HEADER HORMONE 03-MAR-19 6O5J TITLE CRYSTAL STRUCTURE OF DAD2 BOUND TO QUINAZOLINONE DERIVATIVE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROBABLE STRIGOLACTONE ESTERASE DAD2; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: PROTEIN DECREASED APICAL DOMINANCE 2; COMPND 5 EC: 3.1.-.-; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PETUNIA HYBRIDA; SOURCE 3 ORGANISM_COMMON: PETUNIA; SOURCE 4 ORGANISM_TAXID: 4102; SOURCE 5 GENE: DAD2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA GAMI 2; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PDEST566 KEYWDS ALPHA/BETA HYDROLASE, HORMONE EXPDTA X-RAY DIFFRACTION AUTHOR C.HAMIAUX REVDAT 3 11-OCT-23 6O5J 1 REMARK REVDAT 2 10-JUL-19 6O5J 1 JRNL REVDAT 1 26-JUN-19 6O5J 0 JRNL AUTH C.HAMIAUX,L.LARSEN,H.W.LEE,Z.LUO,P.SHARMA,B.C.HAWKINS, JRNL AUTH 2 N.B.PERRY,K.C.SNOWDEN JRNL TITL CHEMICAL SYNTHESIS AND CHARACTERIZATION OF A NEW JRNL TITL 2 QUINAZOLINEDIONE COMPETITIVE ANTAGONIST FOR STRIGOLACTONE JRNL TITL 3 RECEPTORS WITH AN UNEXPECTED BINDING MODE. JRNL REF BIOCHEM.J. V. 476 1843 2019 JRNL REFN ESSN 1470-8728 JRNL PMID 31186286 JRNL DOI 10.1042/BCJ20190288 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH C.HAMIAUX,R.S.M.DRUMMOND,Z.LUO,H.W.LEE,P.SHARMA,B.J.JANSSEN, REMARK 1 AUTH 2 N.B.PERRY,W.A.DENNY,K.C.SNOWDEN REMARK 1 TITL INHIBITION OF STRIGOLACTONE RECEPTORS BY N-PHENYLANTHRANILIC REMARK 1 TITL 2 ACID DERIVATIVES: STRUCTURAL AND FUNCTIONAL INSIGHTS REMARK 1 REF J. BIOL. CHEM. V. 293 6530 2018 REMARK 1 REFN ESSN 1083-351X REMARK 1 PMID 29523686 REMARK 1 DOI 10.1074/JBC.RA117.001154 REMARK 1 REFERENCE 2 REMARK 1 AUTH C.HAMIAUX,R.S.DRUMMOND,B.J.JANSSEN,S.E.LEDGER,J.M.COONEY, REMARK 1 AUTH 2 R.D.NEWCOMB,K.C.SNOWDEN REMARK 1 TITL DAD2 IS AN A/B HYDROLASE LIKELY TO BE INVOLVED IN THE REMARK 1 TITL 2 PERCEPTION OF THE PLANT BRANCHING HORMONE, STRIGOLACTONE REMARK 1 REF CURR. BIOL. V. 22 2032 2012 REMARK 1 REFN ISSN 1879-0445 REMARK 1 PMID 22959345 REMARK 1 DOI 10.1016/J.CUB.2012.08.007 REMARK 2 REMARK 2 RESOLUTION. 1.63 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0238 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) : 1.63 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.37 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.5 REMARK 3 NUMBER OF REFLECTIONS : 56359 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) : 0.146 REMARK 3 R VALUE (WORKING SET) : 0.144 REMARK 3 FREE R VALUE : 0.182 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2954 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) : 1.63 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.67 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2613 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 56.34 REMARK 3 BIN R VALUE (WORKING SET) : 0.2030 REMARK 3 BIN FREE R VALUE SET COUNT : 131 REMARK 3 BIN FREE R VALUE : 0.2160 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4154 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 67 REMARK 3 SOLVENT ATOMS : 514 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.48 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.09000 REMARK 3 B22 (A**2) : -0.52000 REMARK 3 B33 (A**2) : 0.48000 REMARK 3 B12 (A**2) : 0.10000 REMARK 3 B13 (A**2) : -0.02000 REMARK 3 B23 (A**2) : -0.08000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.089 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.091 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.063 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.659 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.971 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.955 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4445 ; 0.016 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 4085 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6070 ; 1.947 ; 1.646 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9401 ; 1.594 ; 1.574 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 553 ; 6.042 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 243 ;26.841 ;20.782 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 683 ;13.222 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 37 ;18.613 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 554 ; 0.113 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5092 ; 0.012 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1031 ; 0.001 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 1 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 3 266 B 3 266 8761 0.080 0.050 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 3 A 266 REMARK 3 ORIGIN FOR THE GROUP (A): -18.2770 57.7940 -17.2090 REMARK 3 T TENSOR REMARK 3 T11: 0.0087 T22: 0.1457 REMARK 3 T33: 0.0220 T12: -0.0342 REMARK 3 T13: 0.0057 T23: -0.0299 REMARK 3 L TENSOR REMARK 3 L11: 1.6998 L22: 0.6332 REMARK 3 L33: 1.1198 L12: 0.0936 REMARK 3 L13: 0.2729 L23: 0.1247 REMARK 3 S TENSOR REMARK 3 S11: -0.0008 S12: -0.0703 S13: -0.0111 REMARK 3 S21: -0.0067 S22: -0.0244 S23: -0.0158 REMARK 3 S31: 0.0039 S32: -0.0252 S33: 0.0252 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 3 B 266 REMARK 3 ORIGIN FOR THE GROUP (A): -15.4540 76.3930 17.8040 REMARK 3 T TENSOR REMARK 3 T11: 0.0087 T22: 0.1708 REMARK 3 T33: 0.0211 T12: -0.0228 REMARK 3 T13: 0.0040 T23: -0.0296 REMARK 3 L TENSOR REMARK 3 L11: 1.8575 L22: 0.8672 REMARK 3 L33: 1.2750 L12: 0.2160 REMARK 3 L13: 0.0734 L23: 0.4164 REMARK 3 S TENSOR REMARK 3 S11: 0.0561 S12: 0.1568 S13: -0.0267 REMARK 3 S21: -0.0073 S22: 0.0186 S23: 0.0133 REMARK 3 S31: -0.0324 S32: -0.0342 S33: -0.0747 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.00 REMARK 3 ION PROBE RADIUS : 0.70 REMARK 3 SHRINKAGE RADIUS : 0.70 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : WITH TLS ADDED REMARK 4 REMARK 4 6O5J COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-MAR-19. REMARK 100 THE DEPOSITION ID IS D_1000240002. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-FEB-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9537 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.17 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 62194 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.630 REMARK 200 RESOLUTION RANGE LOW (A) : 31.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.63 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.66 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.90 REMARK 200 R MERGE FOR SHELL (I) : 0.60900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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: PHASER 2.5.7 REMARK 200 STARTING MODEL: 4DNP REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.98 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS/ACETATE, 0.2M MGCL2, 31% PEG REMARK 280 3350, PH 8.5, VAPOR DIFFUSION, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 O HOH B 463 O HOH B 539 1.87 REMARK 500 NE2 HIS A 218 O HOH A 401 2.06 REMARK 500 OD2 ASP A 61 O HOH A 402 2.09 REMARK 500 OE1 GLU B 129 O HOH B 401 2.09 REMARK 500 NH1 ARG B 109 O HOH B 402 2.11 REMARK 500 O HOH B 583 O HOH B 596 2.18 REMARK 500 O HOH A 634 O HOH A 645 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 O HOH B 588 O HOH B 596 1455 2.13 REMARK 500 O HOH A 427 O HOH B 424 1554 2.13 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 ASP A 184 C ASP A 184 O 0.119 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 108 NE - CZ - NH2 ANGL. DEV. = -4.1 DEGREES REMARK 500 PHE A 212 CB - CG - CD1 ANGL. DEV. = 4.5 DEGREES REMARK 500 ARG B 108 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 ARG B 109 NE - CZ - NH2 ANGL. DEV. = -3.1 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 29 -169.15 -125.93 REMARK 500 SER A 96 -128.10 60.22 REMARK 500 LEU A 247 61.32 -119.54 REMARK 500 ALA A 252 57.66 -144.11 REMARK 500 SER B 96 -128.76 60.74 REMARK 500 ARG B 124 122.47 -171.61 REMARK 500 LEU B 247 63.80 -118.15 REMARK 500 ALA B 252 58.55 -144.78 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 A 649 DISTANCE = 5.85 ANGSTROMS REMARK 525 HOH A 650 DISTANCE = 6.22 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue LM7 A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue LM7 B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 303 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4DNP RELATED DB: PDB REMARK 900 DAD2 APO STRUCTURE REMARK 900 RELATED ID: 6AP6 RELATED DB: PDB REMARK 900 DAD2 BOUND TO TOLFENAMIC ACID REMARK 900 RELATED ID: 6AP7 RELATED DB: PDB REMARK 900 DAD2 BOUND TO 2-(2-METHYL-3-NITROANILINO)BENZOIC ACID DBREF 6O5J A 3 266 UNP J9U5U9 DAD2_PETHY 3 266 DBREF 6O5J B 3 266 UNP J9U5U9 DAD2_PETHY 3 266 SEQADV 6O5J GLN A 89 UNP J9U5U9 CYS 89 ENGINEERED MUTATION SEQADV 6O5J GLN B 89 UNP J9U5U9 CYS 89 ENGINEERED MUTATION SEQRES 1 A 264 GLN THR LEU LEU ASP ALA LEU ASN VAL ARG VAL VAL GLY SEQRES 2 A 264 SER GLY GLU ARG VAL LEU VAL LEU ALA HIS GLY PHE GLY SEQRES 3 A 264 THR ASP GLN SER ALA TRP ASN ARG ILE LEU PRO PHE PHE SEQRES 4 A 264 LEU ARG ASP TYR ARG VAL VAL LEU TYR ASP LEU VAL CYS SEQRES 5 A 264 ALA GLY SER VAL ASN PRO ASP PHE PHE ASP PHE ARG ARG SEQRES 6 A 264 TYR THR THR LEU ASP PRO TYR VAL ASP ASP LEU LEU HIS SEQRES 7 A 264 ILE LEU ASP ALA LEU GLY ILE ASP GLN CYS ALA TYR VAL SEQRES 8 A 264 GLY HIS SER VAL SER ALA MET ILE GLY ILE LEU ALA SER SEQRES 9 A 264 ILE ARG ARG PRO GLU LEU PHE SER LYS LEU ILE LEU ILE SEQRES 10 A 264 GLY ALA SER PRO ARG PHE LEU ASN ASP GLU ASP TYR HIS SEQRES 11 A 264 GLY GLY PHE GLU GLN GLY GLU ILE GLU LYS VAL PHE SER SEQRES 12 A 264 ALA MET GLU ALA ASN TYR GLU ALA TRP VAL ASN GLY PHE SEQRES 13 A 264 ALA PRO LEU ALA VAL GLY ALA ASP VAL PRO ALA ALA VAL SEQRES 14 A 264 ARG GLU PHE SER ARG THR LEU PHE ASN MET ARG PRO ASP SEQRES 15 A 264 ILE THR LEU PHE VAL SER ARG THR VAL PHE ASN SER ASP SEQRES 16 A 264 MET ARG GLY VAL LEU GLY LEU VAL LYS VAL PRO CYS HIS SEQRES 17 A 264 ILE PHE GLN THR ALA ARG ASP HIS SER VAL PRO ALA SER SEQRES 18 A 264 VAL ALA THR TYR LEU LYS ASN HIS LEU GLY GLY LYS ASN SEQRES 19 A 264 THR VAL HIS TRP LEU ASN ILE GLU GLY HIS LEU PRO HIS SEQRES 20 A 264 LEU SER ALA PRO THR LEU LEU ALA GLN GLU LEU ARG ARG SEQRES 21 A 264 ALA LEU SER HIS SEQRES 1 B 264 GLN THR LEU LEU ASP ALA LEU ASN VAL ARG VAL VAL GLY SEQRES 2 B 264 SER GLY GLU ARG VAL LEU VAL LEU ALA HIS GLY PHE GLY SEQRES 3 B 264 THR ASP GLN SER ALA TRP ASN ARG ILE LEU PRO PHE PHE SEQRES 4 B 264 LEU ARG ASP TYR ARG VAL VAL LEU TYR ASP LEU VAL CYS SEQRES 5 B 264 ALA GLY SER VAL ASN PRO ASP PHE PHE ASP PHE ARG ARG SEQRES 6 B 264 TYR THR THR LEU ASP PRO TYR VAL ASP ASP LEU LEU HIS SEQRES 7 B 264 ILE LEU ASP ALA LEU GLY ILE ASP GLN CYS ALA TYR VAL SEQRES 8 B 264 GLY HIS SER VAL SER ALA MET ILE GLY ILE LEU ALA SER SEQRES 9 B 264 ILE ARG ARG PRO GLU LEU PHE SER LYS LEU ILE LEU ILE SEQRES 10 B 264 GLY ALA SER PRO ARG PHE LEU ASN ASP GLU ASP TYR HIS SEQRES 11 B 264 GLY GLY PHE GLU GLN GLY GLU ILE GLU LYS VAL PHE SER SEQRES 12 B 264 ALA MET GLU ALA ASN TYR GLU ALA TRP VAL ASN GLY PHE SEQRES 13 B 264 ALA PRO LEU ALA VAL GLY ALA ASP VAL PRO ALA ALA VAL SEQRES 14 B 264 ARG GLU PHE SER ARG THR LEU PHE ASN MET ARG PRO ASP SEQRES 15 B 264 ILE THR LEU PHE VAL SER ARG THR VAL PHE ASN SER ASP SEQRES 16 B 264 MET ARG GLY VAL LEU GLY LEU VAL LYS VAL PRO CYS HIS SEQRES 17 B 264 ILE PHE GLN THR ALA ARG ASP HIS SER VAL PRO ALA SER SEQRES 18 B 264 VAL ALA THR TYR LEU LYS ASN HIS LEU GLY GLY LYS ASN SEQRES 19 B 264 THR VAL HIS TRP LEU ASN ILE GLU GLY HIS LEU PRO HIS SEQRES 20 B 264 LEU SER ALA PRO THR LEU LEU ALA GLN GLU LEU ARG ARG SEQRES 21 B 264 ALA LEU SER HIS HET LM7 A 301 22 HET GOL A 302 6 HET ACT A 303 4 HET LM7 B 301 22 HET PEG B 302 7 HET GOL B 303 6 HETNAM LM7 1-(4-HYDROXY-3-NITROPHENYL)QUINAZOLINE-2,4(1H,3H)-DIONE HETNAM GOL GLYCEROL HETNAM ACT ACETATE ION HETNAM PEG DI(HYDROXYETHYL)ETHER HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 LM7 2(C14 H9 N3 O5) FORMUL 4 GOL 2(C3 H8 O3) FORMUL 5 ACT C2 H3 O2 1- FORMUL 7 PEG C4 H10 O3 FORMUL 9 HOH *514(H2 O) HELIX 1 AA1 GLN A 3 LEU A 9 1 7 HELIX 2 AA2 ASP A 30 ASN A 35 5 6 HELIX 3 AA3 ILE A 37 PHE A 41 5 5 HELIX 4 AA4 ASN A 59 PHE A 63 5 5 HELIX 5 AA5 LEU A 71 LEU A 85 1 15 HELIX 6 AA6 SER A 96 ARG A 109 1 14 HELIX 7 AA7 GLU A 136 ASN A 150 1 15 HELIX 8 AA8 ASN A 150 GLY A 164 1 15 HELIX 9 AA9 VAL A 167 MET A 181 1 15 HELIX 10 AB1 ARG A 182 SER A 196 1 15 HELIX 11 AB2 MET A 198 VAL A 205 5 8 HELIX 12 AB3 PRO A 221 LEU A 232 1 12 HELIX 13 AB4 LEU A 247 ALA A 252 1 6 HELIX 14 AB5 ALA A 252 HIS A 266 1 15 HELIX 15 AB6 THR B 4 LEU B 9 1 6 HELIX 16 AB7 ASP B 30 ASN B 35 5 6 HELIX 17 AB8 ILE B 37 PHE B 41 5 5 HELIX 18 AB9 ASN B 59 PHE B 63 5 5 HELIX 19 AC1 LEU B 71 LEU B 85 1 15 HELIX 20 AC2 SER B 96 ARG B 109 1 14 HELIX 21 AC3 GLU B 136 ASN B 150 1 15 HELIX 22 AC4 ASN B 150 GLY B 164 1 15 HELIX 23 AC5 VAL B 167 PHE B 179 1 13 HELIX 24 AC6 ARG B 182 SER B 196 1 15 HELIX 25 AC7 MET B 198 VAL B 205 5 8 HELIX 26 AC8 PRO B 221 LEU B 232 1 12 HELIX 27 AC9 LEU B 247 ALA B 252 1 6 HELIX 28 AD1 ALA B 252 HIS B 266 1 15 SHEET 1 AA1 7 ARG A 12 VAL A 14 0 SHEET 2 AA1 7 ARG A 46 TYR A 50 -1 O VAL A 47 N VAL A 14 SHEET 3 AA1 7 VAL A 20 ALA A 24 1 N LEU A 21 O VAL A 48 SHEET 4 AA1 7 CYS A 90 HIS A 95 1 O VAL A 93 N VAL A 22 SHEET 5 AA1 7 PHE A 113 ILE A 119 1 O ILE A 117 N TYR A 92 SHEET 6 AA1 7 CYS A 209 ALA A 215 1 O PHE A 212 N LEU A 118 SHEET 7 AA1 7 ASN A 236 GLU A 244 1 O HIS A 239 N ILE A 211 SHEET 1 AA2 7 ARG B 12 VAL B 14 0 SHEET 2 AA2 7 ARG B 46 TYR B 50 -1 O VAL B 47 N VAL B 14 SHEET 3 AA2 7 VAL B 20 ALA B 24 1 N LEU B 21 O VAL B 48 SHEET 4 AA2 7 CYS B 90 HIS B 95 1 O VAL B 93 N VAL B 22 SHEET 5 AA2 7 PHE B 113 ILE B 119 1 O ILE B 117 N TYR B 92 SHEET 6 AA2 7 CYS B 209 ALA B 215 1 O PHE B 212 N LEU B 118 SHEET 7 AA2 7 ASN B 236 GLU B 244 1 O HIS B 239 N ILE B 211 SITE 1 AC1 17 PHE A 27 SER A 96 PHE A 125 PHE A 135 SITE 2 AC1 17 VAL A 143 TRP A 154 PHE A 158 PHE A 174 SITE 3 AC1 17 SER A 190 PHE A 194 HIS A 218 SER A 219 SITE 4 AC1 17 HIS A 246 HOH A 401 HOH A 448 HOH A 483 SITE 5 AC1 17 HOH A 515 SITE 1 AC2 5 TYR A 131 HIS A 132 SER A 223 VAL A 224 SITE 2 AC2 5 ASN B 230 SITE 1 AC3 5 ARG A 36 ASP A 72 PRO A 253 THR A 254 SITE 2 AC3 5 HOH A 420 SITE 1 AC4 16 PHE B 27 SER B 96 PHE B 125 PHE B 135 SITE 2 AC4 16 VAL B 143 TRP B 154 PHE B 158 PHE B 174 SITE 3 AC4 16 SER B 190 PHE B 194 HIS B 218 SER B 219 SITE 4 AC4 16 HIS B 246 HOH B 425 HOH B 473 HOH B 493 SITE 1 AC5 3 LEU B 6 ASP B 7 VAL B 11 SITE 1 AC6 6 HOH A 423 ASP B 130 HIS B 132 SER B 223 SITE 2 AC6 6 VAL B 224 HOH B 578 CRYST1 36.630 56.830 68.800 95.69 94.59 108.74 P 1 2 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 0.027300 0.009262 0.003447 0.00000 SCALE2 0.000000 0.018581 0.002480 0.00000 SCALE3 0.000000 0.000000 0.014711 0.00000