HEADER TRANSFERASE 08-FEB-14 4OQE
TITLE CRYSTAL STRUCTURE OF THE TYLM1 N,N-DIMETHYLTRANSFERASE IN COMPLEX WITH
TITLE 2 SAH AND TDP-FUC3NME
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: DTDP-3-AMINO-3,6-DIDEOXY-ALPHA-D-GLUCOPYRANOSE N,N-
COMPND 3 DIMETHYLTRANSFERASE;
COMPND 4 CHAIN: A, B;
COMPND 5 SYNONYM: TYLOSIN BIOSYNTHESIS PROTEIN M1;
COMPND 6 EC: 2.1.1.235;
COMPND 7 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES FRADIAE;
SOURCE 3 ORGANISM_TAXID: 1906;
SOURCE 4 GENE: TYLM1, TYLMI;
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008;
SOURCE 7 EXPRESSION_SYSTEM_STRAIN: ROSETTA2(DE3);
SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET31
KEYWDS SAM METHYLTRANSFERASE, N-METHYLTRANSFERASE, S-ADENOSYLMETHIONINE,
KEYWDS 2 TRANSFERASE
EXPDTA X-RAY DIFFRACTION
AUTHOR J.B.THODEN,H.M.HOLDEN
REVDAT 3 20-SEP-23 4OQE 1 REMARK SEQADV
REVDAT 2 19-MAR-14 4OQE 1 JRNL
REVDAT 1 26-FEB-14 4OQE 0
JRNL AUTH J.B.THODEN,H.M.HOLDEN
JRNL TITL PRODUCTION OF A NOVEL N-MONOMETHYLATED DIDEOXYSUGAR.
JRNL REF BIOCHEMISTRY V. 53 1105 2014
JRNL REFN ISSN 0006-2960
JRNL PMID 24512254
JRNL DOI 10.1021/BI500098A
REMARK 2
REMARK 2 RESOLUTION. 2.20 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.7.0029
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) : 2.20
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.05
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 86.5
REMARK 3 NUMBER OF REFLECTIONS : 24812
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) : 0.219
REMARK 3 R VALUE (WORKING SET) : 0.215
REMARK 3 FREE R VALUE : 0.277
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 1251
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) : 2.20
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26
REMARK 3 REFLECTION IN BIN (WORKING SET) : 1432
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 71.39
REMARK 3 BIN R VALUE (WORKING SET) : 0.3430
REMARK 3 BIN FREE R VALUE SET COUNT : 63
REMARK 3 BIN FREE R VALUE : 0.3660
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 3651
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 124
REMARK 3 SOLVENT ATOMS : 212
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.97
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 5.44000
REMARK 3 B22 (A**2) : -4.11000
REMARK 3 B33 (A**2) : -1.81000
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : 4.22000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): 0.368
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.268
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.235
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.824
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.942
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.901
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3880 ; 0.013 ; 0.019
REMARK 3 BOND LENGTHS OTHERS (A): 3549 ; 0.001 ; 0.020
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5277 ; 1.702 ; 1.977
REMARK 3 BOND ANGLES OTHERS (DEGREES): 8133 ; 0.840 ; 3.000
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 478 ; 7.520 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 179 ;32.314 ;21.955
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 561 ;17.354 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 39 ;20.863 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 574 ; 0.088 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4388 ; 0.006 ; 0.021
REMARK 3 GENERAL PLANES OTHERS (A): 941 ; 0.001 ; 0.020
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: NULL
REMARK 4
REMARK 4 4OQE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-FEB-14.
REMARK 100 THE DEPOSITION ID IS D_1000084819.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 10-MAY-13
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 9
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) : 1.5418
REMARK 200 MONOCHROMATOR : NI 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 : 24812
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 (%) : 86.5
REMARK 200 DATA REDUNDANCY : 3.200
REMARK 200 R MERGE (I) : 0.05700
REMARK 200 R SYM (I) : 0.05700
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.0000
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) : 2.30
REMARK 200 COMPLETENESS FOR SHELL (%) : 71.8
REMARK 200 DATA REDUNDANCY IN SHELL : 1.20
REMARK 200 R MERGE FOR SHELL (I) : 0.14000
REMARK 200 R SYM FOR SHELL (I) : 0.14000
REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.700
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 4OQD
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 50.97
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.51
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 15-20% PEG3400, 200 MM SODIUM
REMARK 280 CHLORIDE, 5 MM S-ADENOSYLHOMOCYSTEINE, 10 MM TDP-3-N-METHYLAMINO-
REMARK 280 3,6-DIDEOXYGALACTOSE, PH 9, BATCH, 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 46.46900
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: 1580 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 19000 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -17.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B
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 PRO A 10
REMARK 465 LYS A 50
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 B 1
REMARK 465 ALA B 2
REMARK 465 HIS B 3
REMARK 465 SER B 4
REMARK 465 SER B 5
REMARK 465 ALA B 6
REMARK 465 THR B 7
REMARK 465 ALA B 8
REMARK 465 GLY B 9
REMARK 465 ALA B 250
REMARK 465 LYS B 251
REMARK 465 GLY B 252
REMARK 465 GLU B 253
REMARK 465 THR B 254
REMARK 465 ARG B 255
REMARK 465 LEU B 256
REMARK 465 GLU B 257
REMARK 465 HIS B 258
REMARK 465 HIS B 259
REMARK 465 HIS B 260
REMARK 465 HIS B 261
REMARK 465 HIS B 262
REMARK 465 HIS B 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 NH1 ARG B 45 O SER B 71 2.07
REMARK 500 O PHE A 72 O HOH A 415 2.10
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 136 NE - CZ - NH2 ANGL. DEV. = 3.1 DEGREES
REMARK 500 ASP B 131 CB - CG - OD2 ANGL. DEV. = -5.4 DEGREES
REMARK 500 PRO B 143 C - N - CA ANGL. DEV. = 9.5 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 ALA A 12 34.38 -153.19
REMARK 500 ASP A 13 21.06 -145.35
REMARK 500 SER A 48 72.81 -118.24
REMARK 500 ALA A 58 43.19 79.86
REMARK 500 ASP A 104 87.29 -156.92
REMARK 500 TRP A 153 141.15 -38.55
REMARK 500 GLU A 186 48.89 -92.31
REMARK 500 LEU A 243 120.54 -173.68
REMARK 500 ALA B 52 6.43 -161.71
REMARK 500 ALA B 58 73.49 35.29
REMARK 500 PHE B 118 35.46 71.51
REMARK 500 SER B 239 11.08 -145.62
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS
REMARK 500
REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH
REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED
REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND
REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES.
REMARK 500 MODEL OMEGA
REMARK 500 GLY B 100 ASP B 101 -147.45
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 300
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MMF A 301
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SAH B 300
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MMF B 301
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 4OQD RELATED DB: PDB
REMARK 900 TYLM1 N,N-DIMETHYLTRANSFERASE IN COMPLEX WITH SAH AND TDP-QUI3NME2
DBREF 4OQE A 1 255 UNP P95748 TYLM1_STRFR 1 255
DBREF 4OQE B 1 255 UNP P95748 TYLM1_STRFR 1 255
SEQADV 4OQE LEU A 256 UNP P95748 EXPRESSION TAG
SEQADV 4OQE GLU A 257 UNP P95748 EXPRESSION TAG
SEQADV 4OQE HIS A 258 UNP P95748 EXPRESSION TAG
SEQADV 4OQE HIS A 259 UNP P95748 EXPRESSION TAG
SEQADV 4OQE HIS A 260 UNP P95748 EXPRESSION TAG
SEQADV 4OQE HIS A 261 UNP P95748 EXPRESSION TAG
SEQADV 4OQE HIS A 262 UNP P95748 EXPRESSION TAG
SEQADV 4OQE HIS A 263 UNP P95748 EXPRESSION TAG
SEQADV 4OQE LEU B 256 UNP P95748 EXPRESSION TAG
SEQADV 4OQE GLU B 257 UNP P95748 EXPRESSION TAG
SEQADV 4OQE HIS B 258 UNP P95748 EXPRESSION TAG
SEQADV 4OQE HIS B 259 UNP P95748 EXPRESSION TAG
SEQADV 4OQE HIS B 260 UNP P95748 EXPRESSION TAG
SEQADV 4OQE HIS B 261 UNP P95748 EXPRESSION TAG
SEQADV 4OQE HIS B 262 UNP P95748 EXPRESSION TAG
SEQADV 4OQE HIS B 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 HIS 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 B 263 MET ALA HIS SER SER ALA THR ALA GLY PRO GLN ALA ASP
SEQRES 2 B 263 TYR SER GLY GLU ILE ALA GLU LEU TYR ASP LEU VAL HIS
SEQRES 3 B 263 GLN GLY LYS GLY LYS ASP TYR HIS ARG GLU ALA ALA ASP
SEQRES 4 B 263 LEU ALA ALA LEU VAL ARG ARG HIS SER PRO LYS ALA ALA
SEQRES 5 B 263 SER LEU LEU ASP VAL ALA CYS GLY THR GLY MET HIS LEU
SEQRES 6 B 263 ARG HIS LEU ALA ASP SER PHE GLY THR VAL GLU GLY LEU
SEQRES 7 B 263 GLU LEU SER ALA ASP MET LEU ALA ILE ALA ARG ARG ARG
SEQRES 8 B 263 ASN PRO ASP ALA VAL LEU HIS HIS GLY ASP MET ARG ASP
SEQRES 9 B 263 PHE SER LEU GLY ARG ARG PHE SER ALA VAL THR CYS MET
SEQRES 10 B 263 PHE SER SER ILE GLY HIS LEU ALA GLY GLN ALA GLU LEU
SEQRES 11 B 263 ASP ALA ALA LEU GLU ARG PHE ALA ALA HIS VAL LEU PRO
SEQRES 12 B 263 ASP GLY VAL VAL VAL VAL GLU PRO TRP TRP PHE PRO GLU
SEQRES 13 B 263 ASN PHE THR PRO GLY TYR VAL ALA ALA GLY THR VAL GLU
SEQRES 14 B 263 ALA GLY GLY THR THR VAL THR ARG VAL SER HIS SER SER
SEQRES 15 B 263 ARG GLU GLY GLU ALA THR ARG ILE GLU VAL HIS TYR LEU
SEQRES 16 B 263 VAL ALA GLY PRO ASP ARG GLY ILE THR HIS HIS GLU GLU
SEQRES 17 B 263 SER HIS ARG ILE THR LEU PHE THR ARG GLU GLN TYR GLU
SEQRES 18 B 263 ARG ALA PHE THR ALA ALA GLY LEU SER VAL GLU PHE MET
SEQRES 19 B 263 PRO GLY GLY PRO SER GLY ARG GLY LEU PHE THR GLY LEU
SEQRES 20 B 263 PRO GLY ALA LYS GLY GLU THR ARG LEU GLU HIS HIS HIS
SEQRES 21 B 263 HIS HIS HIS
HET SAH A 300 26
HET MMF A 301 36
HET SAH B 300 26
HET MMF B 301 36
HETNAM SAH S-ADENOSYL-L-HOMOCYSTEINE
HETNAM MMF DTDP-3-N-METHYLAMINO-3,6-DIDEOXYGALACTOSE
FORMUL 3 SAH 2(C14 H20 N6 O5 S)
FORMUL 4 MMF 2(C17 H29 N3 O14 P2)
FORMUL 7 HOH *212(H2 O)
HELIX 1 1 GLY A 16 LYS A 29 1 14
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 ASP A 70 PHE A 72 5 3
HELIX 5 5 SER A 81 ASN A 92 1 12
HELIX 6 6 SER A 119 LEU A 124 5 6
HELIX 7 7 GLY A 126 HIS A 140 1 15
HELIX 8 8 THR A 216 ALA A 227 1 12
HELIX 9 9 SER B 15 LYS B 29 1 15
HELIX 10 10 ASP B 32 SER B 48 1 17
HELIX 11 11 GLY B 62 ASP B 70 1 9
HELIX 12 12 SER B 81 ASN B 92 1 12
HELIX 13 13 SER B 119 LEU B 124 5 6
HELIX 14 14 GLY B 126 HIS B 140 1 15
HELIX 15 15 PHE B 154 PHE B 158 5 5
HELIX 16 16 THR B 216 ALA B 227 1 12
SHEET 1 A 7 LEU A 97 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 LEU A 54 O THR A 74
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 VAL A 148 N CYS A 116
SHEET 6 A 7 LEU A 243 PRO A 248 -1 O GLY A 246 N VAL A 147
SHEET 7 A 7 LEU A 229 MET A 234 -1 N SER A 230 O LEU A 247
SHEET 1 B 4 TYR A 162 ALA A 170 0
SHEET 2 B 4 THR A 173 ARG A 183 -1 O VAL A 175 N VAL A 168
SHEET 3 B 4 ALA A 187 GLY A 198 -1 O HIS A 193 N VAL A 178
SHEET 4 B 4 GLY A 202 THR A 213 -1 O GLU A 208 N VAL A 192
SHEET 1 C 7 VAL B 96 HIS B 99 0
SHEET 2 C 7 THR B 74 GLU B 79 1 N GLY B 77 O HIS B 98
SHEET 3 C 7 SER B 53 VAL B 57 1 N LEU B 54 O GLU B 76
SHEET 4 C 7 PHE B 111 CYS B 116 1 O THR B 115 N VAL B 57
SHEET 5 C 7 VAL B 141 VAL B 149 1 O VAL B 148 N VAL B 114
SHEET 6 C 7 LEU B 243 PRO B 248 -1 O GLY B 246 N VAL B 147
SHEET 7 C 7 LEU B 229 MET B 234 -1 N MET B 234 O LEU B 243
SHEET 1 D 4 VAL B 163 ALA B 170 0
SHEET 2 D 4 THR B 173 GLU B 184 -1 O VAL B 175 N VAL B 168
SHEET 3 D 4 ALA B 187 GLY B 198 -1 O GLU B 191 N HIS B 180
SHEET 4 D 4 GLY B 202 THR B 213 -1 O THR B 204 N VAL B 196
SITE 1 AC1 18 TYR A 14 TYR A 22 TYR A 33 ALA A 58
SITE 2 AC1 18 GLY A 60 HIS A 64 GLU A 79 LEU A 80
SITE 3 AC1 18 SER A 81 ASP A 101 MET A 102 MET A 117
SITE 4 AC1 18 PHE A 118 SER A 120 MMF A 301 HOH A 409
SITE 5 AC1 18 HOH A 411 HOH A 428
SITE 1 AC2 19 TYR A 14 LYS A 29 PHE A 118 TRP A 152
SITE 2 AC2 19 TRP A 153 ASN A 157 PHE A 158 THR A 159
SITE 3 AC2 19 TYR A 162 ALA A 164 ARG A 177 SER A 179
SITE 4 AC2 19 SER A 181 ILE A 190 HIS A 210 ILE A 212
SITE 5 AC2 19 ARG A 241 SAH A 300 HOH A 479
SITE 1 AC3 19 TYR B 14 TYR B 22 TYR B 33 ALA B 58
SITE 2 AC3 19 CYS B 59 GLY B 60 HIS B 64 GLU B 79
SITE 3 AC3 19 LEU B 80 SER B 81 MET B 84 ASP B 101
SITE 4 AC3 19 MET B 102 MET B 117 PHE B 118 SER B 120
SITE 5 AC3 19 MMF B 301 HOH B 427 HOH B 465
SITE 1 AC4 20 TYR B 14 LYS B 29 PHE B 118 HIS B 123
SITE 2 AC4 20 TRP B 152 TRP B 153 ASN B 157 PHE B 158
SITE 3 AC4 20 THR B 159 TYR B 162 ALA B 164 ARG B 177
SITE 4 AC4 20 SER B 179 SER B 181 HIS B 210 ARG B 241
SITE 5 AC4 20 SAH B 300 HOH B 444 HOH B 455 HOH B 459
CRYST1 39.885 92.938 77.879 90.00 97.29 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 0.025072 0.000000 0.003207 0.00000
SCALE2 0.000000 0.010760 0.000000 0.00000
SCALE3 0.000000 0.000000 0.012945 0.00000
(ATOM LINES ARE NOT SHOWN.)
END