HEADER TRANSFERASE 09-JUL-25 9VSS TITLE HIGH TEMPERATURE (363K) CRYSTAL STRUCTURE OF 5'-DEOXY-5'- TITLE 2 METHYLTHIOADENOSINE PHOSPHORYLASE FROM AEROPYRUM PERNIX AFTER 30 TITLE 3 MINUTES REACTION WITH SUBSTRATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: S-METHYL-5'-THIOADENOSINE PHOSPHORYLASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: 5'-METHYLTHIOADENOSINE PHOSPHORYLASE,MTA PHOSPHORYLASE,MTAP; COMPND 5 EC: 2.4.2.28; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: THE FIRST M AND SECOND F ARE MISSING IN THE UPLOADED COMPND 8 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, APE_1885; 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 22-JUL-26 9VSS 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 363K JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.79 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0430 (REFMACAT 0.4.105) 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) : 1.79 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.35 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 26842 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) : 0.149 REMARK 3 FREE R VALUE : 0.176 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.182 REMARK 3 FREE R VALUE TEST SET COUNT : 1391 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) : 1.79 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.84 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1849 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2130 REMARK 3 BIN FREE R VALUE SET COUNT : 122 REMARK 3 BIN FREE R VALUE : 0.2530 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2140 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 32 REMARK 3 SOLVENT ATOMS : 40 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.44 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.02100 REMARK 3 B22 (A**2) : 0.02100 REMARK 3 B33 (A**2) : -0.06800 REMARK 3 B12 (A**2) : 0.01000 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): 0.103 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.097 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.067 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.168 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.967 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.965 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2334 ; 0.010 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 2198 ; 0.001 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3189 ; 1.852 ; 1.815 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5050 ; 0.620 ; 1.752 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 295 ; 6.939 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 25 ; 8.531 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 366 ;14.104 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 352 ; 0.089 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2806 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 551 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 358 ; 0.210 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 108 ; 0.204 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1100 ; 0.180 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 60 ; 0.134 ; 0.200 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): 1144 ; 2.789 ; 2.366 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1144 ; 2.788 ; 2.366 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1433 ; 4.184 ; 4.237 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1434 ; 4.183 ; 4.237 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1190 ; 4.885 ; 3.073 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1190 ; 4.884 ; 3.073 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1750 ; 7.712 ; 5.307 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1751 ; 7.710 ; 5.305 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 9VSS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-JUL-25. REMARK 100 THE DEPOSITION ID IS D_1300061349. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-JUL-25 REMARK 200 TEMPERATURE (KELVIN) : 363 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 : 26844 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.790 REMARK 200 RESOLUTION RANGE LOW (A) : 44.350 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 9.600 REMARK 200 R MERGE (I) : 0.22400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 8.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 44.35 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3 REMARK 200 DATA REDUNDANCY IN SHELL : 6.70 REMARK 200 R MERGE FOR SHELL (I) : 0.12700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 25.10 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 (%): 45.98 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, METHYLCELLUROSE WAS FILLED INTO A GLASS CAPILLARY, AND REMARK 280 THE CAPILLARY WAS IMMERSED IN THE RESERVOIR SOLUTION FOR REMARK 280 CRYSTALLIZATION. THE COMPOSITION OF THE RESERVOIR SOLUTION WAS REMARK 280 AS FOLLOWS. 15%(V/V)PEG#200, 0.1M PHOSPHATE CITRATE PH 5.4, 5MM REMARK 280 MTA, COUNTER-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 39.49850 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 22.80447 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 77.65633 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 39.49850 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 22.80447 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 77.65633 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 39.49850 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 22.80447 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 77.65633 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 39.49850 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 22.80447 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 77.65633 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 39.49850 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 22.80447 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 77.65633 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 39.49850 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 22.80447 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 77.65633 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 45.60894 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 155.31267 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 45.60894 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 155.31267 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 45.60894 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 155.31267 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 45.60894 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 155.31267 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 45.60894 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 155.31267 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 45.60894 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 155.31267 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: 10240 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29060 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -79.0 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 0.00000 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG A 68 NH1 NH2 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 105 CD - NE - CZ ANGL. DEV. = 8.5 DEGREES REMARK 500 ARG A 122 NE - CZ - NH2 ANGL. DEV. = -3.5 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 PRO A 25 -96.02 -82.09 REMARK 500 VAL A 28 114.97 -164.25 REMARK 500 LYS A 120 -16.56 -145.08 REMARK 500 ARG A 123 -50.09 81.00 REMARK 500 ASP A 221 -129.65 58.41 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 REMARK 500 REMARK: NULL DBREF 9VSS A 3 275 UNP Q9YAQ8 MTAP_AERPE 3 275 SEQRES 1 A 273 GLU ILE THR ARG PRO PRO GLY VAL ARG ALA HIS VAL GLY SEQRES 2 A 273 VAL ILE GLY GLY SER GLY LEU TYR ASP PRO GLY ILE VAL SEQRES 3 A 273 GLU ASN PRO VAL GLU VAL LYS VAL SER THR PRO TYR GLY SEQRES 4 A 273 ASN PRO SER ASP PHE ILE VAL VAL GLY ASP VAL ALA GLY SEQRES 5 A 273 VAL LYS VAL ALA PHE LEU PRO ARG HIS GLY ARG GLY HIS SEQRES 6 A 273 ARG ILE PRO PRO HIS ALA ILE ASN TYR ARG ALA ASN ILE SEQRES 7 A 273 TRP ALA LEU LYS ALA LEU GLY VAL LYS TRP VAL ILE SER SEQRES 8 A 273 VAL SER ALA VAL GLY SER LEU ARG GLU ASP TYR ARG PRO SEQRES 9 A 273 GLY ASP PHE VAL VAL PRO ASP GLN PHE ILE ASP MET THR SEQRES 10 A 273 LYS ASN ARG ARG HIS TYR THR PHE TYR ASP GLY PRO VAL SEQRES 11 A 273 THR VAL HIS VAL SER MET ALA ASP PRO PHE CYS GLU ASP SEQRES 12 A 273 LEU ARG GLN ARG LEU ILE ASP SER GLY ARG ARG LEU GLY SEQRES 13 A 273 TYR THR VAL HIS GLU ARG GLY THR TYR VAL CYS ILE GLU SEQRES 14 A 273 GLY PRO ARG PHE SER THR ARG ALA GLU SER ARG VAL TRP SEQRES 15 A 273 LYS ASP VAL PHE LYS ALA ASP ILE ILE GLY MET THR LEU SEQRES 16 A 273 VAL PRO GLU ILE ASN LEU ALA CYS GLU ALA GLN LEU CYS SEQRES 17 A 273 TYR ALA THR LEU ALA MET VAL THR ASP TYR ASP VAL TRP SEQRES 18 A 273 ALA ASP ARG PRO VAL THR ALA GLU GLU VAL GLU ARG VAL SEQRES 19 A 273 MET ILE SER ASN VAL GLU ARG ALA ARG ARG MET LEU TYR SEQRES 20 A 273 ASP VAL ILE PRO LYS LEU ALA GLY GLU PRO GLU LEU GLU SEQRES 21 A 273 ARG CYS SER CYS CYS ARG ALA LEU ASP THR ALA ALA ILE HET PO4 A 301 10 HET PEG A 302 7 HET MTA A 303 20 HETNAM PO4 PHOSPHATE ION HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM MTA 5'-DEOXY-5'-METHYLTHIOADENOSINE FORMUL 2 PO4 O4 P 3- FORMUL 3 PEG C4 H10 O3 FORMUL 4 MTA C11 H15 N5 O3 S FORMUL 5 HOH *40(H2 O) HELIX 1 AA1 GLY A 19 TYR A 23 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 LEU A 157 1 15 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 ASN A 240 1 12 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 2.02 SSBOND 2 CYS A 205 CYS A 266 1555 1555 2.05 SSBOND 3 CYS A 264 CYS A 267 1555 1555 2.00 CISPEP 1 ARG A 6 PRO A 7 0 -3.54 CISPEP 2 GLY A 130 PRO A 131 0 8.55 CISPEP 3 GLY A 172 PRO A 173 0 1.60 CISPEP 4 VAL A 198 PRO A 199 0 7.84 CRYST1 78.997 78.997 232.969 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 0.012659 0.007309 0.000000 0.00000 SCALE2 0.000000 0.014617 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004292 0.00000 CONECT 1184 1721 CONECT 1684 2170 CONECT 1721 1184 CONECT 2158 2176 CONECT 2170 1684 CONECT 2176 2158 CONECT 2236 2238 2240 2242 2244 CONECT 2237 2239 2241 2243 2245 CONECT 2238 2236 CONECT 2239 2237 CONECT 2240 2236 CONECT 2241 2237 CONECT 2242 2236 CONECT 2243 2237 CONECT 2244 2236 CONECT 2245 2237 CONECT 2246 2247 2248 CONECT 2247 2246 CONECT 2248 2246 2249 CONECT 2249 2248 2250 CONECT 2250 2249 2251 CONECT 2251 2250 2252 CONECT 2252 2251 CONECT 2253 2254 CONECT 2254 2253 2255 CONECT 2255 2254 2256 CONECT 2256 2255 2257 2260 CONECT 2257 2256 2262 CONECT 2258 2259 2260 2262 CONECT 2259 2258 CONECT 2260 2256 2258 2261 CONECT 2261 2260 CONECT 2262 2257 2258 2263 CONECT 2263 2262 2264 2272 CONECT 2264 2263 2265 CONECT 2265 2264 2266 CONECT 2266 2265 2267 2272 CONECT 2267 2266 2268 2269 CONECT 2268 2267 CONECT 2269 2267 2270 CONECT 2270 2269 2271 CONECT 2271 2270 2272 CONECT 2272 2263 2266 2271 MASTER 369 0 3 11 18 0 0 6 2212 1 43 21 END