HEADER TRANSFERASE 07-JUN-16 5KDA TITLE CRYSTAL STRUCTURE OF THE AROMATIC PRENYLTRANSFERASE ATAPT FROM TITLE 2 ASPERGILLUS TERREUS A8-4 IN COMPLEX WITH DIMETHYLALLYL S- TITLE 3 THIOLODIPHOSPHATE AND GENISTEIN 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 GENE: ATEG_04999; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS AROMATIC PRENYLTRANSFERASE, ABBA FOLD, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR F.SUN,B.GAO REVDAT 4 08-NOV-23 5KDA 1 HETSYN REVDAT 3 16-OCT-19 5KDA 1 COMPND REMARK HET HETNAM REVDAT 3 2 1 FORMUL ATOM REVDAT 2 05-JUL-17 5KDA 1 JRNL REVDAT 1 21-DEC-16 5KDA 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. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0135 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 78.80 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 88.6 REMARK 3 NUMBER OF REFLECTIONS : 52312 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) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.188 REMARK 3 FREE R VALUE : 0.238 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2731 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3280 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 75.94 REMARK 3 BIN R VALUE (WORKING SET) : 0.2120 REMARK 3 BIN FREE R VALUE SET COUNT : 180 REMARK 3 BIN FREE R VALUE : 0.2640 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6311 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 48 REMARK 3 SOLVENT ATOMS : 410 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.12 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.68000 REMARK 3 B22 (A**2) : 0.94000 REMARK 3 B33 (A**2) : -0.26000 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): 0.207 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.181 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.118 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.224 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.944 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.916 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6521 ; 0.018 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 6245 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8875 ; 1.884 ; 1.980 REMARK 3 BOND ANGLES OTHERS (DEGREES): 14389 ; 1.062 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 797 ; 6.715 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 281 ;34.593 ;23.879 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1086 ;15.802 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 35 ;16.469 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 990 ; 0.116 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 7281 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1470 ; 0.002 ; 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): 3194 ; 2.148 ; 2.343 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 3193 ; 2.148 ; 2.343 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3989 ; 3.056 ; 3.502 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3990 ; 3.056 ; 3.502 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3327 ; 3.059 ; 2.737 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 3328 ; 3.059 ; 2.738 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 4887 ; 4.657 ; 3.950 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 7612 ; 6.203 ;19.805 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 7493 ; 6.137 ;19.652 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 : 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 5KDA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-JUN-16. REMARK 100 THE DEPOSITION ID IS D_1000219190. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-APR-14 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) : 0.99999 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 3.321 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 52312 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 78.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 88.9 REMARK 200 DATA REDUNDANCY : 4.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 7.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.11 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL 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 (%): 50.88 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS PH 6.0, 0.2 M REMARK 280 (NH4)2SO4, 17% PEG 3350, 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 48.32500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 68.04000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 48.32500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 68.04000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 11820 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 54990 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -24.0 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 193.30000 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 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 811 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 GLY A 6 REMARK 465 PRO A 7 REMARK 465 LEU A 8 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 ALA A 422 REMARK 465 ARG A 423 REMARK 465 VAL A 424 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 465 ALA B 422 REMARK 465 ARG B 423 REMARK 465 VAL B 424 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 OH TYR B 268 S9 DST B 501 1.96 REMARK 500 C VAL B 421 O HOH B 631 2.10 REMARK 500 NZ LYS A 188 O8 DST A 502 2.17 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 104 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 LYS A 406 N - CA - C ANGL. DEV. = 19.6 DEGREES REMARK 500 ASP B 119 CB - CG - OD1 ANGL. DEV. = 7.0 DEGREES REMARK 500 ASP B 179 CB - CG - OD1 ANGL. DEV. = 6.0 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 THR A 34 -31.17 -132.71 REMARK 500 ASP A 119 64.93 -159.87 REMARK 500 ASP A 259 124.13 -39.90 REMARK 500 ASP A 291 170.17 -58.90 REMARK 500 TRP A 368 72.74 -101.08 REMARK 500 THR A 405 4.29 81.73 REMARK 500 LYS A 406 -15.95 -145.89 REMARK 500 THR B 34 -31.40 -142.58 REMARK 500 ASP B 97 -167.12 -126.83 REMARK 500 ASP B 119 73.63 -157.69 REMARK 500 ASP B 182 -129.66 57.76 REMARK 500 TRP B 368 72.40 -100.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B 792 DISTANCE = 6.56 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GEN A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DST A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DST 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: 5KD0 RELATED DB: PDB REMARK 900 RELATED ID: 5KD6 RELATED DB: PDB DBREF 5KDA A 6 424 PDB 5KDA 5KDA 6 424 DBREF 5KDA B 6 424 PDB 5KDA 5KDA 6 424 SEQRES 1 A 419 GLY PRO LEU GLY SER ARG PRO TRP GLN ILE LEU SER GLN SEQRES 2 A 419 ALA LEU GLY PHE PRO ASN TYR ASP GLN GLU LEU TRP TRP SEQRES 3 A 419 GLN ASN THR ALA GLU THR LEU ASN ARG VAL LEU GLU GLN SEQRES 4 A 419 CYS ASP TYR SER VAL HIS LEU GLN TYR LYS TYR LEU ALA SEQRES 5 A 419 PHE TYR HIS LYS TYR ILE LEU PRO SER LEU GLY PRO PHE SEQRES 6 A 419 ARG ARG PRO GLY VAL GLU PRO GLU TYR ILE SER GLY LEU SEQRES 7 A 419 SER HIS GLY GLY HIS PRO LEU GLU ILE SER VAL LYS ILE SEQRES 8 A 419 ASP LYS SER LYS THR ILE CYS ARG LEU GLY LEU GLN ALA SEQRES 9 A 419 ILE GLY PRO LEU ALA GLY THR ALA ARG ASP PRO LEU ASN SEQRES 10 A 419 SER PHE GLY ASP ARG GLU LEU LEU LYS ASN LEU ALA THR SEQRES 11 A 419 LEU LEU PRO HIS VAL ASP LEU ARG LEU PHE ASP HIS PHE SEQRES 12 A 419 ASN ALA GLN VAL GLY LEU ASP ARG ALA GLN CYS ALA VAL SEQRES 13 A 419 ALA THR THR LYS LEU ILE LYS GLU SER HIS ASN ILE VAL SEQRES 14 A 419 CYS THR SER LEU ASP LEU LYS ASP GLY GLU VAL ILE PRO SEQRES 15 A 419 LYS VAL TYR PHE SER THR ILE PRO LYS GLY LEU VAL THR SEQRES 16 A 419 GLU THR PRO LEU PHE ASP LEU THR PHE ALA ALA ILE GLU SEQRES 17 A 419 GLN MET GLU VAL TYR HIS LYS ASP ALA PRO LEU ARG THR SEQRES 18 A 419 ALA LEU SER SER LEU LYS ASP PHE LEU ARG PRO ARG VAL SEQRES 19 A 419 PRO THR ASP ALA SER ILE THR PRO PRO LEU THR GLY LEU SEQRES 20 A 419 ILE GLY VAL ASP CYS ILE ASP PRO MET LEU SER ARG LEU SEQRES 21 A 419 LYS VAL TYR LEU ALA THR PHE ARG MET ASP LEU SER LEU SEQRES 22 A 419 ILE ARG ASP TYR TRP THR LEU GLY GLY LEU LEU THR ASP SEQRES 23 A 419 ALA GLY THR MET LYS GLY LEU GLU MET VAL GLU THR LEU SEQRES 24 A 419 ALA LYS THR LEU LYS LEU GLY ASP GLU ALA CYS GLU THR SEQRES 25 A 419 LEU ASP ALA GLU ARG LEU PRO PHE GLY ILE ASN TYR ALA SEQRES 26 A 419 MET LYS PRO GLY THR ALA GLU LEU ALA PRO PRO GLN ILE SEQRES 27 A 419 TYR PHE PRO LEU LEU GLY ILE ASN ASP GLY PHE ILE ALA SEQRES 28 A 419 ASP ALA LEU VAL GLU PHE PHE GLN TYR MET GLY TRP GLU SEQRES 29 A 419 ASP GLN ALA ASN ARG TYR LYS ASP GLU LEU LYS ALA LYS SEQRES 30 A 419 PHE PRO ASN VAL ASP ILE SER GLN THR LYS ASN VAL HIS SEQRES 31 A 419 ARG TRP LEU GLY VAL ALA TYR SER GLU THR LYS GLY PRO SEQRES 32 A 419 SER MET ASN ILE TYR TYR ASP VAL VAL ALA GLY ASN VAL SEQRES 33 A 419 ALA ARG VAL SEQRES 1 B 419 GLY PRO LEU GLY SER ARG PRO TRP GLN ILE LEU SER GLN SEQRES 2 B 419 ALA LEU GLY PHE PRO ASN TYR ASP GLN GLU LEU TRP TRP SEQRES 3 B 419 GLN ASN THR ALA GLU THR LEU ASN ARG VAL LEU GLU GLN SEQRES 4 B 419 CYS ASP TYR SER VAL HIS LEU GLN TYR LYS TYR LEU ALA SEQRES 5 B 419 PHE TYR HIS LYS TYR ILE LEU PRO SER LEU GLY PRO PHE SEQRES 6 B 419 ARG ARG PRO GLY VAL GLU PRO GLU TYR ILE SER GLY LEU SEQRES 7 B 419 SER HIS GLY GLY HIS PRO LEU GLU ILE SER VAL LYS ILE SEQRES 8 B 419 ASP LYS SER LYS THR ILE CYS ARG LEU GLY LEU GLN ALA SEQRES 9 B 419 ILE GLY PRO LEU ALA GLY THR ALA ARG ASP PRO LEU ASN SEQRES 10 B 419 SER PHE GLY ASP ARG GLU LEU LEU LYS ASN LEU ALA THR SEQRES 11 B 419 LEU LEU PRO HIS VAL ASP LEU ARG LEU PHE ASP HIS PHE SEQRES 12 B 419 ASN ALA GLN VAL GLY LEU ASP ARG ALA GLN CYS ALA VAL SEQRES 13 B 419 ALA THR THR LYS LEU ILE LYS GLU SER HIS ASN ILE VAL SEQRES 14 B 419 CYS THR SER LEU ASP LEU LYS ASP GLY GLU VAL ILE PRO SEQRES 15 B 419 LYS VAL TYR PHE SER THR ILE PRO LYS GLY LEU VAL THR SEQRES 16 B 419 GLU THR PRO LEU PHE ASP LEU THR PHE ALA ALA ILE GLU SEQRES 17 B 419 GLN MET GLU VAL TYR HIS LYS ASP ALA PRO LEU ARG THR SEQRES 18 B 419 ALA LEU SER SER LEU LYS ASP PHE LEU ARG PRO ARG VAL SEQRES 19 B 419 PRO THR ASP ALA SER ILE THR PRO PRO LEU THR GLY LEU SEQRES 20 B 419 ILE GLY VAL ASP CYS ILE ASP PRO MET LEU SER ARG LEU SEQRES 21 B 419 LYS VAL TYR LEU ALA THR PHE ARG MET ASP LEU SER LEU SEQRES 22 B 419 ILE ARG ASP TYR TRP THR LEU GLY GLY LEU LEU THR ASP SEQRES 23 B 419 ALA GLY THR MET LYS GLY LEU GLU MET VAL GLU THR LEU SEQRES 24 B 419 ALA LYS THR LEU LYS LEU GLY ASP GLU ALA CYS GLU THR SEQRES 25 B 419 LEU ASP ALA GLU ARG LEU PRO PHE GLY ILE ASN TYR ALA SEQRES 26 B 419 MET LYS PRO GLY THR ALA GLU LEU ALA PRO PRO GLN ILE SEQRES 27 B 419 TYR PHE PRO LEU LEU GLY ILE ASN ASP GLY PHE ILE ALA SEQRES 28 B 419 ASP ALA LEU VAL GLU PHE PHE GLN TYR MET GLY TRP GLU SEQRES 29 B 419 ASP GLN ALA ASN ARG TYR LYS ASP GLU LEU LYS ALA LYS SEQRES 30 B 419 PHE PRO ASN VAL ASP ILE SER GLN THR LYS ASN VAL HIS SEQRES 31 B 419 ARG TRP LEU GLY VAL ALA TYR SER GLU THR LYS GLY PRO SEQRES 32 B 419 SER MET ASN ILE TYR TYR ASP VAL VAL ALA GLY ASN VAL SEQRES 33 B 419 ALA ARG VAL HET GEN A 501 20 HET DST A 502 14 HET DST B 501 14 HETNAM GEN GENISTEIN HETNAM DST DIMETHYLALLYL S-THIOLODIPHOSPHATE HETSYN GEN 5,7-DIHYDROXY-3-(4-HYDROXYPHENYL)-4H-1-BENZOPYRAN-4- HETSYN 2 GEN ONE; 4',5,7-TRIHYDROXYISOFLAVONE; PRUNETOL; GENISTEOL HETSYN DST DMASPP; DMAPP; DMADP; DIMETHYLALLYL PYROPHOSPHATE; HETSYN 2 DST DIMETHYLALLYL DIPHOSPHATE; ISOPRENYL PYROPHOSPHATE FORMUL 3 GEN C15 H10 O5 FORMUL 4 DST 2(C5 H12 O6 P2 S) FORMUL 6 HOH *410(H2 O) HELIX 1 AA1 ARG A 11 GLY A 21 1 11 HELIX 2 AA2 ASN A 24 CYS A 45 1 22 HELIX 3 AA3 SER A 48 ILE A 63 1 16 HELIX 4 AA4 LEU A 64 GLY A 68 5 5 HELIX 5 AA5 PHE A 124 LEU A 137 1 14 HELIX 6 AA6 LEU A 142 GLY A 153 1 12 HELIX 7 AA7 ASP A 155 LYS A 165 1 11 HELIX 8 AA8 LEU A 166 HIS A 171 5 6 HELIX 9 AA9 THR A 193 GLU A 201 1 9 HELIX 10 AB1 PRO A 203 GLN A 214 1 12 HELIX 11 AB2 MET A 215 LYS A 220 1 6 HELIX 12 AB3 ASP A 221 ARG A 236 1 16 HELIX 13 AB4 ASP A 275 LEU A 285 1 11 HELIX 14 AB5 ASP A 291 LEU A 308 1 18 HELIX 15 AB6 ASN A 351 GLY A 367 1 17 HELIX 16 AB7 TRP A 368 PHE A 383 1 16 HELIX 17 AB8 ASP A 387 THR A 391 5 5 HELIX 18 AB9 PRO B 12 GLY B 21 1 10 HELIX 19 AC1 ASN B 24 CYS B 45 1 22 HELIX 20 AC2 SER B 48 ILE B 63 1 16 HELIX 21 AC3 LEU B 64 GLY B 68 5 5 HELIX 22 AC4 PHE B 124 LEU B 137 1 14 HELIX 23 AC5 LEU B 142 GLY B 153 1 12 HELIX 24 AC6 ASP B 155 LYS B 165 1 11 HELIX 25 AC7 LEU B 166 HIS B 171 5 6 HELIX 26 AC8 THR B 193 GLU B 201 1 9 HELIX 27 AC9 PRO B 203 GLN B 214 1 12 HELIX 28 AD1 MET B 215 ASP B 221 1 7 HELIX 29 AD2 ASP B 221 ARG B 236 1 16 HELIX 30 AD3 ASP B 275 LEU B 285 1 11 HELIX 31 AD4 ASP B 291 LEU B 308 1 18 HELIX 32 AD5 ASN B 351 GLY B 367 1 17 HELIX 33 AD6 TRP B 368 PHE B 383 1 16 SHEET 1 AA111 LEU A 90 ILE A 96 0 SHEET 2 AA111 THR A 101 LEU A 107 -1 O ARG A 104 N SER A 93 SHEET 3 AA111 VAL A 174 LYS A 181 -1 O LEU A 178 N LEU A 105 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 ILE A 327 N LEU A 269 SHEET 8 AA111 GLN A 342 PRO A 346 -1 O TYR A 344 N GLY A 326 SHEET 9 AA111 HIS A 395 SER A 403 -1 O LEU A 398 N PHE A 345 SHEET 10 AA111 GLY A 407 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 92 O TYR A 414 SHEET 1 AA211 LEU B 90 ILE B 96 0 SHEET 2 AA211 THR B 101 LEU B 107 -1 O ARG B 104 N SER B 93 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 TYR B 268 N LEU B 252 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 GLN B 342 N ASN B 328 SHEET 9 AA211 HIS B 395 SER B 403 -1 O LEU B 398 N PHE B 345 SHEET 10 AA211 GLY B 407 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 CISPEP 1 PRO A 247 PRO A 248 0 -4.00 CISPEP 2 PRO B 247 PRO B 248 0 1.38 SITE 1 AC1 3 GLY A 82 GLU A 169 ARG A 396 SITE 1 AC2 7 ARG A 104 LYS A 188 TYR A 190 GLN A 342 SITE 2 AC2 7 TYR A 344 ASN A 411 TYR A 413 SITE 1 AC3 9 ARG B 104 LYS B 188 TYR B 190 ARG B 264 SITE 2 AC3 9 TYR B 268 GLN B 342 TYR B 344 ASN B 411 SITE 3 AC3 9 TYR B 413 CRYST1 96.650 136.080 68.840 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 0.010347 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007349 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014527 0.00000