HEADER TRANSFERASE 07-JUN-16 5KD0 TITLE CRYSTAL STRUCTURE OF THE AROMATIC PRENYLTRANSFERASE ATAPT(E91A) MUTANT TITLE 2 FROM ASPERGILLUS TERREUS A8-4 IN COMPLEX WITH GERANYL S- TITLE 3 THIOLODIPHOSPHATE AND (+)-BUTYROLACTONE II COMPND MOL_ID: 1; COMPND 2 MOLECULE: AROMATIC PRENYLTRANSFERASE; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ASPERGILLUS TERREUS; SOURCE 3 ORGANISM_TAXID: 33178; SOURCE 4 STRAIN: A8-4; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SUBSTRATE PROMISCUITY, ABBA FOLD, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR F.SUN,B.GAO REVDAT 4 06-NOV-24 5KD0 1 REMARK REVDAT 3 08-NOV-23 5KD0 1 REMARK REVDAT 2 05-JUL-17 5KD0 1 JRNL REVDAT 1 21-DEC-16 5KD0 0 JRNL AUTH R.CHEN,B.GAO,X.LIU,F.RUAN,Y.ZHANG,J.LOU,K.FENG,C.WUNSCH, JRNL AUTH 2 S.M.LI,J.DAI,F.SUN JRNL TITL MOLECULAR INSIGHTS INTO THE ENZYME PROMISCUITY OF AN JRNL TITL 2 AROMATIC PRENYLTRANSFERASE. JRNL REF NAT. CHEM. BIOL. V. 13 226 2017 JRNL REFN ESSN 1552-4469 JRNL PMID 27992881 JRNL DOI 10.1038/NCHEMBIO.2263 REMARK 2 REMARK 2 RESOLUTION. 2.82 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0073 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.82 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 139.24 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 21593 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) : 0.208 REMARK 3 R VALUE (WORKING SET) : 0.205 REMARK 3 FREE R VALUE : 0.268 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1144 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) : 2.82 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.89 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1570 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.81 REMARK 3 BIN R VALUE (WORKING SET) : 0.3000 REMARK 3 BIN FREE R VALUE SET COUNT : 80 REMARK 3 BIN FREE R VALUE : 0.3630 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6293 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 64 REMARK 3 SOLVENT ATOMS : 9 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.61 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.09000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : -0.08000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.419 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.310 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 16.001 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.921 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.866 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6517 ; 0.019 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 6260 ; 0.010 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8869 ; 1.903 ; 1.986 REMARK 3 BOND ANGLES OTHERS (DEGREES): 14413 ; 2.201 ; 3.002 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 791 ; 6.081 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 277 ;35.545 ;23.863 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1079 ;18.181 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 35 ;16.406 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 992 ; 0.090 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 7238 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1461 ; 0.007 ; 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): 3176 ; 2.392 ; 4.009 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 3175 ; 2.392 ; 4.009 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3963 ; 3.868 ; 6.011 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3964 ; 3.868 ; 6.012 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3341 ; 2.518 ; 4.312 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 3342 ; 2.518 ; 4.313 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 4907 ; 4.218 ; 6.342 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 7340 ; 6.410 ;32.323 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 7341 ; 6.410 ;32.326 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 : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 11 A 421 1 REMARK 3 1 B 11 B 421 1 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 TIGHT THERMAL 1 A (A**2): 3686 ; 4.89 ; 0.50 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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 THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 5KD0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 11-JUL-16. REMARK 100 THE DEPOSITION ID IS D_1000219186. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-DEC-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97892 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.21 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22776 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.820 REMARK 200 RESOLUTION RANGE LOW (A) : 139.240 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 8.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.09300 REMARK 200 FOR THE DATA SET : 15.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.82 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.4 REMARK 200 DATA REDUNDANCY IN SHELL : 7.70 REMARK 200 R MERGE FOR SHELL (I) : 0.38100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.000 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: 5KCG REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.03 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.51 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25 MM BIS-TRIS PH 6.0, 0.2 M REMARK 280 (NH4)2SO4, 17% PEG3350, 3.3% DDM, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 289K 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 48.34500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 69.62000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 48.34500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 69.62000 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: TETRAMERIC 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 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 193.38000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 GLY A 6 REMARK 465 PRO A 7 REMARK 465 LEU A 8 REMARK 465 GLY A 9 REMARK 465 SER A 10 REMARK 465 LYS A 309 REMARK 465 LEU A 310 REMARK 465 GLY A 311 REMARK 465 ASP A 312 REMARK 465 GLU A 313 REMARK 465 ALA A 314 REMARK 465 CYS A 315 REMARK 465 GLU A 316 REMARK 465 THR A 317 REMARK 465 LEU A 318 REMARK 465 ASP A 319 REMARK 465 ALA A 320 REMARK 465 GLU A 321 REMARK 465 GLY B 6 REMARK 465 PRO B 7 REMARK 465 LEU B 8 REMARK 465 GLY B 9 REMARK 465 SER B 10 REMARK 465 LYS B 309 REMARK 465 LEU B 310 REMARK 465 GLY B 311 REMARK 465 ASP B 312 REMARK 465 GLU B 313 REMARK 465 ALA B 314 REMARK 465 CYS B 315 REMARK 465 GLU B 316 REMARK 465 THR B 317 REMARK 465 LEU B 318 REMARK 465 ASP B 319 REMARK 465 ALA B 320 REMARK 465 GLU B 321 REMARK 465 ARG B 322 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 A 11 OE1 GLN A 14 1.89 REMARK 500 OG1 THR A 34 OH TYR A 59 2.09 REMARK 500 C LEU B 308 O HOH B 603 2.19 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 NH1 ARG A 273 OE1 GLU B 299 4556 1.98 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 PHE A 22 CG PHE A 22 CD2 -0.094 REMARK 500 PHE A 58 CG PHE A 58 CD1 -0.101 REMARK 500 ARG A 236 CZ ARG A 236 NH1 -0.130 REMARK 500 PHE A 272 CG PHE A 272 CD1 -0.091 REMARK 500 TYR A 365 CG TYR A 365 CD2 -0.093 REMARK 500 TYR A 365 CE1 TYR A 365 CZ -0.107 REMARK 500 PHE B 22 CG PHE B 22 CD1 -0.097 REMARK 500 PHE B 58 CG PHE B 58 CD1 -0.093 REMARK 500 ARG B 236 CZ ARG B 236 NH1 -0.124 REMARK 500 PHE B 272 CG PHE B 272 CD2 -0.097 REMARK 500 PHE B 345 CG PHE B 345 CD1 -0.092 REMARK 500 TYR B 365 CG TYR B 365 CD2 -0.081 REMARK 500 TYR B 365 CG TYR B 365 CD1 -0.080 REMARK 500 TYR B 365 CE1 TYR B 365 CZ -0.119 REMARK 500 SER B 409 CB SER B 409 OG -0.078 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 LEU A 207 CA - CB - CG ANGL. DEV. = 18.1 DEGREES REMARK 500 LEU A 207 CB - CG - CD2 ANGL. DEV. = -10.5 DEGREES REMARK 500 ARG A 225 CD - NE - CZ ANGL. DEV. = 8.5 DEGREES REMARK 500 ARG A 225 NE - CZ - NH1 ANGL. DEV. = -9.2 DEGREES REMARK 500 ARG A 225 NE - CZ - NH2 ANGL. DEV. = 7.5 DEGREES REMARK 500 ARG A 236 NE - CZ - NH1 ANGL. DEV. = -3.9 DEGREES REMARK 500 ARG A 236 NE - CZ - NH2 ANGL. DEV. = 6.2 DEGREES REMARK 500 ARG A 264 NE - CZ - NH2 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG A 280 NE - CZ - NH2 ANGL. DEV. = -4.2 DEGREES REMARK 500 ILE B 102 CG1 - CB - CG2 ANGL. DEV. = -21.9 DEGREES REMARK 500 ASP B 141 CB - CG - OD1 ANGL. DEV. = 6.0 DEGREES REMARK 500 LEU B 207 CA - CB - CG ANGL. DEV. = 18.9 DEGREES REMARK 500 ARG B 225 CD - NE - CZ ANGL. DEV. = 8.6 DEGREES REMARK 500 ARG B 225 NE - CZ - NH1 ANGL. DEV. = 7.7 DEGREES REMARK 500 ARG B 225 NE - CZ - NH2 ANGL. DEV. = -8.7 DEGREES REMARK 500 ARG B 236 NE - CZ - NH1 ANGL. DEV. = -3.5 DEGREES REMARK 500 ARG B 236 NE - CZ - NH2 ANGL. DEV. = 6.6 DEGREES REMARK 500 ARG B 264 NE - CZ - NH2 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG B 273 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 ARG B 280 NE - CZ - NH1 ANGL. DEV. = -4.2 DEGREES REMARK 500 GLU B 369 OE1 - CD - OE2 ANGL. DEV. = -7.6 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 THR A 34 -53.86 -138.21 REMARK 500 PRO A 77 154.47 -49.98 REMARK 500 ASP A 119 74.92 -158.76 REMARK 500 ILE A 245 67.00 -107.25 REMARK 500 THR A 290 -1.67 -141.32 REMARK 500 ASP A 291 170.86 -55.17 REMARK 500 TRP A 368 78.88 -103.44 REMARK 500 THR B 34 -28.05 -145.95 REMARK 500 ASP B 119 73.97 -160.86 REMARK 500 ASP B 182 -129.11 62.31 REMARK 500 ASP B 242 -168.34 -110.66 REMARK 500 ILE B 245 62.77 -109.86 REMARK 500 THR B 290 -3.86 -143.66 REMARK 500 ASP B 291 172.14 -52.63 REMARK 500 PRO B 341 -177.88 -66.44 REMARK 500 TRP B 368 73.73 -106.98 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 XBU A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GST A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GST B 501 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5KCG RELATED DB: PDB REMARK 900 RELATED ID: 5KCL RELATED DB: PDB REMARK 900 RELATED ID: 5KCQ RELATED DB: PDB REMARK 900 RELATED ID: 5KCY RELATED DB: PDB REMARK 900 RELATED ID: 5KD6 RELATED DB: PDB REMARK 900 RELATED ID: 5KDA RELATED DB: PDB DBREF 5KD0 A 6 421 PDB 5KD0 5KD0 6 421 DBREF 5KD0 B 6 421 PDB 5KD0 5KD0 6 421 SEQRES 1 A 416 GLY PRO LEU GLY SER ARG PRO TRP GLN ILE LEU SER GLN SEQRES 2 A 416 ALA LEU GLY PHE PRO ASN TYR ASP GLN GLU LEU TRP TRP SEQRES 3 A 416 GLN ASN THR ALA GLU THR LEU ASN ARG VAL LEU GLU GLN SEQRES 4 A 416 CYS ASP TYR SER VAL HIS LEU GLN TYR LYS TYR LEU ALA SEQRES 5 A 416 PHE TYR HIS LYS TYR ILE LEU PRO SER LEU GLY PRO PHE SEQRES 6 A 416 ARG ARG PRO GLY VAL GLU PRO GLU TYR ILE SER GLY LEU SEQRES 7 A 416 SER HIS GLY GLY HIS PRO LEU ALA ILE SER VAL LYS ILE SEQRES 8 A 416 ASP LYS SER LYS THR ILE CYS ARG LEU GLY LEU GLN ALA SEQRES 9 A 416 ILE GLY PRO LEU ALA GLY THR ALA ARG ASP PRO LEU ASN SEQRES 10 A 416 SER PHE GLY ASP ARG GLU LEU LEU LYS ASN LEU ALA THR SEQRES 11 A 416 LEU LEU PRO HIS VAL ASP LEU ARG LEU PHE ASP HIS PHE SEQRES 12 A 416 ASN ALA GLN VAL GLY LEU ASP ARG ALA GLN CYS ALA VAL SEQRES 13 A 416 ALA THR THR LYS LEU ILE LYS GLU SER HIS ASN ILE VAL SEQRES 14 A 416 CYS THR SER LEU ASP LEU LYS ASP GLY GLU VAL ILE PRO SEQRES 15 A 416 LYS VAL TYR PHE SER THR ILE PRO LYS GLY LEU VAL THR SEQRES 16 A 416 GLU THR PRO LEU PHE ASP LEU THR PHE ALA ALA ILE GLU SEQRES 17 A 416 GLN MET GLU VAL TYR HIS LYS ASP ALA PRO LEU ARG THR SEQRES 18 A 416 ALA LEU SER SER LEU LYS ASP PHE LEU ARG PRO ARG VAL SEQRES 19 A 416 PRO THR ASP ALA SER ILE THR PRO PRO LEU THR GLY LEU SEQRES 20 A 416 ILE GLY VAL ASP CYS ILE ASP PRO MET LEU SER ARG LEU SEQRES 21 A 416 LYS VAL TYR LEU ALA THR PHE ARG MET ASP LEU SER LEU SEQRES 22 A 416 ILE ARG ASP TYR TRP THR LEU GLY GLY LEU LEU THR ASP SEQRES 23 A 416 ALA GLY THR MET LYS GLY LEU GLU MET VAL GLU THR LEU SEQRES 24 A 416 ALA LYS THR LEU LYS LEU GLY ASP GLU ALA CYS GLU THR SEQRES 25 A 416 LEU ASP ALA GLU ARG LEU PRO PHE GLY ILE ASN TYR ALA SEQRES 26 A 416 MET LYS PRO GLY THR ALA GLU LEU ALA PRO PRO GLN ILE SEQRES 27 A 416 TYR PHE PRO LEU LEU GLY ILE ASN ASP GLY PHE ILE ALA SEQRES 28 A 416 ASP ALA LEU VAL GLU PHE PHE GLN TYR MET GLY TRP GLU SEQRES 29 A 416 ASP GLN ALA ASN ARG TYR LYS ASP GLU LEU LYS ALA LYS SEQRES 30 A 416 PHE PRO ASN VAL ASP ILE SER GLN THR LYS ASN VAL HIS SEQRES 31 A 416 ARG TRP LEU GLY VAL ALA TYR SER GLU THR LYS GLY PRO SEQRES 32 A 416 SER MET ASN ILE TYR TYR ASP VAL VAL ALA GLY ASN VAL SEQRES 1 B 416 GLY PRO LEU GLY SER ARG PRO TRP GLN ILE LEU SER GLN SEQRES 2 B 416 ALA LEU GLY PHE PRO ASN TYR ASP GLN GLU LEU TRP TRP SEQRES 3 B 416 GLN ASN THR ALA GLU THR LEU ASN ARG VAL LEU GLU GLN SEQRES 4 B 416 CYS ASP TYR SER VAL HIS LEU GLN TYR LYS TYR LEU ALA SEQRES 5 B 416 PHE TYR HIS LYS TYR ILE LEU PRO SER LEU GLY PRO PHE SEQRES 6 B 416 ARG ARG PRO GLY VAL GLU PRO GLU TYR ILE SER GLY LEU SEQRES 7 B 416 SER HIS GLY GLY HIS PRO LEU ALA ILE SER VAL LYS ILE SEQRES 8 B 416 ASP LYS SER LYS THR ILE CYS ARG LEU GLY LEU GLN ALA SEQRES 9 B 416 ILE GLY PRO LEU ALA GLY THR ALA ARG ASP PRO LEU ASN SEQRES 10 B 416 SER PHE GLY ASP ARG GLU LEU LEU LYS ASN LEU ALA THR SEQRES 11 B 416 LEU LEU PRO HIS VAL ASP LEU ARG LEU PHE ASP HIS PHE SEQRES 12 B 416 ASN ALA GLN VAL GLY LEU ASP ARG ALA GLN CYS ALA VAL SEQRES 13 B 416 ALA THR THR LYS LEU ILE LYS GLU SER HIS ASN ILE VAL SEQRES 14 B 416 CYS THR SER LEU ASP LEU LYS ASP GLY GLU VAL ILE PRO SEQRES 15 B 416 LYS VAL TYR PHE SER THR ILE PRO LYS GLY LEU VAL THR SEQRES 16 B 416 GLU THR PRO LEU PHE ASP LEU THR PHE ALA ALA ILE GLU SEQRES 17 B 416 GLN MET GLU VAL TYR HIS LYS ASP ALA PRO LEU ARG THR SEQRES 18 B 416 ALA LEU SER SER LEU LYS ASP PHE LEU ARG PRO ARG VAL SEQRES 19 B 416 PRO THR ASP ALA SER ILE THR PRO PRO LEU THR GLY LEU SEQRES 20 B 416 ILE GLY VAL ASP CYS ILE ASP PRO MET LEU SER ARG LEU SEQRES 21 B 416 LYS VAL TYR LEU ALA THR PHE ARG MET ASP LEU SER LEU SEQRES 22 B 416 ILE ARG ASP TYR TRP THR LEU GLY GLY LEU LEU THR ASP SEQRES 23 B 416 ALA GLY THR MET LYS GLY LEU GLU MET VAL GLU THR LEU SEQRES 24 B 416 ALA LYS THR LEU LYS LEU GLY ASP GLU ALA CYS GLU THR SEQRES 25 B 416 LEU ASP ALA GLU ARG LEU PRO PHE GLY ILE ASN TYR ALA SEQRES 26 B 416 MET LYS PRO GLY THR ALA GLU LEU ALA PRO PRO GLN ILE SEQRES 27 B 416 TYR PHE PRO LEU LEU GLY ILE ASN ASP GLY PHE ILE ALA SEQRES 28 B 416 ASP ALA LEU VAL GLU PHE PHE GLN TYR MET GLY TRP GLU SEQRES 29 B 416 ASP GLN ALA ASN ARG TYR LYS ASP GLU LEU LYS ALA LYS SEQRES 30 B 416 PHE PRO ASN VAL ASP ILE SER GLN THR LYS ASN VAL HIS SEQRES 31 B 416 ARG TRP LEU GLY VAL ALA TYR SER GLU THR LYS GLY PRO SEQRES 32 B 416 SER MET ASN ILE TYR TYR ASP VAL VAL ALA GLY ASN VAL HET XBU A 501 26 HET GST A 502 19 HET GST B 501 19 HETNAM XBU METHYL (2~{R})-3-(4-HYDROXYPHENYL)-2-[(4- HETNAM 2 XBU HYDROXYPHENYL)METHYL]-4-OXIDANYL-5-OXIDANYLIDENE- HETNAM 3 XBU FURAN-2-CARBOXYLATE HETNAM GST GERANYL S-THIOLODIPHOSPHATE HETSYN GST S-[(2E)-3,7-DIMETHYLOCTA-2,6-DIENYL] TRIHYDROGEN HETSYN 2 GST THIODIPHOSPHATE FORMUL 3 XBU C19 H16 O7 FORMUL 4 GST 2(C10 H20 O6 P2 S) FORMUL 6 HOH *9(H2 O) HELIX 1 AA1 ARG A 11 GLY A 21 1 11 HELIX 2 AA2 ASN A 24 ASN A 33 1 10 HELIX 3 AA3 THR A 34 CYS A 45 1 12 HELIX 4 AA4 SER A 48 ILE A 63 1 16 HELIX 5 AA5 LEU A 64 GLY A 68 5 5 HELIX 6 AA6 PHE A 124 LEU A 137 1 14 HELIX 7 AA7 LEU A 142 GLY A 153 1 12 HELIX 8 AA8 ASP A 155 LYS A 165 1 11 HELIX 9 AA9 LEU A 166 HIS A 171 5 6 HELIX 10 AB1 THR A 193 GLU A 201 1 9 HELIX 11 AB2 PRO A 203 GLN A 214 1 12 HELIX 12 AB3 MET A 215 LYS A 220 1 6 HELIX 13 AB4 ASP A 221 VAL A 239 1 19 HELIX 14 AB5 ASP A 259 SER A 263 5 5 HELIX 15 AB6 ASP A 275 LEU A 285 1 11 HELIX 16 AB7 ASP A 291 THR A 307 1 17 HELIX 17 AB8 ASN A 351 GLY A 367 1 17 HELIX 18 AB9 TRP A 368 PHE A 383 1 16 HELIX 19 AC1 PRO B 12 GLY B 21 1 10 HELIX 20 AC2 ASN B 24 ASN B 33 1 10 HELIX 21 AC3 THR B 34 CYS B 45 1 12 HELIX 22 AC4 SER B 48 ILE B 63 1 16 HELIX 23 AC5 LEU B 64 GLY B 68 5 5 HELIX 24 AC6 PHE B 124 LEU B 137 1 14 HELIX 25 AC7 LEU B 142 GLY B 153 1 12 HELIX 26 AC8 ASP B 155 LYS B 165 1 11 HELIX 27 AC9 ILE B 167 HIS B 171 5 5 HELIX 28 AD1 THR B 193 GLU B 201 1 9 HELIX 29 AD2 PRO B 203 GLN B 214 1 12 HELIX 30 AD3 MET B 215 LYS B 220 1 6 HELIX 31 AD4 ASP B 221 VAL B 239 1 19 HELIX 32 AD5 ASP B 259 SER B 263 5 5 HELIX 33 AD6 ASP B 275 LEU B 285 1 11 HELIX 34 AD7 ASP B 291 THR B 307 1 17 HELIX 35 AD8 ASN B 351 MET B 366 1 16 HELIX 36 AD9 TRP B 368 PHE B 383 1 16 HELIX 37 AE1 VAL B 417 VAL B 421 5 5 SHEET 1 AA111 LEU A 90 ILE A 96 0 SHEET 2 AA111 THR A 101 LEU A 107 -1 O GLY A 106 N ALA A 91 SHEET 3 AA111 VAL A 174 LYS A 181 -1 O THR A 176 N LEU A 107 SHEET 4 AA111 GLU A 184 SER A 192 -1 O ILE A 186 N ASP A 179 SHEET 5 AA111 LEU A 249 ASP A 256 -1 O ILE A 253 N PHE A 191 SHEET 6 AA111 LEU A 265 THR A 271 -1 O LYS A 266 N GLY A 254 SHEET 7 AA111 PHE A 325 MET A 331 -1 O PHE A 325 N THR A 271 SHEET 8 AA111 GLN A 342 PRO A 346 -1 O TYR A 344 N GLY A 326 SHEET 9 AA111 HIS A 395 TYR A 402 -1 O LEU A 398 N PHE A 345 SHEET 10 AA111 PRO A 408 TYR A 414 -1 O ASN A 411 N GLY A 399 SHEET 11 AA111 LEU A 90 ILE A 96 -1 N ILE A 96 O MET A 410 SHEET 1 AA211 LEU B 90 ILE B 96 0 SHEET 2 AA211 THR B 101 LEU B 107 -1 O GLY B 106 N ALA B 91 SHEET 3 AA211 VAL B 174 LYS B 181 -1 O THR B 176 N LEU B 107 SHEET 4 AA211 GLU B 184 SER B 192 -1 O LYS B 188 N SER B 177 SHEET 5 AA211 LEU B 249 ASP B 256 -1 O ILE B 253 N PHE B 191 SHEET 6 AA211 LEU B 265 THR B 271 -1 O LYS B 266 N GLY B 254 SHEET 7 AA211 PHE B 325 MET B 331 -1 O PHE B 325 N THR B 271 SHEET 8 AA211 GLN B 342 PRO B 346 -1 O TYR B 344 N GLY B 326 SHEET 9 AA211 HIS B 395 TYR B 402 -1 O LEU B 398 N PHE B 345 SHEET 10 AA211 PRO B 408 TYR B 414 -1 O ASN B 411 N GLY B 399 SHEET 11 AA211 LEU B 90 ILE B 96 -1 N ILE B 96 O MET B 410 LINK O TRP A 30 CG2 THR A 34 1555 1555 1.18 CISPEP 1 PRO A 247 PRO A 248 0 -8.02 CISPEP 2 PRO B 247 PRO B 248 0 -12.01 SITE 1 AC1 11 LEU A 83 ALA A 91 SER A 93 ARG A 104 SITE 2 AC1 11 LEU A 105 GLY A 106 SER A 177 ARG A 396 SITE 3 AC1 11 TRP A 397 TYR A 413 GST A 502 SITE 1 AC2 14 LYS A 95 ARG A 104 LYS A 188 TYR A 190 SITE 2 AC2 14 ARG A 264 LYS A 266 TYR A 268 GLY A 326 SITE 3 AC2 14 GLN A 342 TYR A 344 TRP A 397 ASN A 411 SITE 4 AC2 14 TYR A 413 XBU A 501 SITE 1 AC3 11 LYS B 95 ARG B 104 LYS B 188 TYR B 190 SITE 2 AC3 11 ARG B 264 LYS B 266 TYR B 268 GLN B 342 SITE 3 AC3 11 TYR B 344 TRP B 397 TYR B 413 CRYST1 96.690 139.240 68.800 90.00 90.00 90.00 P 21 21 2 8 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 0.010342 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007182 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014535 0.00000 MTRIX1 1 1.000000 0.000000 0.000000 0.00000 1 MTRIX2 1 0.000000 1.000000 0.000000 0.00000 1 MTRIX3 1 0.000000 0.000000 1.000000 0.00000 1 MTRIX1 2 -0.410496 -0.911852 0.004423 136.29843 1 MTRIX2 2 -0.911833 0.410517 0.006001 87.97433 1 MTRIX3 2 -0.007288 -0.001569 -0.999972 94.42169 1