEET 1 A 5 THR A 11 ALA A 12 0 SHEET 2 A 5 GLY A 19 PRO A 30 -1 O VAL A 20 N THR A 11 SHEET 3 A 5 THR A 46 CYS A 54 -1 O VAL A 51 N PHE A 23 SHEET 4 A 5 VAL A 60 LEU A 62 -1 O GLN A 61 N GLY A 52 SHEET 5 A 5 PHE A 227 LEU A 228 -1 O LEU A 228 N VAL A 60 SHEET 1 B 7 VAL A 150 ARG A 151 0 SHEET 2 B 7 ARG A 129 PHE A 133 1 N GLY A 132 O ARG A 151 SHEET 3 B 7 PHE A 108 ILE A 112 1 N GLU A 111 O PHE A 133 SHEET 4 B 7 ALA A 170 ALA A 176 1 O TYR A 174 N ILE A 112 SHEET 5 B 7 LEU A 196 PRO A 207 1 O ALA A 197 N ALA A 170 SHEET 6 B 7 GLU A 257 ARG A 264 -1 O LEU A 262 N PHE A 202 SHEET 7 B 7 PHE A 243 LEU A 251 -1 N GLN A 249 O ARG A 259 SHEET 1 C 7 ARG A 356 LEU A 357 0 SHEET 2 C 7 PRO A 364 PRO A 367 -1 O VAL A 365 N ARG A 356 SHEET 3 C 7 VAL A 346 ASP A 348 1 N VAL A 346 O ARG A 366 SHEET 4 C 7 VAL A 320 TYR A 323 1 N GLY A 322 O TYR A 347 SHEET 5 C 7 TYR A 378 LEU A 381 1 O LEU A 380 N VAL A 321 SHEET 6 C 7 ARG A 403 LEU A 406 1 O ILE A 405 N LEU A 381 SHEET 7 C 7 HIS A 412 ILE A 413 -1 O HIS A 412 N LEU A 406 LINK SG CYS A 13 ZN ZN A 501 1555 1555 2.34 LINK SG CYS A 16 ZN ZN A 501 1555 1555 2.31 LINK SG CYS A 54 ZN ZN A 501 1555 1555 2.41 LINK SG CYS A 57 ZN ZN A 501 1555 1555 2.31 CISPEP 1 ASP A 373 PRO A 374 0 1.33 CISPEP 2 VAL A 408 PRO A 409 0 -2.67 SITE 1 AC1 4 CYS A 13 CYS A 16 CYS A 54 CYS A 57 SITE 1 AC2 6 LEU A 93 ASP A 96 PHE A 97 ARG A 259 SITE 2 AC2 6 HOH A 865 HOH A 902 SITE 1 AC3 3 ARG A 164 HOH A1031 HOH A1034 SITE 1 AC4 8 SER A 319 VAL A 320 PRO A 340 ASP A 341 SITE 2 AC4 8 LEU A 342 HIS A 344 HOH A 827 HOH A 967 SITE 1 AC5 5 GLU A 22 ASP A 25 THR A 103 HOH A 606 SITE 2 AC5 5 HOH A1002 SITE 1 AC6 22 PHE A 72 TYR A 76 SER A 80 PHE A 90 SITE 2 AC6 22 ILE A 112 GLY A 113 ASN A 115 PHE A 133 SITE 3 AC6 22 GLU A 134 PRO A 135 SER A 136 PHE A 154 SITE 4 AC6 22 PHE A 155 ALA A 176 ASN A 177 THR A 178 SITE 5 AC6 22 ILE A 182 TYR A 184 HOH A 659 HOH A 701 SITE 6 AC6 22 HOH A 703 HOH A 714 SITE 1 AC7 17 TYR A 78 HIS A 254 GLY A 324 THR A 326 SITE 2 AC7 17 ALA A 327 LYS A 328 ASP A 348 THR A 349 SITE 3 AC7 17 THR A 350 LYS A 353 ASN A 385 HIS A 386 SITE 4 AC7 17 GLU A 389 ILE A 390 LYS A 393 HOH A 615 SITE 5 AC7 17 HOH A 652 CRYST1 100.542 114.174 37.632 90.00 90.00 90.00 P 21 21 2 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 0.009946 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008759 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026573 0.00000