HEADER TRANSFERASE 10-SEP-24 9JHV TITLE CRYSTAL STRUCTURE OF 5'-DEOXY-5'-METHYLTHIOADENOSINE PHOSPHORYLASE TITLE 2 FROM AEROPYRUM PERNIX COMPLEX WITH 5'-DEOXY-5'-METHYLTHIOADENOSINE TITLE 3 343K 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 2 09-OCT-24 9JHV 1 REMARK REVDAT 1 25-SEP-24 9JHV 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 353K JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.65 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) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.36 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 34101 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) : 0.118 REMARK 3 FREE R VALUE : 0.167 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.243 REMARK 3 FREE R VALUE TEST SET COUNT : 1788 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) : 1.65 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.69 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2347 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.92 REMARK 3 BIN R VALUE (WORKING SET) : 0.2640 REMARK 3 BIN FREE R VALUE SET COUNT : 134 REMARK 3 BIN FREE R VALUE : 0.2690 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 : 55 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.91 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.32900 REMARK 3 B22 (A**2) : -0.32900 REMARK 3 B33 (A**2) : 1.06700 REMARK 3 B12 (A**2) : -0.16500 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): 0.086 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.074 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.056 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.047 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.985 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.975 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2251 ; 0.009 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 2124 ; 0.001 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3069 ; 1.668 ; 1.819 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4874 ; 0.580 ; 1.758 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 278 ; 6.961 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 26 ; 6.961 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 356 ;13.072 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 339 ; 0.085 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2710 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 535 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 355 ; 0.215 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 110 ; 0.210 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1105 ; 0.181 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 56 ; 0.127 ; 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): 1103 ; 6.832 ; 2.428 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1103 ; 6.822 ; 2.428 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1381 ;10.245 ; 4.364 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1382 ;10.242 ; 4.364 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1148 ;11.042 ; 3.120 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1148 ;11.041 ; 3.120 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1687 ;16.426 ; 5.426 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1688 ;16.421 ; 5.425 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): 4375 ; 4.030 ; 3.000 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 9JHV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 11-SEP-24. REMARK 100 THE DEPOSITION ID IS D_1300051352. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-JUN-24 REMARK 200 TEMPERATURE (KELVIN) : 343 REMARK 200 PH : NULL 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) : 1.0 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 : 34102 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 44.360 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 10.00 REMARK 200 R MERGE (I) : 0.14100 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 9.04 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 44.36 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.6 REMARK 200 DATA REDUNDANCY IN SHELL : 7.90 REMARK 200 R MERGE FOR SHELL (I) : 0.05200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 30.70 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 (%): 45.88 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: HE MIXTURE OF PROTEIN SOLUTION AND REMARK 280 AGAROSE WAS FILLED INTO A GLASS CAPILLARY, AND THE CAPILLARY WAS REMARK 280 IMMERSED IN THE RESERVOIR SOLUTION FOR CRYSTALLIZATION. THE REMARK 280 COMPOSITION OF THE RESERVOIR SOLUTION WAS AS FOLLOWS.15%(V/V)PEG# REMARK 280 200,0.1 M PHOSPHATE CITRATE PH 5.4, 5 MM MTA, COUNTER-DIFFUSION, REMARK 280 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 39.42700 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 22.76319 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 77.78967 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 39.42700 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 22.76319 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 77.78967 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 39.42700 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 22.76319 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 77.78967 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 39.42700 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 22.76319 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 77.78967 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 39.42700 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 22.76319 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 77.78967 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 39.42700 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 22.76319 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 77.78967 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 45.52638 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 155.57933 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 45.52638 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 155.57933 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 45.52638 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 155.57933 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 45.52638 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 155.57933 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 45.52638 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 155.57933 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 45.52638 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 155.57933 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: 10250 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27840 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -74.0 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 -39.42700 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 -68.28957 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 39.42700 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 -68.28957 REMARK 350 BIOMT3 3 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 406 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 MET A 1 REMARK 465 PHE A 2 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 O1 PEG A 301 O1 PEG A 301 2445 1.57 REMARK 500 O HOH A 430 O HOH A 430 6555 1.72 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 62 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 MET A 118 CG - SD - CE ANGL. DEV. = 10.7 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 LYS A 120 -19.71 -145.32 REMARK 500 ARG A 123 -44.76 76.67 REMARK 500 ASP A 221 -131.48 60.38 REMARK 500 REMARK 500 REMARK: NULL DBREF 9JHV 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 PEG A 301 7 HET PO4 A 302 5 HET MTA A 303 20 HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM PO4 PHOSPHATE ION HETNAM MTA 5'-DEOXY-5'-METHYLTHIOADENOSINE FORMUL 2 PEG C4 H10 O3 FORMUL 3 PO4 O4 P 3- FORMUL 4 MTA C11 H15 N5 O3 S FORMUL 5 HOH *55(H2 O) HELIX 1 AA1 PRO A 70 ILE A 74 5 5 HELIX 2 AA2 ASN A 75 LEU A 86 1 12 HELIX 3 AA3 CYS A 143 GLY A 158 1 16 HELIX 4 AA4 THR A 177 VAL A 187 1 11 HELIX 5 AA5 PRO A 199 ALA A 207 1 9 HELIX 6 AA6 THR A 229 ILE A 252 1 24 HELIX 7 AA7 PRO A 253 ALA A 256 5 4 HELIX 8 AA8 GLU A 260 CYS A 264 5 5 HELIX 9 AA9 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 2.04 SSBOND 3 CYS A 264 CYS A 267 1555 1555 2.01 CISPEP 1 ARG A 6 PRO A 7 0 0.19 CISPEP 2 GLY A 130 PRO A 131 0 8.41 CISPEP 3 GLY A 172 PRO A 173 0 0.29 CISPEP 4 VAL A 198 PRO A 199 0 7.16 CRYST1 78.854 78.854 233.369 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 0.012682 0.007322 0.000000 0.00000 SCALE2 0.000000 0.014644 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004285 0.00000