HEADER TRANSCRIPTION/DNA 17-DEC-17 5YZZ TITLE ATVAL1 B3 DOMAIN IN COMPLEX WITH 13BP-DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*AP*TP*TP*CP*TP*GP*CP*AP*TP*GP*GP*AP*T)-3'); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'-D(*TP*AP*TP*CP*CP*AP*TP*GP*CP*AP*GP*AP*A)-3'); COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: B3 DOMAIN-CONTAINING TRANSCRIPTION REPRESSOR VAL1; COMPND 11 CHAIN: C; COMPND 12 FRAGMENT: B3 DOMAIN, DNA BINDING DOMAIN; COMPND 13 SYNONYM: PROTEIN HIGH-LEVEL EXPRESSION OF SUGAR-INDUCIBLE 2,PROTEIN COMPND 14 VP1/ABI3-LIKE 1; COMPND 15 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 8 ORGANISM_TAXID: 32630; SOURCE 9 MOL_ID: 3; SOURCE 10 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; SOURCE 11 ORGANISM_COMMON: MOUSE-EAR CRESS; SOURCE 12 ORGANISM_TAXID: 3702; SOURCE 13 GENE: VAL1, HSI2, AT2G30470, T6B20.17; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TRANSCRIPTIONAL FACTOR, VAL1, B3 DOMAIN, DNA COMPLEX, FLC, PLANT, KEYWDS 2 TRANSCRIPTION, TRANSCRIPTION-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR B.X.WU,M.M.ZHANG REVDAT 3 22-NOV-23 5YZZ 1 REMARK REVDAT 2 30-MAY-18 5YZZ 1 JRNL REVDAT 1 02-MAY-18 5YZZ 0 JRNL AUTH B.X.WU,M.M.ZHANG,S.C.SU,H.H.LIU,J.H.GAN,J.B.MA JRNL TITL STRUCTURAL INSIGHT INTO THE ROLE OF VAL1 B3 DOMAIN FOR JRNL TITL 2 TARGETING TO FLC LOCUS IN ARABIDOPSIS THALIANA. JRNL REF BIOCHEM. BIOPHYS. RES. 2018 JRNL REF 2 COMMUN. JRNL REFN ESSN 1090-2104 JRNL PMID 29733847 JRNL DOI 10.1016/J.BBRC.2018.05.002 REMARK 2 REMARK 2 RESOLUTION. 2.58 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0189 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) : 2.58 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 84.6 REMARK 3 NUMBER OF REFLECTIONS : 7414 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) : 0.228 REMARK 3 R VALUE (WORKING SET) : 0.226 REMARK 3 FREE R VALUE : 0.255 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.300 REMARK 3 FREE R VALUE TEST SET COUNT : 415 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) : 2.59 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.65 REMARK 3 REFLECTION IN BIN (WORKING SET) : 182 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 28.55 REMARK 3 BIN R VALUE (WORKING SET) : 0.4940 REMARK 3 BIN FREE R VALUE SET COUNT : 11 REMARK 3 BIN FREE R VALUE : 0.4990 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 866 REMARK 3 NUCLEIC ACID ATOMS : 527 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 44.34 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.98000 REMARK 3 B22 (A**2) : -0.98000 REMARK 3 B33 (A**2) : 1.97000 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): 0.547 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.308 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.247 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 13.293 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.926 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.893 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1475 ; 0.013 ; 0.016 REMARK 3 BOND LENGTHS OTHERS (A): 1135 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2104 ; 1.895 ; 1.626 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2647 ; 1.326 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 110 ; 9.497 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 38 ;34.024 ;23.158 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 152 ;19.037 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 8 ;22.200 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 209 ; 0.099 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1280 ; 0.009 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 305 ; 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): 443 ; 3.811 ; 4.473 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 442 ; 3.783 ; 4.464 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 552 ; 6.491 ; 6.667 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 553 ; 6.496 ; 6.681 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1032 ; 3.972 ; 4.469 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1030 ; 3.953 ; 4.460 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1552 ; 6.459 ; 6.629 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 1744 ; 8.865 ;43.304 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 1744 ; 8.865 ;43.279 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 5YZZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-DEC-17. REMARK 100 THE DEPOSITION ID IS D_1300006198. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-NOV-17 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 : SSRF REMARK 200 BEAMLINE : BL18U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97853 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9191 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.580 REMARK 200 RESOLUTION RANGE LOW (A) : 74.970 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 13.90 REMARK 200 R MERGE (I) : 0.07700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 29.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.58 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.67 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 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 REMARK 200 STARTING MODEL: 5YZY REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% (W/V) PEG 5000 MME, 0.1M TRIS REMARK 280 BASE/HYDROCHLORIC ACID PH 8.0, 0.2M LITHIUM SULFATE, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 41 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 3555 -Y,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X,Z+3/4 REMARK 290 5555 -X+1/2,Y,-Z+3/4 REMARK 290 6555 X,-Y+1/2,-Z+1/4 REMARK 290 7555 Y+1/2,X+1/2,-Z+1/2 REMARK 290 8555 -Y,-X,-Z REMARK 290 9555 X+1/2,Y+1/2,Z+1/2 REMARK 290 10555 -X,-Y,Z REMARK 290 11555 -Y+1/2,X,Z+3/4 REMARK 290 12555 Y,-X+1/2,Z+1/4 REMARK 290 13555 -X,Y+1/2,-Z+1/4 REMARK 290 14555 X+1/2,-Y,-Z+3/4 REMARK 290 15555 Y,X,-Z REMARK 290 16555 -Y+1/2,-X+1/2,-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 43.44800 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 43.44800 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 74.11850 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 43.44800 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 37.05925 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 43.44800 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 111.17775 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 43.44800 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 111.17775 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 43.44800 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 37.05925 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 43.44800 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 43.44800 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 74.11850 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 0.00000 REMARK 290 SMTRY1 9 1.000000 0.000000 0.000000 43.44800 REMARK 290 SMTRY2 9 0.000000 1.000000 0.000000 43.44800 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 74.11850 REMARK 290 SMTRY1 10 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 11 0.000000 -1.000000 0.000000 43.44800 REMARK 290 SMTRY2 11 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 1.000000 111.17775 REMARK 290 SMTRY1 12 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 12 -1.000000 0.000000 0.000000 43.44800 REMARK 290 SMTRY3 12 0.000000 0.000000 1.000000 37.05925 REMARK 290 SMTRY1 13 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 43.44800 REMARK 290 SMTRY3 13 0.000000 0.000000 -1.000000 37.05925 REMARK 290 SMTRY1 14 1.000000 0.000000 0.000000 43.44800 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 14 0.000000 0.000000 -1.000000 111.17775 REMARK 290 SMTRY1 15 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 15 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 16 0.000000 -1.000000 0.000000 43.44800 REMARK 290 SMTRY2 16 -1.000000 0.000000 0.000000 43.44800 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 74.11850 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2550 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10360 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 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 PRO C 273 REMARK 465 LYS C 274 REMARK 465 TYR C 275 REMARK 465 THR C 276 REMARK 465 ASP C 277 REMARK 465 LYS C 278 REMARK 465 GLU C 279 REMARK 465 VAL C 280 REMARK 465 GLN C 281 REMARK 465 GLN C 282 REMARK 465 ILE C 283 REMARK 465 SER C 284 REMARK 465 GLY C 285 REMARK 465 ASN C 286 REMARK 465 ALA C 398 REMARK 465 GLY C 399 REMARK 465 ASP C 400 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 DT A 13 O5' - P - OP1 ANGL. DEV. = -5.5 DEGREES REMARK 500 DC B 5 O5' - P - OP1 ANGL. DEV. = -6.9 DEGREES REMARK 500 DC B 5 O5' - P - OP2 ANGL. DEV. = 7.2 DEGREES REMARK 500 DC B 9 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DA B 10 C5' - C4' - O4' 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 LEU C 294 -63.89 -99.98 REMARK 500 PRO C 322 155.71 -49.55 REMARK 500 ARG C 338 40.04 -101.02 REMARK 500 ASN C 352 -118.83 54.69 REMARK 500 SER C 354 -135.45 -110.83 REMARK 500 ALA C 396 -47.45 -27.66 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 VAL C 358 LEU C 359 149.45 REMARK 500 REMARK 500 REMARK: NULL DBREF 5YZZ A 1 13 PDB 5YZZ 5YZZ 1 13 DBREF 5YZZ B 1 13 PDB 5YZZ 5YZZ 1 13 DBREF 5YZZ C 273 400 UNP Q8W4L5 VAL1_ARATH 273 400 SEQRES 1 A 13 DA DT DT DC DT DG DC DA DT DG DG DA DT SEQRES 1 B 13 DT DA DT DC DC DA DT DG DC DA DG DA DA SEQRES 1 C 128 PRO LYS TYR THR ASP LYS GLU VAL GLN GLN ILE SER GLY SEQRES 2 C 128 ASN LEU ASN LEU ASN ILE VAL PRO LEU PHE GLU LYS THR SEQRES 3 C 128 LEU SER ALA SER ASP ALA GLY ARG ILE GLY ARG LEU VAL SEQRES 4 C 128 LEU PRO LYS ALA CYS ALA GLU ALA TYR PHE PRO PRO ILE SEQRES 5 C 128 SER GLN SER GLU GLY ILE PRO LEU LYS ILE GLN ASP VAL SEQRES 6 C 128 ARG GLY ARG GLU TRP THR PHE GLN PHE ARG TYR TRP PRO SEQRES 7 C 128 ASN ASN ASN SER ARG MET TYR VAL LEU GLU GLY VAL THR SEQRES 8 C 128 PRO CYS ILE GLN SER MET MET LEU GLN ALA GLY ASP THR SEQRES 9 C 128 VAL THR PHE SER ARG VAL ASP PRO GLY GLY LYS LEU ILE SEQRES 10 C 128 MET GLY SER ARG LYS ALA ALA ASN ALA GLY ASP HELIX 1 AA1 SER C 300 GLY C 305 1 6 HELIX 2 AA2 PRO C 313 PHE C 321 1 9 HELIX 3 AA3 VAL C 362 MET C 369 1 8 SHEET 1 AA1 7 ASN C 290 THR C 298 0 SHEET 2 AA1 7 THR C 376 ASP C 383 -1 O ARG C 381 N VAL C 292 SHEET 3 AA1 7 LYS C 387 ARG C 393 -1 O ARG C 393 N THR C 376 SHEET 4 AA1 7 ILE C 330 ASP C 336 1 N GLN C 335 O LEU C 388 SHEET 5 AA1 7 GLU C 341 ASN C 351 -1 O TRP C 342 N ILE C 334 SHEET 6 AA1 7 SER C 354 GLU C 360 -1 O SER C 354 N ASN C 351 SHEET 7 AA1 7 ARG C 309 LEU C 312 -1 N LEU C 310 O LEU C 359 CISPEP 1 ASP C 383 PRO C 384 0 -12.45 CRYST1 86.896 86.896 148.237 90.00 90.00 90.00 I 41 2 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 0.011508 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011508 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006746 0.00000