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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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