HEADER TRANSFERASE 06-MAR-25 9M5W TITLE CRYSTAL STRUCTURE OF 5'-DEOXY-5'-METHYLTHIOADENOSINE PHOSPHORYLASE TITLE 2 FROM AEROPYRUM PERNIX COMPLEX WITH 5'-DEOXY-5'-METHYLTHIOADENOSINE TITLE 3 343K 1.58 ANGSTROM COMPND MOL_ID: 1; COMPND 2 MOLECULE: S-METHYL-5'-THIOADENOSINE PHOSPHORYLASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: THE FIRST M AND SECOND F ARE MISSING IN THE UPLOADED COMPND 6 STRUCTURE BECAUSE THE ELECTRON DENSITY COULD NOT BE OBSERVED. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AEROPYRUM PERNIX K1; SOURCE 3 ORGANISM_TAXID: 272557; SOURCE 4 GENE: MTNP; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS MTAP, COMPLEX, PHOSPHORYLASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.IIZUKA,M.KIKUCHI,T.YAMAUCHI,M.TSUNODA REVDAT 1 11-MAR-26 9M5W 0 JRNL AUTH Y.IIZUKA,M.KIKUCHI,T.YAMAUCHI,M.TSUNODA JRNL TITL CRYSTAL STRUCTURE OF 5'-DEOXY-5'-METHYLTHIOADENOSINE JRNL TITL 2 PHOSPHORYLASE FROM AEROPYRUM PERNIX COMPLEX WITH JRNL TITL 3 5'-DEOXY-5'-METHYLTHIOADENOSINE 343K 1.58 ANGSTROM JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.58 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0430 (REFMACAT 0.4.82) REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.58 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.39 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 38816 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.141 REMARK 3 FREE R VALUE : 0.163 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.008 REMARK 3 FREE R VALUE TEST SET COUNT : 1944 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) : 1.58 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.62 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2681 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2490 REMARK 3 BIN FREE R VALUE SET COUNT : 125 REMARK 3 BIN FREE R VALUE : 0.2710 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2142 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 32 REMARK 3 SOLVENT ATOMS : 48 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.38 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.20500 REMARK 3 B22 (A**2) : 0.20500 REMARK 3 B33 (A**2) : -0.66600 REMARK 3 B12 (A**2) : 0.10300 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): 0.064 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.064 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.045 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.321 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.980 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.974 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2245 ; 0.012 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 2122 ; 0.001 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3061 ; 1.981 ; 1.820 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4870 ; 0.651 ; 1.758 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 278 ; 6.999 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 26 ; 9.857 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 356 ;13.456 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 339 ; 0.101 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2696 ; 0.012 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 533 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 343 ; 0.218 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 80 ; 0.201 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1125 ; 0.181 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 46 ; 0.121 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): 2 ; 0.054 ; 0.200 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): 1097 ; 2.602 ; 2.242 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1097 ; 2.602 ; 2.241 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1371 ; 3.785 ; 4.013 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1372 ; 3.784 ; 4.013 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1148 ; 5.210 ; 2.979 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1149 ; 5.208 ; 2.981 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1687 ; 7.996 ; 5.118 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1688 ; 7.994 ; 5.118 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 BULK SOLVENT 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: HYDROGENS HAVE BEEN ADDED IN THEIR REMARK 3 RIDING POSITIONS REMARK 4 REMARK 4 9M5W COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-MAR-25. REMARK 100 THE DEPOSITION ID IS D_1300056967. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-NOV-24 REMARK 200 TEMPERATURE (KELVIN) : 343 REMARK 200 PH : 5.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-17A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 38817 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.580 REMARK 200 RESOLUTION RANGE LOW (A) : 44.390 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 10.00 REMARK 200 R MERGE (I) : 0.05800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 25.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 8.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 44.39 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.5 REMARK 200 DATA REDUNDANCY IN SHELL : 8.20 REMARK 200 R MERGE FOR SHELL (I) : 0.01800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 93.50 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 1WTA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.03 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: THE MIXTURE OF PROTEIN SOLUTION AND REMARK 280 AGAROSE WAS WAS FILLED INTO A GLASS CAPILLARY, AND THE CAPILLARY REMARK 280 WAS IMMERSED IN THE RESERVOIR SOLUTION FOR CRYSTALLIZATION. THE REMARK 280 COMPOSITION OF THE RESERVOIR SOLUTION WAS AS FOLLOWS. 15%(V/V) REMARK 280 PEG#200, 0.1M PHOSPHATE CITRATE PH 5.4, 5MM MTA, COUNTER- REMARK 280 DIFFUSION, TEMPERATURE 293.2K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-Z REMARK 290 7555 X+2/3,Y+1/3,Z+1/3 REMARK 290 8555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 9555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 10555 Y+2/3,X+1/3,-Z+1/3 REMARK 290 11555 X-Y+2/3,-Y+1/3,-Z+1/3 REMARK 290 12555 -X+2/3,-X+Y+1/3,-Z+1/3 REMARK 290 13555 X+1/3,Y+2/3,Z+2/3 REMARK 290 14555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 15555 -X+Y+1/3,-X+2/3,Z+2/3 REMARK 290 16555 Y+1/3,X+2/3,-Z+2/3 REMARK 290 17555 X-Y+1/3,-Y+2/3,-Z+2/3 REMARK 290 18555 -X+1/3,-X+Y+2/3,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 39.47000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 22.78802 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 77.82700 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 39.47000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 22.78802 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 77.82700 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 39.47000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 22.78802 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 77.82700 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 39.47000 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 22.78802 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 77.82700 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 39.47000 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 22.78802 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 77.82700 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 39.47000 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 22.78802 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 77.82700 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 45.57603 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 155.65400 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 45.57603 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 155.65400 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 45.57603 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 155.65400 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 45.57603 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 155.65400 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 45.57603 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 155.65400 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 45.57603 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 155.65400 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 11590 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27400 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -60.0 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 -0.500000 -0.866025 0.000000 -39.47000 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 -68.36405 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 39.47000 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 -68.36405 REMARK 350 BIOMT3 3 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 PHE A 2 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 62 NE - CZ - NH2 ANGL. DEV. = 4.4 DEGREES REMARK 500 MET A 216 CG - SD - CE ANGL. DEV. = -14.1 DEGREES REMARK 500 MET A 237 CG - SD - CE ANGL. DEV. = 11.0 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 ARG A 123 -42.14 76.28 REMARK 500 ASP A 221 -132.33 59.75 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 77 0.09 SIDE CHAIN REMARK 500 ARG A 178 0.08 SIDE CHAIN REMARK 500 ARG A 182 0.14 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 9M5W A 1 275 UNP Q9YAQ8 MTAP_AERPE 1 275 SEQRES 1 A 275 MET PHE GLU ILE THR ARG PRO PRO GLY VAL ARG ALA HIS SEQRES 2 A 275 VAL GLY VAL ILE GLY GLY SER GLY LEU TYR ASP PRO GLY SEQRES 3 A 275 ILE VAL GLU ASN PRO VAL GLU VAL LYS VAL SER THR PRO SEQRES 4 A 275 TYR GLY ASN PRO SER ASP PHE ILE VAL VAL GLY ASP VAL SEQRES 5 A 275 ALA GLY VAL LYS VAL ALA PHE LEU PRO ARG HIS GLY ARG SEQRES 6 A 275 GLY HIS ARG ILE PRO PRO HIS ALA ILE ASN TYR ARG ALA SEQRES 7 A 275 ASN ILE TRP ALA LEU LYS ALA LEU GLY VAL LYS TRP VAL SEQRES 8 A 275 ILE SER VAL SER ALA VAL GLY SER LEU ARG GLU ASP TYR SEQRES 9 A 275 ARG PRO GLY ASP PHE VAL VAL PRO ASP GLN PHE ILE ASP SEQRES 10 A 275 MET THR LYS ASN ARG ARG HIS TYR THR PHE TYR ASP GLY SEQRES 11 A 275 PRO VAL THR VAL HIS VAL SER MET ALA ASP PRO PHE CYS SEQRES 12 A 275 GLU ASP LEU ARG GLN ARG LEU ILE ASP SER GLY ARG ARG SEQRES 13 A 275 LEU GLY TYR THR VAL HIS GLU ARG GLY THR TYR VAL CYS SEQRES 14 A 275 ILE GLU GLY PRO ARG PHE SER THR ARG ALA GLU SER ARG SEQRES 15 A 275 VAL TRP LYS ASP VAL PHE LYS ALA ASP ILE ILE GLY MET SEQRES 16 A 275 THR LEU VAL PRO GLU ILE ASN LEU ALA CYS GLU ALA GLN SEQRES 17 A 275 LEU CYS TYR ALA THR LEU ALA MET VAL THR ASP TYR ASP SEQRES 18 A 275 VAL TRP ALA ASP ARG PRO VAL THR ALA GLU GLU VAL GLU SEQRES 19 A 275 ARG VAL MET ILE SER ASN VAL GLU ARG ALA ARG ARG MET SEQRES 20 A 275 LEU TYR ASP VAL ILE PRO LYS LEU ALA GLY GLU PRO GLU SEQRES 21 A 275 LEU GLU ARG CYS SER CYS CYS ARG ALA LEU ASP THR ALA SEQRES 22 A 275 ALA ILE HET PO4 A 400 5 HET MTA A 401 20 HET PEG A 402 7 HETNAM PO4 PHOSPHATE ION HETNAM MTA 5'-DEOXY-5'-METHYLTHIOADENOSINE HETNAM PEG DI(HYDROXYETHYL)ETHER FORMUL 2 PO4 O4 P 3- FORMUL 3 MTA C11 H15 N5 O3 S FORMUL 4 PEG C4 H10 O3 FORMUL 5 HOH *48(H2 O) HELIX 1 AA1 GLY A 64 ARG A 68 5 5 HELIX 2 AA2 PRO A 70 ILE A 74 5 5 HELIX 3 AA3 ASN A 75 LEU A 86 1 12 HELIX 4 AA4 CYS A 143 GLY A 158 1 16 HELIX 5 AA5 THR A 177 VAL A 187 1 11 HELIX 6 AA6 THR A 196 ALA A 207 1 12 HELIX 7 AA7 THR A 229 SER A 239 1 11 HELIX 8 AA8 ASN A 240 ILE A 252 1 13 HELIX 9 AA9 PRO A 253 ALA A 256 5 4 HELIX 10 AB1 GLU A 260 CYS A 264 5 5 HELIX 11 AB2 ALA A 269 ALA A 274 1 6 SHEET 1 AA1 9 THR A 5 ARG A 6 0 SHEET 2 AA1 9 GLU A 29 VAL A 36 -1 O LYS A 35 N ARG A 6 SHEET 3 AA1 9 ILE A 47 VAL A 52 -1 O ILE A 47 N VAL A 34 SHEET 4 AA1 9 VAL A 55 PRO A 61 -1 O VAL A 57 N GLY A 50 SHEET 5 AA1 9 VAL A 14 GLY A 18 1 N VAL A 14 O ALA A 58 SHEET 6 AA1 9 TRP A 90 SER A 99 1 O TRP A 90 N GLY A 15 SHEET 7 AA1 9 ILE A 192 GLY A 194 -1 O ILE A 193 N GLY A 98 SHEET 8 AA1 9 THR A 166 ILE A 170 1 N VAL A 168 O ILE A 192 SHEET 9 AA1 9 GLN A 114 MET A 118 1 N ILE A 116 O CYS A 169 SHEET 1 AA2 9 THR A 5 ARG A 6 0 SHEET 2 AA2 9 GLU A 29 VAL A 36 -1 O LYS A 35 N ARG A 6 SHEET 3 AA2 9 ILE A 47 VAL A 52 -1 O ILE A 47 N VAL A 34 SHEET 4 AA2 9 VAL A 55 PRO A 61 -1 O VAL A 57 N GLY A 50 SHEET 5 AA2 9 VAL A 14 GLY A 18 1 N VAL A 14 O ALA A 58 SHEET 6 AA2 9 TRP A 90 SER A 99 1 O TRP A 90 N GLY A 15 SHEET 7 AA2 9 CYS A 210 ASP A 219 1 O LEU A 214 N SER A 93 SHEET 8 AA2 9 PHE A 109 VAL A 110 -1 N VAL A 110 O ALA A 215 SHEET 9 AA2 9 VAL A 161 HIS A 162 1 O HIS A 162 N PHE A 109 SSBOND 1 CYS A 143 CYS A 210 1555 1555 2.03 SSBOND 2 CYS A 205 CYS A 266 1555 1555 2.03 SSBOND 3 CYS A 264 CYS A 267 1555 1555 2.02 CISPEP 1 ARG A 6 PRO A 7 0 -5.86 CISPEP 2 GLY A 130 PRO A 131 0 10.61 CISPEP 3 GLY A 172 PRO A 173 0 0.09 CISPEP 4 VAL A 198 PRO A 199 0 7.64 CRYST1 78.940 78.940 233.481 90.00 90.00 120.00 H 3 2 18 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 0.012668 0.007314 0.000000 0.00000 SCALE2 0.000000 0.014628 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004283 0.00000 CONECT 1106 1643 CONECT 1606 2092 CONECT 1643 1106 CONECT 2080 2098 CONECT 2092 1606 CONECT 2098 2080 CONECT 2158 2159 2160 2161 2162 CONECT 2159 2158 CONECT 2160 2158 CONECT 2161 2158 CONECT 2162 2158 CONECT 2163 2164 CONECT 2164 2163 2165 CONECT 2165 2164 2166 CONECT 2166 2165 2167 2170 CONECT 2167 2166 2172 CONECT 2168 2169 2170 2172 CONECT 2169 2168 CONECT 2170 2166 2168 2171 CONECT 2171 2170 CONECT 2172 2167 2168 2173 CONECT 2173 2172 2174 2182 CONECT 2174 2173 2175 CONECT 2175 2174 2176 CONECT 2176 2175 2177 2182 CONECT 2177 2176 2178 2179 CONECT 2178 2177 CONECT 2179 2177 2180 CONECT 2180 2179 2181 CONECT 2181 2180 2182 CONECT 2182 2173 2176 2181 CONECT 2183 2184 2185 CONECT 2184 2183 CONECT 2185 2183 2186 CONECT 2186 2185 2187 CONECT 2187 2186 2188 CONECT 2188 2187 2189 CONECT 2189 2188 MASTER 371 0 3 11 18 0 0 6 2222 1 38 22 END