HEADER DNA BINDING PROTEIN/DNA 11-APR-19 6JTQ TITLE RVD HA SPECIFICALLY CONTACTS 5MC THROUGH VAN DER WAALS 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; 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, DNA BINDING PROTEIN-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR L.LIU,C.YI REVDAT 2 27-MAR-24 6JTQ 1 REMARK REVDAT 1 15-APR-20 6JTQ 0 JRNL AUTH L.LIU,C.YI JRNL TITL RVD HA SPECIFICALLY CONTACTS 5MC THROUGH VAN DER WAALS JRNL TITL 2 INTERACTIONS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.48 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0135 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) : 2.48 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 91.8 REMARK 3 NUMBER OF REFLECTIONS : 39755 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) : 0.221 REMARK 3 R VALUE (WORKING SET) : 0.218 REMARK 3 FREE R VALUE : 0.283 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2095 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) : 2.48 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.55 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1558 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 48.63 REMARK 3 BIN R VALUE (WORKING SET) : 0.2230 REMARK 3 BIN FREE R VALUE SET COUNT : 71 REMARK 3 BIN FREE R VALUE : 0.2700 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 7210 REMARK 3 NUCLEIC ACID ATOMS : 1382 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 112 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 46.04 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.15000 REMARK 3 B22 (A**2) : -1.15000 REMARK 3 B33 (A**2) : 0.81000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.15000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.751 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.345 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.255 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 11.308 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.923 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.872 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 8868 ; 0.013 ; 0.018 REMARK 3 BOND LENGTHS OTHERS (A): 8178 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 12384 ; 1.813 ; 1.828 REMARK 3 BOND ANGLES OTHERS (DEGREES): 18792 ; 1.207 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 992 ; 9.690 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 274 ;42.154 ;25.912 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1184 ;19.028 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 32 ;21.503 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1442 ; 0.096 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 9322 ; 0.009 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1866 ; 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): 3974 ; 3.558 ; 4.593 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 3973 ; 3.549 ; 4.587 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4964 ; 5.852 ; 6.872 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 4965 ; 5.852 ; 6.879 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 4894 ; 3.420 ; 4.760 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 4895 ; 3.419 ; 4.760 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 7421 ; 5.580 ; 7.069 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 10244 ;10.198 ;37.538 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 10215 ;10.206 ;37.579 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 6JTQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-APR-19. REMARK 100 THE DEPOSITION ID IS D_1300011759. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-JUN-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 : BL17U1 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-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39755 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.480 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 2.0300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.48 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.55 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.01 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.62 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 8-10% PEG3350 (W/V), 10% ETHANOL, 0.1 REMARK 280 M 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 44.01100 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: 6460 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24370 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -55.0 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: 6400 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 26860 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -57.0 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 727 REMARK 465 HIS A 728 REMARK 465 HIS B 727 REMARK 465 HIS B 728 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 HIS A 525 CG ND1 CD2 CE1 NE2 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 525 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 O LEU B 613 N THR B 615 2.13 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 MET A 230 N SER B 233 1656 1.95 REMARK 500 O GLN A 231 C GLN B 231 1656 1.98 REMARK 500 O GLN A 231 O GLN B 231 1656 2.00 REMARK 500 N LEU B 595 O HIS B 725 2545 2.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 LEU A 416 CA - CB - CG ANGL. DEV. = 14.1 DEGREES REMARK 500 PRO B 251 C - N - CA ANGL. DEV. = 11.1 DEGREES REMARK 500 LEU B 595 CA - CB - CG ANGL. DEV. = 18.6 DEGREES REMARK 500 HIS B 724 N - CA - CB ANGL. DEV. = 11.8 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 SER A 233 -49.91 175.29 REMARK 500 ARG A 236 -13.72 57.45 REMARK 500 ALA A 237 33.32 -74.26 REMARK 500 ALA A 285 -133.24 52.02 REMARK 500 SER A 367 43.13 -86.92 REMARK 500 GLN A 387 -85.76 -69.91 REMARK 500 SER A 401 36.85 -78.86 REMARK 500 SER A 469 21.71 -75.17 REMARK 500 SER A 503 44.12 -82.77 REMARK 500 LEU A 517 -36.00 60.38 REMARK 500 CYS A 522 41.68 -107.74 REMARK 500 HIS A 525 -65.92 83.19 REMARK 500 SER A 571 39.90 -84.02 REMARK 500 GLN A 591 -76.32 -70.24 REMARK 500 SER A 639 49.13 -88.18 REMARK 500 CYS A 658 -74.17 -78.14 REMARK 500 SER A 673 49.39 -80.91 REMARK 500 PRO A 691 103.81 -23.96 REMARK 500 ALA A 696 -63.43 74.81 REMARK 500 HIS A 725 -86.23 -65.80 REMARK 500 TRP B 232 -69.00 -104.27 REMARK 500 PRO B 251 -60.26 -24.80 REMARK 500 TRP B 278 4.78 -69.48 REMARK 500 ALA B 285 -137.31 59.67 REMARK 500 SER B 299 48.50 -94.02 REMARK 500 SER B 333 47.85 -89.31 REMARK 500 SER B 367 46.47 -93.49 REMARK 500 SER B 401 45.29 -84.29 REMARK 500 SER B 435 39.75 -87.27 REMARK 500 GLN B 489 -84.99 -65.12 REMARK 500 ASN B 505 135.81 -36.95 REMARK 500 ALA B 524 118.67 50.80 REMARK 500 HIS B 525 50.43 79.98 REMARK 500 SER B 537 37.08 -80.51 REMARK 500 ASP B 539 135.39 -33.36 REMARK 500 VAL B 582 33.06 -78.11 REMARK 500 GLN B 583 -52.51 -131.93 REMARK 500 LEU B 586 -45.20 104.63 REMARK 500 LEU B 589 53.95 -107.72 REMARK 500 ALA B 592 39.62 113.35 REMARK 500 HIS B 593 -86.43 -163.23 REMARK 500 SER B 605 35.91 -84.07 REMARK 500 LEU B 613 -161.83 -62.64 REMARK 500 GLU B 614 -56.15 54.66 REMARK 500 CYS B 624 -67.35 66.73 REMARK 500 HIS B 627 -72.40 -156.24 REMARK 500 LEU B 629 -105.30 -151.50 REMARK 500 GLU B 632 55.61 -103.54 REMARK 500 GLN B 633 -86.38 -122.73 REMARK 500 ALA B 636 -48.46 96.04 REMARK 500 REMARK 500 THIS ENTRY HAS 87 RAMACHANDRAN OUTLIERS. 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 ARG A 236 ALA A 237 139.61 REMARK 500 ALA A 237 LEU A 238 143.87 REMARK 500 PRO A 251 PRO A 252 66.69 REMARK 500 ALA A 694 LEU A 695 -145.89 REMARK 500 GLY B 234 ALA B 235 139.09 REMARK 500 ALA B 524 HIS B 525 -145.08 REMARK 500 HIS B 525 GLY B 526 -145.50 REMARK 500 VAL B 622 LEU B 623 148.39 REMARK 500 THR B 630 PRO B 631 131.05 REMARK 500 PRO B 631 GLU B 632 139.96 REMARK 500 GLU B 648 THR B 649 -140.34 REMARK 500 CYS B 658 GLN B 659 -137.33 REMARK 500 HIS B 661 GLY B 662 149.23 REMARK 500 THR B 664 PRO B 665 138.50 REMARK 500 ILE B 671 ALA B 672 138.68 REMARK 500 ALA B 672 SER B 673 -144.92 REMARK 500 ARG B 678 PRO B 679 142.90 REMARK 500 HIS B 723 HIS B 724 144.66 REMARK 500 HIS B 724 HIS B 725 145.65 REMARK 500 REMARK 500 REMARK: NULL DBREF 6JTQ A 230 728 PDB 6JTQ 6JTQ 230 728 DBREF 6JTQ I -2 14 PDB 6JTQ 6JTQ -2 14 DBREF 6JTQ J -14 2 PDB 6JTQ 6JTQ -14 2 DBREF 6JTQ B 230 728 PDB 6JTQ 6JTQ 230 728 DBREF 6JTQ C -2 14 PDB 6JTQ 6JTQ -2 14 DBREF 6JTQ D -14 2 PDB 6JTQ 6JTQ -14 2 SEQRES 1 A 499 MET GLN TRP SER GLY ALA ARG ALA LEU GLU ALA LEU LEU SEQRES 2 A 499 THR VAL ALA GLY GLU LEU ARG GLY PRO PRO LEU GLN LEU SEQRES 3 A 499 ASP THR GLY GLN LEU LEU LYS ILE ALA LYS ARG GLY GLY SEQRES 4 A 499 VAL THR ALA VAL GLU ALA VAL HIS ALA TRP ARG ASN ALA SEQRES 5 A 499 LEU THR GLY ALA PRO LEU ASN LEU THR PRO GLU GLN VAL SEQRES 6 A 499 VAL ALA ILE ALA SER HIS ASP GLY GLY LYS GLN ALA LEU SEQRES 7 A 499 GLU THR VAL GLN ARG LEU LEU PRO VAL LEU CYS GLN ALA SEQRES 8 A 499 HIS GLY LEU THR PRO GLN GLN VAL VAL ALA ILE ALA SER SEQRES 9 A 499 HIS ASP GLY GLY LYS GLN ALA LEU GLU THR VAL GLN ARG SEQRES 10 A 499 LEU LEU PRO VAL LEU CYS GLN ALA HIS GLY LEU THR PRO SEQRES 11 A 499 GLU GLN VAL VAL ALA ILE ALA SER HIS ASP GLY GLY LYS SEQRES 12 A 499 GLN ALA LEU GLU THR VAL GLN ALA LEU LEU PRO VAL LEU SEQRES 13 A 499 CYS GLN ALA HIS GLY LEU THR PRO GLU GLN VAL VAL ALA SEQRES 14 A 499 ILE ALA SER ASN GLY GLY GLY LYS GLN ALA LEU GLU THR SEQRES 15 A 499 VAL GLN ARG LEU LEU PRO VAL LEU CYS GLN ALA HIS GLY SEQRES 16 A 499 LEU THR PRO GLN GLN VAL VAL ALA ILE ALA SER ASN GLY SEQRES 17 A 499 GLY GLY LYS GLN ALA LEU GLU THR VAL GLN ARG LEU LEU SEQRES 18 A 499 PRO VAL LEU CYS GLN ALA HIS GLY LEU THR PRO GLN GLN SEQRES 19 A 499 VAL VAL ALA ILE ALA SER HIS ALA GLY GLY LYS GLN ALA SEQRES 20 A 499 LEU GLU THR VAL GLN ARG LEU LEU PRO VAL LEU CYS GLN SEQRES 21 A 499 ALA HIS GLY LEU THR PRO GLN GLN VAL VAL ALA ILE ALA SEQRES 22 A 499 SER ASN ASN GLY GLY LYS GLN ALA LEU GLU THR VAL GLN SEQRES 23 A 499 ARG LEU LEU PRO VAL LEU CYS GLN ALA HIS GLY LEU THR SEQRES 24 A 499 PRO GLN GLN VAL VAL ALA ILE ALA SER HIS ASP GLY GLY SEQRES 25 A 499 LYS GLN ALA LEU GLU THR VAL GLN ARG LEU LEU PRO VAL SEQRES 26 A 499 LEU CYS GLN ALA HIS GLY LEU THR PRO GLN GLN VAL VAL SEQRES 27 A 499 ALA ILE ALA SER ASN ASN GLY GLY LYS GLN ALA LEU GLU SEQRES 28 A 499 THR VAL GLN ARG LEU LEU PRO VAL LEU CYS GLN ALA HIS SEQRES 29 A 499 GLY LEU THR PRO GLU GLN VAL VAL ALA ILE ALA SER ASN SEQRES 30 A 499 GLY GLY GLY LYS GLN ALA LEU GLU THR VAL GLN ARG LEU SEQRES 31 A 499 LEU PRO VAL LEU CYS GLN ALA HIS GLY LEU THR PRO GLU SEQRES 32 A 499 GLN VAL VAL ALA ILE ALA SER HIS ASP GLY GLY LYS GLN SEQRES 33 A 499 ALA LEU GLU THR VAL GLN ARG LEU LEU PRO VAL LEU CYS SEQRES 34 A 499 GLN ALA HIS GLY LEU THR PRO GLN GLN VAL VAL ALA ILE SEQRES 35 A 499 ALA SER ASN GLY GLY GLY ARG PRO ALA LEU GLU SER ILE SEQRES 36 A 499 VAL ALA GLN LEU SER ARG PRO ASP PRO ALA LEU ALA ALA SEQRES 37 A 499 LEU THR ASN ASP HIS LEU VAL ALA LEU ALA CYS LEU GLY SEQRES 38 A 499 GLY ARG PRO ALA LEU ASP ALA VAL LYS LYS LEU GLU HIS SEQRES 39 A 499 HIS 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 499 MET GLN TRP SER GLY ALA ARG ALA LEU GLU ALA LEU LEU SEQRES 2 B 499 THR VAL ALA GLY GLU LEU ARG GLY PRO PRO LEU GLN LEU SEQRES 3 B 499 ASP THR GLY GLN LEU LEU LYS ILE ALA LYS ARG GLY GLY SEQRES 4 B 499 VAL THR ALA VAL GLU ALA VAL HIS ALA TRP ARG ASN ALA SEQRES 5 B 499 LEU THR GLY ALA PRO LEU ASN LEU THR PRO GLU GLN VAL SEQRES 6 B 499 VAL ALA ILE ALA SER HIS ASP GLY GLY LYS GLN ALA LEU SEQRES 7 B 499 GLU THR VAL GLN ARG LEU LEU PRO VAL LEU CYS GLN ALA SEQRES 8 B 499 HIS GLY LEU THR PRO GLN GLN VAL VAL ALA ILE ALA SER SEQRES 9 B 499 HIS ASP GLY GLY LYS GLN ALA LEU GLU THR VAL GLN ARG SEQRES 10 B 499 LEU LEU PRO VAL LEU CYS GLN ALA HIS GLY LEU THR PRO SEQRES 11 B 499 GLU GLN VAL VAL ALA ILE ALA SER HIS ASP GLY GLY LYS SEQRES 12 B 499 GLN ALA LEU GLU THR VAL GLN ALA LEU LEU PRO VAL LEU SEQRES 13 B 499 CYS GLN ALA HIS GLY LEU THR PRO GLU GLN VAL VAL ALA SEQRES 14 B 499 ILE ALA SER ASN GLY GLY GLY LYS GLN ALA LEU GLU THR SEQRES 15 B 499 VAL GLN ARG LEU LEU PRO VAL LEU CYS GLN ALA HIS GLY SEQRES 16 B 499 LEU THR PRO GLN GLN VAL VAL ALA ILE ALA SER ASN GLY SEQRES 17 B 499 GLY GLY LYS GLN ALA LEU GLU THR VAL GLN ARG LEU LEU SEQRES 18 B 499 PRO VAL LEU CYS GLN ALA HIS GLY LEU THR PRO GLN GLN SEQRES 19 B 499 VAL VAL ALA ILE ALA SER HIS ALA GLY GLY LYS GLN ALA SEQRES 20 B 499 LEU GLU THR VAL GLN ARG LEU LEU PRO VAL LEU CYS GLN SEQRES 21 B 499 ALA HIS GLY LEU THR PRO GLN GLN VAL VAL ALA ILE ALA SEQRES 22 B 499 SER ASN ASN GLY GLY LYS GLN ALA LEU GLU THR VAL GLN SEQRES 23 B 499 ARG LEU LEU PRO VAL LEU CYS GLN ALA HIS GLY LEU THR SEQRES 24 B 499 PRO GLN GLN VAL VAL ALA ILE ALA SER HIS ASP GLY GLY SEQRES 25 B 499 LYS GLN ALA LEU GLU THR VAL GLN ARG LEU LEU PRO VAL SEQRES 26 B 499 LEU CYS GLN ALA HIS GLY LEU THR PRO GLN GLN VAL VAL SEQRES 27 B 499 ALA ILE ALA SER ASN ASN GLY GLY LYS GLN ALA LEU GLU SEQRES 28 B 499 THR VAL GLN ARG LEU LEU PRO VAL LEU CYS GLN ALA HIS SEQRES 29 B 499 GLY LEU THR PRO GLU GLN VAL VAL ALA ILE ALA SER ASN SEQRES 30 B 499 GLY GLY GLY LYS GLN ALA LEU GLU THR VAL GLN ARG LEU SEQRES 31 B 499 LEU PRO VAL LEU CYS GLN ALA HIS GLY LEU THR PRO GLU SEQRES 32 B 499 GLN VAL VAL ALA ILE ALA SER HIS ASP GLY GLY LYS GLN SEQRES 33 B 499 ALA LEU GLU THR VAL GLN ARG LEU LEU PRO VAL LEU CYS SEQRES 34 B 499 GLN ALA HIS GLY LEU THR PRO GLN GLN VAL VAL ALA ILE SEQRES 35 B 499 ALA SER ASN GLY GLY GLY ARG PRO ALA LEU GLU SER ILE SEQRES 36 B 499 VAL ALA GLN LEU SER ARG PRO ASP PRO ALA LEU ALA ALA SEQRES 37 B 499 LEU THR ASN ASP HIS LEU VAL ALA LEU ALA CYS LEU GLY SEQRES 38 B 499 GLY ARG PRO ALA LEU ASP ALA VAL LYS LYS LEU GLU HIS SEQRES 39 B 499 HIS 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 *112(H2 O) HELIX 1 AA1 ALA A 237 LEU A 248 1 12 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 GLY A 322 1 21 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 GLN A 387 1 18 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 SER A 469 1 10 HELIX 15 AB6 GLY A 472 ALA A 490 1 19 HELIX 16 AB7 THR A 494 SER A 503 1 10 HELIX 17 AB8 GLY A 506 ARG A 516 1 11 HELIX 18 AB9 PRO A 519 GLN A 523 5 5 HELIX 19 AC1 THR A 528 SER A 537 1 10 HELIX 20 AC2 GLY A 540 HIS A 559 1 20 HELIX 21 AC3 THR A 562 SER A 571 1 10 HELIX 22 AC4 GLY A 574 GLY A 594 1 21 HELIX 23 AC5 THR A 596 SER A 605 1 10 HELIX 24 AC6 GLY A 608 GLN A 625 1 18 HELIX 25 AC7 THR A 630 SER A 639 1 10 HELIX 26 AC8 GLY A 642 GLN A 659 1 18 HELIX 27 AC9 THR A 664 SER A 673 1 10 HELIX 28 AD1 GLY A 676 ARG A 690 1 15 HELIX 29 AD2 THR A 699 HIS A 725 1 27 HELIX 30 AD3 GLY B 234 ARG B 249 1 16 HELIX 31 AD4 ASP B 256 GLY B 284 1 29 HELIX 32 AD5 THR B 290 SER B 299 1 10 HELIX 33 AD6 GLY B 302 ALA B 320 1 19 HELIX 34 AD7 THR B 324 SER B 333 1 10 HELIX 35 AD8 GLY B 336 ALA B 354 1 19 HELIX 36 AD9 THR B 358 SER B 367 1 10 HELIX 37 AE1 GLY B 370 ALA B 388 1 19 HELIX 38 AE2 THR B 392 SER B 401 1 10 HELIX 39 AE3 GLY B 404 ALA B 422 1 19 HELIX 40 AE4 THR B 426 SER B 435 1 10 HELIX 41 AE5 GLY B 438 ALA B 456 1 19 HELIX 42 AE6 THR B 460 SER B 469 1 10 HELIX 43 AE7 GLY B 472 GLN B 489 1 18 HELIX 44 AE8 THR B 494 SER B 503 1 10 HELIX 45 AE9 GLY B 506 GLN B 523 1 18 HELIX 46 AF1 THR B 528 SER B 537 1 10 HELIX 47 AF2 GLY B 540 ALA B 558 1 19 HELIX 48 AF3 THR B 562 SER B 571 1 10 HELIX 49 AF4 GLY B 574 LEU B 585 1 12 HELIX 50 AF5 THR B 596 SER B 605 1 10 HELIX 51 AF6 GLY B 608 LEU B 620 1 13 HELIX 52 AF7 GLU B 648 CYS B 658 1 11 HELIX 53 AF8 PRO B 679 GLN B 687 1 9 LINK O3' DT I 5 P 5CM I 6 1555 1555 1.62 LINK O3' 5CM I 6 P DG I 7 1555 1555 1.61 LINK O3' DT C 5 P 5CM C 6 1555 1555 1.60 LINK O3' 5CM C 6 P DG C 7 1555 1555 1.58 CRYST1 85.786 88.022 89.349 90.00 104.77 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 0.003072 0.00000 SCALE2 0.000000 0.011361 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011574 0.00000