HEADER LYASE/LYASE INHIBITOR 06-APR-21 7MDS TITLE CRYSTAL STRUCTURE OF ATDHDPS1 IN COMPLEX WITH MBDTA-2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: 4-HYDROXY-TETRAHYDRODIPICOLINATE SYNTHASE 1, CHLOROPLASTIC; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: HTPA SYNTHASE 1; COMPND 5 EC: 4.3.3.7; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; SOURCE 3 ORGANISM_COMMON: MOUSE-EAR CRESS; SOURCE 4 ORGANISM_TAXID: 3702; SOURCE 5 GENE: DHDPS1, DHDPS, DHPS1, AT3G60880, T4C21_290; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS HERBICIDE, LYSINE BIOSYNTHESIS, BIOSYNTHETIC PROTEIN, LYASE-LYASE KEYWDS 2 INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR C.J.HALL,T.P.SOARES DA COSTA,S.PANJIKAR REVDAT 2 18-OCT-23 7MDS 1 REMARK REVDAT 1 04-AUG-21 7MDS 0 JRNL AUTH T.P.SOARES DA COSTA,C.J.HALL,S.PANJIKAR,J.A.WYLLIE, JRNL AUTH 2 R.M.CHRISTOFF,S.BAYAT,M.D.HULETT,B.M.ABBOTT,A.R.GENDALL, JRNL AUTH 3 M.A.PERUGINI JRNL TITL TOWARDS NOVEL HERBICIDE MODES OF ACTION BY INHIBITING LYSINE JRNL TITL 2 BIOSYNTHESIS IN PLANTS. JRNL REF ELIFE V. 10 2021 JRNL REFN ESSN 2050-084X JRNL PMID 34313586 JRNL DOI 10.7554/ELIFE.69444 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0257 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 37242 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.876 REMARK 3 FREE R VALUE TEST SET COUNT : 1071 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.35 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2405 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.46 REMARK 3 BIN R VALUE (WORKING SET) : 0.2220 REMARK 3 BIN FREE R VALUE SET COUNT : 73 REMARK 3 BIN FREE R VALUE : 0.2450 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4796 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 83 REMARK 3 SOLVENT ATOMS : 113 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 34.68 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 44.68 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.88700 REMARK 3 B22 (A**2) : 0.88700 REMARK 3 B33 (A**2) : -1.77400 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): 0.236 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.195 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.126 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.088 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.948 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.924 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4985 ; 0.007 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6772 ; 1.415 ; 1.637 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 616 ; 6.724 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 274 ;34.123 ;22.044 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 810 ;14.943 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 32 ;17.313 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 636 ; 0.107 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3922 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2397 ; 0.207 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3374 ; 0.313 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 231 ; 0.113 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2470 ; 3.424 ; 4.154 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3084 ; 4.429 ; 7.758 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2515 ; 6.130 ; 4.721 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 3688 ; 8.890 ; 8.530 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 NUMBER OF DIFFERENT NCS GROUPS : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : Chains A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 0 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL PLUS MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THEIR REMARK 3 RIDING POSITIONS REMARK 4 REMARK 4 7MDS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-APR-21. REMARK 100 THE DEPOSITION ID IS D_1000256021. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-NOV-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.95 REMARK 200 MONOCHROMATOR : SI REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 37390 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.290 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 13.10 REMARK 200 R MERGE (I) : 0.09900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 27.8500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.29 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.43 REMARK 200 COMPLETENESS FOR SHELL (%) : 1.0 REMARK 200 DATA REDUNDANCY IN SHELL : 12.80 REMARK 200 R MERGE FOR SHELL (I) : 0.39100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 7.920 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AUTO-RICKSHAW REMARK 200 STARTING MODEL: 6VVI REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.31 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.69 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES PH 7.5, 0.1 M NACL, 1.4 M REMARK 280 (NH4)2SO4, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 90.70500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 47.23500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 47.23500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 45.35250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 47.23500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 47.23500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 136.05750 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 47.23500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 47.23500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 45.35250 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 47.23500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 47.23500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 136.05750 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 90.70500 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: 13350 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 39030 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -113.0 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 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 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 654 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 28 REMARK 465 HIS A 29 REMARK 465 HIS A 30 REMARK 465 HIS A 31 REMARK 465 HIS A 32 REMARK 465 HIS A 33 REMARK 465 HIS A 34 REMARK 465 GLY A 35 REMARK 465 LYS A 36 REMARK 465 PRO A 37 REMARK 465 ALA A 38 REMARK 465 LEU A 39 REMARK 465 GLU A 40 REMARK 465 VAL A 41 REMARK 465 LEU A 42 REMARK 465 PHE A 43 REMARK 465 GLN A 44 REMARK 465 GLY A 45 REMARK 465 PRO A 46 REMARK 465 GLY A 47 REMARK 465 SER A 48 REMARK 465 MET A 49 REMARK 465 ARG A 50 REMARK 465 SER A 51 REMARK 465 LEU A 52 REMARK 465 GLU A 53 REMARK 465 ASP A 54 REMARK 465 LYS A 55 REMARK 465 ASN A 56 REMARK 465 ARG A 57 REMARK 465 THR A 58 REMARK 465 MET B 28 REMARK 465 HIS B 29 REMARK 465 HIS B 30 REMARK 465 HIS B 31 REMARK 465 HIS B 32 REMARK 465 HIS B 33 REMARK 465 HIS B 34 REMARK 465 GLY B 35 REMARK 465 LYS B 36 REMARK 465 PRO B 37 REMARK 465 ALA B 38 REMARK 465 LEU B 39 REMARK 465 GLU B 40 REMARK 465 VAL B 41 REMARK 465 LEU B 42 REMARK 465 PHE B 43 REMARK 465 GLN B 44 REMARK 465 GLY B 45 REMARK 465 PRO B 46 REMARK 465 GLY B 47 REMARK 465 SER B 48 REMARK 465 MET B 49 REMARK 465 ARG B 50 REMARK 465 SER B 51 REMARK 465 LEU B 52 REMARK 465 GLU B 53 REMARK 465 ASP B 54 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS B 55 CG CD CE NZ REMARK 470 ASN B 56 CG OD1 ND2 REMARK 470 ARG B 57 CG CD NE CZ NH1 NH2 REMARK 470 THR B 58 OG1 CG2 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 GLU A 118 CD GLU A 118 OE1 -0.075 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 273 CB - CG - CD ANGL. DEV. = 17.6 DEGREES REMARK 500 ARG A 280 CG - CD - NE ANGL. DEV. = -14.2 DEGREES REMARK 500 ARG B 280 NE - CZ - NH1 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 TYR A 170 -69.96 70.37 REMARK 500 ASN A 281 82.76 -157.25 REMARK 500 PRO A 301 33.58 -97.45 REMARK 500 LEU A 354 145.72 72.41 REMARK 500 TYR B 170 -74.75 69.98 REMARK 500 ASN B 281 82.27 -159.37 REMARK 500 PRO B 301 32.80 -98.13 REMARK 500 LEU B 354 145.71 71.32 REMARK 500 REMARK 500 REMARK: NULL DBREF 7MDS A 49 365 UNP Q9LZX6 DAPA1_ARATH 49 365 DBREF 7MDS B 49 365 UNP Q9LZX6 DAPA1_ARATH 49 365 SEQADV 7MDS MET A 28 UNP Q9LZX6 INITIATING METHIONINE SEQADV 7MDS HIS A 29 UNP Q9LZX6 EXPRESSION TAG SEQADV 7MDS HIS A 30 UNP Q9LZX6 EXPRESSION TAG SEQADV 7MDS HIS A 31 UNP Q9LZX6 EXPRESSION TAG SEQADV 7MDS HIS A 32 UNP Q9LZX6 EXPRESSION TAG SEQADV 7MDS HIS A 33 UNP Q9LZX6 EXPRESSION TAG SEQADV 7MDS HIS A 34 UNP Q9LZX6 EXPRESSION TAG SEQADV 7MDS GLY A 35 UNP Q9LZX6 EXPRESSION TAG SEQADV 7MDS LYS A 36 UNP Q9LZX6 EXPRESSION TAG SEQADV 7MDS PRO A 37 UNP Q9LZX6 EXPRESSION TAG SEQADV 7MDS ALA A 38 UNP Q9LZX6 EXPRESSION TAG SEQADV 7MDS LEU A 39 UNP Q9LZX6 EXPRESSION TAG SEQADV 7MDS GLU A 40 UNP Q9LZX6 EXPRESSION TAG SEQADV 7MDS VAL A 41 UNP Q9LZX6 EXPRESSION TAG SEQADV 7MDS LEU A 42 UNP Q9LZX6 EXPRESSION TAG SEQADV 7MDS PHE A 43 UNP Q9LZX6 EXPRESSION TAG SEQADV 7MDS GLN A 44 UNP Q9LZX6 EXPRESSION TAG SEQADV 7MDS GLY A 45 UNP Q9LZX6 EXPRESSION TAG SEQADV 7MDS PRO A 46 UNP Q9LZX6 EXPRESSION TAG SEQADV 7MDS GLY A 47 UNP Q9LZX6 EXPRESSION TAG SEQADV 7MDS SER A 48 UNP Q9LZX6 EXPRESSION TAG SEQADV 7MDS MET B 28 UNP Q9LZX6 INITIATING METHIONINE SEQADV 7MDS HIS B 29 UNP Q9LZX6 EXPRESSION TAG SEQADV 7MDS HIS B 30 UNP Q9LZX6 EXPRESSION TAG SEQADV 7MDS HIS B 31 UNP Q9LZX6 EXPRESSION TAG SEQADV 7MDS HIS B 32 UNP Q9LZX6 EXPRESSION TAG SEQADV 7MDS HIS B 33 UNP Q9LZX6 EXPRESSION TAG SEQADV 7MDS HIS B 34 UNP Q9LZX6 EXPRESSION TAG SEQADV 7MDS GLY B 35 UNP Q9LZX6 EXPRESSION TAG SEQADV 7MDS LYS B 36 UNP Q9LZX6 EXPRESSION TAG SEQADV 7MDS PRO B 37 UNP Q9LZX6 EXPRESSION TAG SEQADV 7MDS ALA B 38 UNP Q9LZX6 EXPRESSION TAG SEQADV 7MDS LEU B 39 UNP Q9LZX6 EXPRESSION TAG SEQADV 7MDS GLU B 40 UNP Q9LZX6 EXPRESSION TAG SEQADV 7MDS VAL B 41 UNP Q9LZX6 EXPRESSION TAG SEQADV 7MDS LEU B 42 UNP Q9LZX6 EXPRESSION TAG SEQADV 7MDS PHE B 43 UNP Q9LZX6 EXPRESSION TAG SEQADV 7MDS GLN B 44 UNP Q9LZX6 EXPRESSION TAG SEQADV 7MDS GLY B 45 UNP Q9LZX6 EXPRESSION TAG SEQADV 7MDS PRO B 46 UNP Q9LZX6 EXPRESSION TAG SEQADV 7MDS GLY B 47 UNP Q9LZX6 EXPRESSION TAG SEQADV 7MDS SER B 48 UNP Q9LZX6 EXPRESSION TAG SEQRES 1 A 338 MET HIS HIS HIS HIS HIS HIS GLY LYS PRO ALA LEU GLU SEQRES 2 A 338 VAL LEU PHE GLN GLY PRO GLY SER MET ARG SER LEU GLU SEQRES 3 A 338 ASP LYS ASN ARG THR ASN THR ASP ASP ILE ARG SER LEU SEQRES 4 A 338 ARG VAL ILE THR ALA ILE LYS THR PRO TYR LEU PRO ASP SEQRES 5 A 338 GLY ARG PHE ASP LEU GLN ALA TYR ASP ASP LEU VAL ASN SEQRES 6 A 338 THR GLN ILE GLU ASN GLY ALA GLU GLY VAL ILE VAL GLY SEQRES 7 A 338 GLY THR THR GLY GLU GLY GLN LEU MET SER TRP ASP GLU SEQRES 8 A 338 HIS ILE MET LEU ILE GLY HIS THR VAL ASN CYS PHE GLY SEQRES 9 A 338 GLY ARG ILE LYS VAL ILE GLY ASN THR GLY SER ASN SER SEQRES 10 A 338 THR ARG GLU ALA ILE HIS ALA THR GLU GLN GLY PHE ALA SEQRES 11 A 338 MET GLY MET HIS GLY ALA LEU HIS ILE ASN PRO TYR TYR SEQRES 12 A 338 GLY LYS THR SER ILE GLU GLY MET ASN ALA HIS PHE GLN SEQRES 13 A 338 THR VAL LEU HIS MET GLY PRO THR ILE ILE TYR ASN VAL SEQRES 14 A 338 PRO GLY ARG THR CYS GLN ASP ILE PRO PRO GLN VAL ILE SEQRES 15 A 338 PHE LYS LEU SER GLN ASN PRO ASN MET ALA GLY VAL LYS SEQRES 16 A 338 GLU CYS VAL GLY ASN ASN ARG VAL GLU GLU TYR THR GLU SEQRES 17 A 338 LYS GLY ILE VAL VAL TRP SER GLY ASN ASP ASP GLN CYS SEQRES 18 A 338 HIS ASP SER ARG TRP ASP HIS GLY ALA THR GLY VAL ILE SEQRES 19 A 338 SER VAL THR SER ASN LEU VAL PRO GLY LEU MET ARG LYS SEQRES 20 A 338 LEU MET PHE GLU GLY ARG ASN SER ALA LEU ASN ALA LYS SEQRES 21 A 338 LEU LEU PRO LEU MET ASP TRP LEU PHE GLN GLU PRO ASN SEQRES 22 A 338 PRO ILE GLY VAL ASN THR ALA LEU ALA GLN LEU GLY VAL SEQRES 23 A 338 ALA ARG PRO VAL PHE ARG LEU PRO TYR VAL PRO LEU PRO SEQRES 24 A 338 LEU SER LYS ARG ILE GLU PHE VAL LYS LEU VAL LYS GLU SEQRES 25 A 338 ILE GLY ARG GLU HIS PHE VAL GLY ASP ARG ASP VAL GLN SEQRES 26 A 338 VAL LEU ASP ASP ASP ASP PHE ILE LEU ILE GLY ARG TYR SEQRES 1 B 338 MET HIS HIS HIS HIS HIS HIS GLY LYS PRO ALA LEU GLU SEQRES 2 B 338 VAL LEU PHE GLN GLY PRO GLY SER MET ARG SER LEU GLU SEQRES 3 B 338 ASP LYS ASN ARG THR ASN THR ASP ASP ILE ARG SER LEU SEQRES 4 B 338 ARG VAL ILE THR ALA ILE LYS THR PRO TYR LEU PRO ASP SEQRES 5 B 338 GLY ARG PHE ASP LEU GLN ALA TYR ASP ASP LEU VAL ASN SEQRES 6 B 338 THR GLN ILE GLU ASN GLY ALA GLU GLY VAL ILE VAL GLY SEQRES 7 B 338 GLY THR THR GLY GLU GLY GLN LEU MET SER TRP ASP GLU SEQRES 8 B 338 HIS ILE MET LEU ILE GLY HIS THR VAL ASN CYS PHE GLY SEQRES 9 B 338 GLY ARG ILE LYS VAL ILE GLY ASN THR GLY SER ASN SER SEQRES 10 B 338 THR ARG GLU ALA ILE HIS ALA THR GLU GLN GLY PHE ALA SEQRES 11 B 338 MET GLY MET HIS GLY ALA LEU HIS ILE ASN PRO TYR TYR SEQRES 12 B 338 GLY LYS THR SER ILE GLU GLY MET ASN ALA HIS PHE GLN SEQRES 13 B 338 THR VAL LEU HIS MET GLY PRO THR ILE ILE TYR ASN VAL SEQRES 14 B 338 PRO GLY ARG THR CYS GLN ASP ILE PRO PRO GLN VAL ILE SEQRES 15 B 338 PHE LYS LEU SER GLN ASN PRO ASN MET ALA GLY VAL LYS SEQRES 16 B 338 GLU CYS VAL GLY ASN ASN ARG VAL GLU GLU TYR THR GLU SEQRES 17 B 338 LYS GLY ILE VAL VAL TRP SER GLY ASN ASP ASP GLN CYS SEQRES 18 B 338 HIS ASP SER ARG TRP ASP HIS GLY ALA THR GLY VAL ILE SEQRES 19 B 338 SER VAL THR SER ASN LEU VAL PRO GLY LEU MET ARG LYS SEQRES 20 B 338 LEU MET PHE GLU GLY ARG ASN SER ALA LEU ASN ALA LYS SEQRES 21 B 338 LEU LEU PRO LEU MET ASP TRP LEU PHE GLN GLU PRO ASN SEQRES 22 B 338 PRO ILE GLY VAL ASN THR ALA LEU ALA GLN LEU GLY VAL SEQRES 23 B 338 ALA ARG PRO VAL PHE ARG LEU PRO TYR VAL PRO LEU PRO SEQRES 24 B 338 LEU SER LYS ARG ILE GLU PHE VAL LYS LEU VAL LYS GLU SEQRES 25 B 338 ILE GLY ARG GLU HIS PHE VAL GLY ASP ARG ASP VAL GLN SEQRES 26 B 338 VAL LEU ASP ASP ASP ASP PHE ILE LEU ILE GLY ARG TYR HET YXP A 501 20 HET CL A 502 1 HET CL A 503 1 HET YXP B 401 20 HET YXP B 402 20 HET YXP B 403 20 HET CL B 404 1 HETNAM YXP {(5Z)-5-[(4-METHOXYPHENYL)METHYLIDENE]-2,4-DIOXO-1,3- HETNAM 2 YXP THIAZOLIDIN-3-YL}ACETIC ACID HETNAM CL CHLORIDE ION FORMUL 3 YXP 4(C13 H11 N O5 S) FORMUL 4 CL 3(CL 1-) FORMUL 10 HOH *113(H2 O) HELIX 1 AA1 ASN A 59 SER A 65 1 7 HELIX 2 AA2 ASP A 83 ASN A 97 1 15 HELIX 3 AA3 GLU A 110 MET A 114 5 5 HELIX 4 AA4 SER A 115 GLY A 131 1 17 HELIX 5 AA5 SER A 144 MET A 158 1 15 HELIX 6 AA6 SER A 174 HIS A 187 1 14 HELIX 7 AA7 VAL A 196 CYS A 201 1 6 HELIX 8 AA8 PRO A 205 GLN A 214 1 10 HELIX 9 AA9 GLY A 226 GLU A 235 1 10 HELIX 10 AB1 ASN A 244 HIS A 255 1 12 HELIX 11 AB2 VAL A 263 LEU A 267 5 5 HELIX 12 AB3 VAL A 268 GLU A 278 1 11 HELIX 13 AB4 ASN A 281 PHE A 296 1 16 HELIX 14 AB5 PRO A 301 LEU A 311 1 11 HELIX 15 AB6 PRO A 326 GLY A 341 1 16 HELIX 16 AB7 ARG A 342 PHE A 345 5 4 HELIX 17 AB8 ASP A 355 PHE A 359 5 5 HELIX 18 AB9 ASN B 56 SER B 65 1 10 HELIX 19 AC1 ASP B 83 ASN B 97 1 15 HELIX 20 AC2 GLU B 110 MET B 114 5 5 HELIX 21 AC3 SER B 115 GLY B 131 1 17 HELIX 22 AC4 SER B 144 MET B 158 1 15 HELIX 23 AC5 SER B 174 HIS B 187 1 14 HELIX 24 AC6 VAL B 196 CYS B 201 1 6 HELIX 25 AC7 PRO B 205 SER B 213 1 9 HELIX 26 AC8 GLY B 226 GLU B 235 1 10 HELIX 27 AC9 ASN B 244 ASP B 246 5 3 HELIX 28 AD1 GLN B 247 HIS B 255 1 9 HELIX 29 AD2 VAL B 263 LEU B 267 5 5 HELIX 30 AD3 VAL B 268 GLU B 278 1 11 HELIX 31 AD4 ASN B 281 PHE B 296 1 16 HELIX 32 AD5 PRO B 301 LEU B 311 1 11 HELIX 33 AD6 PRO B 326 GLY B 341 1 16 HELIX 34 AD7 ARG B 342 PHE B 345 5 4 HELIX 35 AD8 ASP B 355 PHE B 359 5 5 SHEET 1 AA1 9 VAL A 68 ALA A 71 0 SHEET 2 AA1 9 GLY A 101 VAL A 104 1 O GLY A 101 N THR A 70 SHEET 3 AA1 9 LYS A 135 ASN A 139 1 O ILE A 137 N VAL A 102 SHEET 4 AA1 9 GLY A 162 ILE A 166 1 O GLY A 162 N GLY A 138 SHEET 5 AA1 9 THR A 191 ASN A 195 1 O ILE A 192 N ALA A 163 SHEET 6 AA1 9 MET A 218 GLU A 223 1 O LYS A 222 N ILE A 193 SHEET 7 AA1 9 VAL A 240 SER A 242 1 O TRP A 241 N VAL A 221 SHEET 8 AA1 9 GLY A 259 SER A 262 1 O GLY A 259 N SER A 242 SHEET 9 AA1 9 VAL A 68 ALA A 71 1 N ILE A 69 O SER A 262 SHEET 1 AA2 2 VAL A 317 ARG A 319 0 SHEET 2 AA2 2 ILE A 360 ILE A 362 1 O ILE A 362 N PHE A 318 SHEET 1 AA3 9 VAL B 68 ALA B 71 0 SHEET 2 AA3 9 GLY B 101 VAL B 104 1 O ILE B 103 N THR B 70 SHEET 3 AA3 9 LYS B 135 ASN B 139 1 O ILE B 137 N VAL B 102 SHEET 4 AA3 9 GLY B 162 ILE B 166 1 O GLY B 162 N GLY B 138 SHEET 5 AA3 9 THR B 191 ASN B 195 1 O ILE B 192 N ALA B 163 SHEET 6 AA3 9 MET B 218 GLU B 223 1 O LYS B 222 N ILE B 193 SHEET 7 AA3 9 VAL B 240 SER B 242 1 O TRP B 241 N VAL B 221 SHEET 8 AA3 9 GLY B 259 SER B 262 1 O GLY B 259 N SER B 242 SHEET 9 AA3 9 VAL B 68 ALA B 71 1 N ILE B 69 O SER B 262 SHEET 1 AA4 2 VAL B 317 ARG B 319 0 SHEET 2 AA4 2 ILE B 360 ILE B 362 1 O ILE B 360 N PHE B 318 SSBOND 1 CYS A 201 CYS B 201 1555 1555 2.06 CISPEP 1 ASN A 300 PRO A 301 0 2.70 CISPEP 2 LEU A 320 PRO A 321 0 14.05 CISPEP 3 ASN B 300 PRO B 301 0 4.56 CISPEP 4 LEU B 320 PRO B 321 0 13.93 CRYST1 94.470 94.470 181.410 90.00 90.00 90.00 P 41 21 2 16 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 0.010585 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010585 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005512 0.00000