HEADER DNA BINDING PROTEIN/DNA 18-APR-19 6JW1 TITLE UNIVERSAL RVD R* ACCOMMODATES 5MC VIA WATER-MEDIATED INTERACTIONS COMPND MOL_ID: 1; COMPND 2 MOLECULE: TAL EFFECTOR; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'-D(*TP*GP*TP*CP*CP*CP*TP*TP*(5CM) COMPND 7 P*GP*CP*GP*TP*CP*TP*CP*T)-3'); COMPND 8 CHAIN: I, C; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: DNA (5'- COMPND 12 D(*AP*GP*AP*GP*AP*CP*GP*CP*GP*AP*AP*GP*GP*GP*AP*CP*A)-3'); COMPND 13 CHAIN: J, D; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: XANTHOMONAS CAMPESTRIS PV. ARMORACIAE; SOURCE 3 ORGANISM_TAXID: 338; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 MOL_ID: 2; SOURCE 7 SYNTHETIC: YES; SOURCE 8 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 9 ORGANISM_TAXID: 32630; SOURCE 10 MOL_ID: 3; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 13 ORGANISM_TAXID: 32630 KEYWDS METHYLATION TAL EFFECTOR COMPLEX, DNA BINDING PROTEIN-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR L.LIU,C.YI REVDAT 3 22-NOV-23 6JW1 1 REMARK REVDAT 2 04-NOV-20 6JW1 1 JRNL REVDAT 1 22-APR-20 6JW1 0 JRNL AUTH L.LIU,Y.ZHANG,M.LIU,W.WEI,C.YI,J.PENG JRNL TITL STRUCTURAL INSIGHTS INTO THE SPECIFIC RECOGNITION OF JRNL TITL 2 5-METHYLCYTOSINE AND 5-HYDROXYMETHYLCYTOSINE BY TAL JRNL TITL 3 EFFECTORS. JRNL REF J.MOL.BIOL. V. 432 1035 2020 JRNL REFN ESSN 1089-8638 JRNL PMID 31863750 JRNL DOI 10.1016/J.JMB.2019.11.023 REMARK 2 REMARK 2 RESOLUTION. 2.49 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0049 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) : 2.49 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 85.74 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 41879 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) : 0.232 REMARK 3 R VALUE (WORKING SET) : 0.229 REMARK 3 FREE R VALUE : 0.278 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2234 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) : 2.49 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.55 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2693 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 85.79 REMARK 3 BIN R VALUE (WORKING SET) : 0.3330 REMARK 3 BIN FREE R VALUE SET COUNT : 133 REMARK 3 BIN FREE R VALUE : 0.3600 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 7207 REMARK 3 NUCLEIC ACID ATOMS : 1382 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 43 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 59.93 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.11000 REMARK 3 B22 (A**2) : -4.54000 REMARK 3 B33 (A**2) : 5.28000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 1.36000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.632 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.321 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.287 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 13.243 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.936 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.896 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 8864 ; 0.010 ; 0.018 REMARK 3 BOND LENGTHS OTHERS (A): 8183 ; 0.004 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 12376 ; 1.546 ; 1.828 REMARK 3 BOND ANGLES OTHERS (DEGREES): 18802 ; 1.285 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 990 ; 6.322 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 275 ;39.971 ;25.818 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1189 ;18.033 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 34 ;20.497 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1440 ; 0.099 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 9312 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1868 ; 0.004 ; 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 : 3 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 230 725 B 230 725 29926 0.100 0.050 REMARK 3 2 I -2 14 C -2 14 1331 0.140 0.050 REMARK 3 3 J -14 2 D -14 2 1222 0.120 0.050 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 U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 6JW1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-APR-19. REMARK 100 THE DEPOSITION ID IS D_1300011792. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-OCT-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) : 0.9793 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 130 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 41879 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.490 REMARK 200 RESOLUTION RANGE LOW (A) : 85.740 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 2.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.49 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.53 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: 4GJP REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.56 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.59 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 8-10% PEG3350 (W/V), 10% ETHANOL AND REMARK 280 0.1M MES PH 6.7, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 43.68900 REMARK 290 SMTRY3 2 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6530 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23970 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -59.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, I, J 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6280 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24650 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -54.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, C, D 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 HIS A 726 REMARK 465 HIS A 727 REMARK 465 HIS B 726 REMARK 465 HIS B 727 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 MET A 230 CG SD CE REMARK 470 ARG A 236 CG CD NE CZ NH1 NH2 REMARK 470 DT I 14 C7 REMARK 470 MET B 230 CG SD CE REMARK 470 ARG B 236 CG CD NE CZ NH1 NH2 REMARK 470 HIS B 524 CG ND1 CD2 CE1 NE2 REMARK 470 DT C 14 C7 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 NE ARG B 711 OP1 DT C 12 1.57 REMARK 500 CZ ARG B 711 OP2 DT C 12 1.81 REMARK 500 NH1 ARG B 711 OP2 DT C 12 1.85 REMARK 500 NH2 ARG B 711 OP2 DT C 12 1.87 REMARK 500 O LEU B 588 O HIS B 592 2.04 REMARK 500 O ARG B 689 N ASP B 691 2.07 REMARK 500 CZ ARG B 711 P DT C 12 2.11 REMARK 500 CZ ARG B 711 OP1 DT C 12 2.12 REMARK 500 O HOH A 802 O HOH A 820 2.15 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 DT I -2 C5' - C4' - O4' ANGL. DEV. = 10.8 DEGREES REMARK 500 DC I 13 C3' - C2' - C1' ANGL. DEV. = -5.1 DEGREES REMARK 500 DC I 13 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 LEU B 242 CA - CB - CG ANGL. DEV. = 15.8 DEGREES REMARK 500 PRO B 251 C - N - CA ANGL. DEV. = 9.2 DEGREES REMARK 500 LEU B 720 CA - CB - CG ANGL. DEV. = 14.5 DEGREES REMARK 500 DT C -2 C5' - C4' - C3' ANGL. DEV. = 9.6 DEGREES REMARK 500 DT C -2 C5' - C4' - O4' ANGL. DEV. = 10.8 DEGREES REMARK 500 DA D -14 O4' - C4' - C3' ANGL. DEV. = 3.7 DEGREES REMARK 500 DA D -14 C5' - C4' - O4' ANGL. DEV. = 9.6 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 GLN A 231 -172.73 -68.32 REMARK 500 TRP A 232 2.26 -68.39 REMARK 500 SER A 233 54.02 -92.19 REMARK 500 ALA A 285 -146.55 64.04 REMARK 500 SER A 299 54.54 -95.28 REMARK 500 SER A 333 49.51 -92.71 REMARK 500 SER A 367 50.63 -93.58 REMARK 500 SER A 401 45.74 -83.23 REMARK 500 SER A 435 30.92 -88.83 REMARK 500 LEU A 516 -44.32 70.51 REMARK 500 SER A 536 48.56 -88.90 REMARK 500 SER A 570 47.50 -85.53 REMARK 500 GLN A 590 -76.32 -68.05 REMARK 500 SER A 638 46.91 -93.89 REMARK 500 SER A 672 47.46 -90.53 REMARK 500 ARG A 689 69.48 -113.52 REMARK 500 PRO A 690 101.63 -39.33 REMARK 500 LEU A 694 -151.91 -93.36 REMARK 500 ALA A 695 -117.36 74.37 REMARK 500 GLN B 231 170.15 -58.11 REMARK 500 SER B 233 -34.94 139.15 REMARK 500 ARG B 236 -63.02 -145.31 REMARK 500 LEU B 238 47.03 -169.43 REMARK 500 LEU B 241 -24.48 -30.23 REMARK 500 LEU B 242 -22.71 -32.00 REMARK 500 ALA B 285 -148.79 64.85 REMARK 500 SER B 299 54.08 -97.86 REMARK 500 SER B 333 50.41 -94.06 REMARK 500 SER B 367 53.50 -95.66 REMARK 500 SER B 401 48.19 -84.82 REMARK 500 SER B 435 35.84 -89.05 REMARK 500 LEU B 516 -43.74 70.38 REMARK 500 SER B 536 46.39 -88.83 REMARK 500 SER B 570 47.67 -85.35 REMARK 500 GLN B 590 -78.80 -69.59 REMARK 500 SER B 638 45.00 -92.32 REMARK 500 SER B 672 47.30 -88.72 REMARK 500 ARG B 689 60.22 -112.53 REMARK 500 PRO B 690 70.34 -53.47 REMARK 500 ASP B 691 -93.01 -69.74 REMARK 500 ALA B 693 77.56 -51.96 REMARK 500 ALA B 695 177.34 140.39 REMARK 500 ALA B 716 14.60 -66.12 REMARK 500 VAL B 717 56.83 -54.65 REMARK 500 LYS B 718 120.01 71.76 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 PRO B 692 ALA B 693 149.11 REMARK 500 ALA B 716 VAL B 717 145.18 REMARK 500 REMARK 500 REMARK: NULL DBREF 6JW1 A 230 727 PDB 6JW1 6JW1 230 727 DBREF 6JW1 I -2 14 PDB 6JW1 6JW1 -2 14 DBREF 6JW1 J -14 2 PDB 6JW1 6JW1 -14 2 DBREF 6JW1 B 230 727 PDB 6JW1 6JW1 230 727 DBREF 6JW1 C -2 14 PDB 6JW1 6JW1 -2 14 DBREF 6JW1 D -14 2 PDB 6JW1 6JW1 -14 2 SEQRES 1 A 498 MET GLN TRP SER GLY ALA ARG ALA LEU GLU ALA LEU LEU SEQRES 2 A 498 THR VAL ALA GLY GLU LEU ARG GLY PRO PRO LEU GLN LEU SEQRES 3 A 498 ASP THR GLY GLN LEU LEU LYS ILE ALA LYS ARG GLY GLY SEQRES 4 A 498 VAL THR ALA VAL GLU ALA VAL HIS ALA TRP ARG ASN ALA SEQRES 5 A 498 LEU THR GLY ALA PRO LEU ASN LEU THR PRO GLU GLN VAL SEQRES 6 A 498 VAL ALA ILE ALA SER HIS ASP GLY GLY LYS GLN ALA LEU SEQRES 7 A 498 GLU THR VAL GLN ARG LEU LEU PRO VAL LEU CYS GLN ALA SEQRES 8 A 498 HIS GLY LEU THR PRO GLN GLN VAL VAL ALA ILE ALA SER SEQRES 9 A 498 HIS ASP GLY GLY LYS GLN ALA LEU GLU THR VAL GLN ARG SEQRES 10 A 498 LEU LEU PRO VAL LEU CYS GLN ALA HIS GLY LEU THR PRO SEQRES 11 A 498 GLU GLN VAL VAL ALA ILE ALA SER HIS ASP GLY GLY LYS SEQRES 12 A 498 GLN ALA LEU GLU THR VAL GLN ALA LEU LEU PRO VAL LEU SEQRES 13 A 498 CYS GLN ALA HIS GLY LEU THR PRO GLU GLN VAL VAL ALA SEQRES 14 A 498 ILE ALA SER ASN GLY GLY GLY LYS GLN ALA LEU GLU THR SEQRES 15 A 498 VAL GLN ARG LEU LEU PRO VAL LEU CYS GLN ALA HIS GLY SEQRES 16 A 498 LEU THR PRO GLN GLN VAL VAL ALA ILE ALA SER ASN GLY SEQRES 17 A 498 GLY GLY LYS GLN ALA LEU GLU THR VAL GLN ARG LEU LEU SEQRES 18 A 498 PRO VAL LEU CYS GLN ALA HIS GLY LEU THR PRO GLN GLN SEQRES 19 A 498 VAL VAL ALA ILE ALA SER ARG GLY GLY LYS GLN ALA LEU SEQRES 20 A 498 GLU THR VAL GLN ARG LEU LEU PRO VAL LEU CYS GLN ALA SEQRES 21 A 498 HIS GLY LEU THR PRO GLN GLN VAL VAL ALA ILE ALA SER SEQRES 22 A 498 ASN ASN GLY GLY LYS GLN ALA LEU GLU THR VAL GLN ARG SEQRES 23 A 498 LEU LEU PRO VAL LEU CYS GLN ALA HIS GLY LEU THR PRO SEQRES 24 A 498 GLN GLN VAL VAL ALA ILE ALA SER HIS ASP GLY GLY LYS SEQRES 25 A 498 GLN ALA LEU GLU THR VAL GLN ARG LEU LEU PRO VAL LEU SEQRES 26 A 498 CYS GLN ALA HIS GLY LEU THR PRO GLN GLN VAL VAL ALA SEQRES 27 A 498 ILE ALA SER ASN ASN GLY GLY LYS GLN ALA LEU GLU THR SEQRES 28 A 498 VAL GLN ARG LEU LEU PRO VAL LEU CYS GLN ALA HIS GLY SEQRES 29 A 498 LEU THR PRO GLU GLN VAL VAL ALA ILE ALA SER ASN GLY SEQRES 30 A 498 GLY GLY LYS GLN ALA LEU GLU THR VAL GLN ARG LEU LEU SEQRES 31 A 498 PRO VAL LEU CYS GLN ALA HIS GLY LEU THR PRO GLU GLN SEQRES 32 A 498 VAL VAL ALA ILE ALA SER HIS ASP GLY GLY LYS GLN ALA SEQRES 33 A 498 LEU GLU THR VAL GLN ARG LEU LEU PRO VAL LEU CYS GLN SEQRES 34 A 498 ALA HIS GLY LEU THR PRO GLN GLN VAL VAL ALA ILE ALA SEQRES 35 A 498 SER ASN GLY GLY GLY ARG PRO ALA LEU GLU SER ILE VAL SEQRES 36 A 498 ALA GLN LEU SER ARG PRO ASP PRO ALA LEU ALA ALA LEU SEQRES 37 A 498 THR ASN ASP HIS LEU VAL ALA LEU ALA CYS LEU GLY GLY SEQRES 38 A 498 ARG PRO ALA LEU ASP ALA VAL LYS LYS LEU GLU HIS HIS SEQRES 39 A 498 HIS HIS HIS HIS SEQRES 1 I 17 DT DG DT DC DC DC DT DT 5CM DG DC DG DT SEQRES 2 I 17 DC DT DC DT SEQRES 1 J 17 DA DG DA DG DA DC DG DC DG DA DA DG DG SEQRES 2 J 17 DG DA DC DA SEQRES 1 B 498 MET GLN TRP SER GLY ALA ARG ALA LEU GLU ALA LEU LEU SEQRES 2 B 498 THR VAL ALA GLY GLU LEU ARG GLY PRO PRO LEU GLN LEU SEQRES 3 B 498 ASP THR GLY GLN LEU LEU LYS ILE ALA LYS ARG GLY GLY SEQRES 4 B 498 VAL THR ALA VAL GLU ALA VAL HIS ALA TRP ARG ASN ALA SEQRES 5 B 498 LEU THR GLY ALA PRO LEU ASN LEU THR PRO GLU GLN VAL SEQRES 6 B 498 VAL ALA ILE ALA SER HIS ASP GLY GLY LYS GLN ALA LEU SEQRES 7 B 498 GLU THR VAL GLN ARG LEU LEU PRO VAL LEU CYS GLN ALA SEQRES 8 B 498 HIS GLY LEU THR PRO GLN GLN VAL VAL ALA ILE ALA SER SEQRES 9 B 498 HIS ASP GLY GLY LYS GLN ALA LEU GLU THR VAL GLN ARG SEQRES 10 B 498 LEU LEU PRO VAL LEU CYS GLN ALA HIS GLY LEU THR PRO SEQRES 11 B 498 GLU GLN VAL VAL ALA ILE ALA SER HIS ASP GLY GLY LYS SEQRES 12 B 498 GLN ALA LEU GLU THR VAL GLN ALA LEU LEU PRO VAL LEU SEQRES 13 B 498 CYS GLN ALA HIS GLY LEU THR PRO GLU GLN VAL VAL ALA SEQRES 14 B 498 ILE ALA SER ASN GLY GLY GLY LYS GLN ALA LEU GLU THR SEQRES 15 B 498 VAL GLN ARG LEU LEU PRO VAL LEU CYS GLN ALA HIS GLY SEQRES 16 B 498 LEU THR PRO GLN GLN VAL VAL ALA ILE ALA SER ASN GLY SEQRES 17 B 498 GLY GLY LYS GLN ALA LEU GLU THR VAL GLN ARG LEU LEU SEQRES 18 B 498 PRO VAL LEU CYS GLN ALA HIS GLY LEU THR PRO GLN GLN SEQRES 19 B 498 VAL VAL ALA ILE ALA SER ARG GLY GLY LYS GLN ALA LEU SEQRES 20 B 498 GLU THR VAL GLN ARG LEU LEU PRO VAL LEU CYS GLN ALA SEQRES 21 B 498 HIS GLY LEU THR PRO GLN GLN VAL VAL ALA ILE ALA SER SEQRES 22 B 498 ASN ASN GLY GLY LYS GLN ALA LEU GLU THR VAL GLN ARG SEQRES 23 B 498 LEU LEU PRO VAL LEU CYS GLN ALA HIS GLY LEU THR PRO SEQRES 24 B 498 GLN GLN VAL VAL ALA ILE ALA SER HIS ASP GLY GLY LYS SEQRES 25 B 498 GLN ALA LEU GLU THR VAL GLN ARG LEU LEU PRO VAL LEU SEQRES 26 B 498 CYS GLN ALA HIS GLY LEU THR PRO GLN GLN VAL VAL ALA SEQRES 27 B 498 ILE ALA SER ASN ASN GLY GLY LYS GLN ALA LEU GLU THR SEQRES 28 B 498 VAL GLN ARG LEU LEU PRO VAL LEU CYS GLN ALA HIS GLY SEQRES 29 B 498 LEU THR PRO GLU GLN VAL VAL ALA ILE ALA SER ASN GLY SEQRES 30 B 498 GLY GLY LYS GLN ALA LEU GLU THR VAL GLN ARG LEU LEU SEQRES 31 B 498 PRO VAL LEU CYS GLN ALA HIS GLY LEU THR PRO GLU GLN SEQRES 32 B 498 VAL VAL ALA ILE ALA SER HIS ASP GLY GLY LYS GLN ALA SEQRES 33 B 498 LEU GLU THR VAL GLN ARG LEU LEU PRO VAL LEU CYS GLN SEQRES 34 B 498 ALA HIS GLY LEU THR PRO GLN GLN VAL VAL ALA ILE ALA SEQRES 35 B 498 SER ASN GLY GLY GLY ARG PRO ALA LEU GLU SER ILE VAL SEQRES 36 B 498 ALA GLN LEU SER ARG PRO ASP PRO ALA LEU ALA ALA LEU SEQRES 37 B 498 THR ASN ASP HIS LEU VAL ALA LEU ALA CYS LEU GLY GLY SEQRES 38 B 498 ARG PRO ALA LEU ASP ALA VAL LYS LYS LEU GLU HIS HIS SEQRES 39 B 498 HIS HIS HIS HIS SEQRES 1 C 17 DT DG DT DC DC DC DT DT 5CM DG DC DG DT SEQRES 2 C 17 DC DT DC DT SEQRES 1 D 17 DA DG DA DG DA DC DG DC DG DA DA DG DG SEQRES 2 D 17 DG DA DC DA HET 5CM I 6 20 HET 5CM C 6 20 HETNAM 5CM 5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE FORMUL 2 5CM 2(C10 H16 N3 O7 P) FORMUL 7 HOH *43(H2 O) HELIX 1 AA1 ALA A 235 ARG A 249 1 15 HELIX 2 AA2 ASP A 256 GLY A 267 1 12 HELIX 3 AA3 GLY A 267 GLY A 284 1 18 HELIX 4 AA4 THR A 290 SER A 299 1 10 HELIX 5 AA5 GLY A 302 ALA A 320 1 19 HELIX 6 AA6 THR A 324 SER A 333 1 10 HELIX 7 AA7 GLY A 336 ALA A 354 1 19 HELIX 8 AA8 THR A 358 SER A 367 1 10 HELIX 9 AA9 GLY A 370 ALA A 388 1 19 HELIX 10 AB1 THR A 392 SER A 401 1 10 HELIX 11 AB2 GLY A 404 GLY A 424 1 21 HELIX 12 AB3 THR A 426 SER A 435 1 10 HELIX 13 AB4 GLY A 438 ALA A 456 1 19 HELIX 14 AB5 THR A 460 ALA A 489 1 30 HELIX 15 AB6 THR A 493 SER A 502 1 10 HELIX 16 AB7 GLY A 505 ARG A 515 1 11 HELIX 17 AB8 LEU A 516 ALA A 523 1 8 HELIX 18 AB9 THR A 527 SER A 536 1 10 HELIX 19 AC1 GLY A 539 ALA A 557 1 19 HELIX 20 AC2 THR A 561 SER A 570 1 10 HELIX 21 AC3 GLY A 573 ALA A 591 1 19 HELIX 22 AC4 THR A 595 SER A 604 1 10 HELIX 23 AC5 GLY A 607 ALA A 625 1 19 HELIX 24 AC6 THR A 629 SER A 638 1 10 HELIX 25 AC7 GLY A 641 ALA A 659 1 19 HELIX 26 AC8 THR A 663 SER A 672 1 10 HELIX 27 AC9 GLY A 675 ARG A 689 1 15 HELIX 28 AD1 THR A 698 HIS A 725 1 28 HELIX 29 AD2 LEU B 241 ARG B 249 1 9 HELIX 30 AD3 ASP B 256 GLY B 284 1 29 HELIX 31 AD4 THR B 290 SER B 299 1 10 HELIX 32 AD5 GLY B 302 ALA B 320 1 19 HELIX 33 AD6 THR B 324 SER B 333 1 10 HELIX 34 AD7 GLY B 336 ALA B 354 1 19 HELIX 35 AD8 THR B 358 SER B 367 1 10 HELIX 36 AD9 GLY B 370 ALA B 388 1 19 HELIX 37 AE1 THR B 392 SER B 401 1 10 HELIX 38 AE2 GLY B 404 ALA B 422 1 19 HELIX 39 AE3 THR B 426 SER B 435 1 10 HELIX 40 AE4 GLY B 438 ALA B 456 1 19 HELIX 41 AE5 THR B 460 ALA B 489 1 30 HELIX 42 AE6 THR B 493 SER B 502 1 10 HELIX 43 AE7 GLY B 505 ARG B 515 1 11 HELIX 44 AE8 LEU B 516 ALA B 523 1 8 HELIX 45 AE9 THR B 527 SER B 536 1 10 HELIX 46 AF1 GLY B 539 ALA B 557 1 19 HELIX 47 AF2 THR B 561 SER B 570 1 10 HELIX 48 AF3 GLY B 573 ALA B 591 1 19 HELIX 49 AF4 THR B 595 SER B 604 1 10 HELIX 50 AF5 GLY B 607 ALA B 625 1 19 HELIX 51 AF6 THR B 629 SER B 638 1 10 HELIX 52 AF7 GLY B 641 ALA B 659 1 19 HELIX 53 AF8 THR B 663 SER B 672 1 10 HELIX 54 AF9 GLY B 675 ARG B 689 1 15 HELIX 55 AG1 THR B 698 ALA B 716 1 19 HELIX 56 AG2 LEU B 720 HIS B 725 1 6 LINK O3' DT I 5 P 5CM I 6 1555 1555 1.62 LINK O3' 5CM I 6 P DG I 7 1555 1555 1.60 LINK O3' DT C 5 P 5CM C 6 1555 1555 1.58 LINK O3' 5CM C 6 P DG C 7 1555 1555 1.60 CRYST1 85.787 87.378 88.456 90.00 104.23 90.00 P 1 21 1 4 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 0.011657 0.000000 0.002956 0.00000 SCALE2 0.000000 0.011445 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011663 0.00000