HEADER TRANSFERASE/DNA 19-DEC-07 3BQ2 TITLE POST-INSERTION BINARY COMPLEX OF DBH DNA POLYMERASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*DGP*DAP*DAP*DGP*DCP*DCP*DGP*DGP*DCP*DGP*DG)-3'); COMPND 3 CHAIN: P; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: PRIMER; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA (5'- COMPND 8 D(*DTP*DTP*DCP*DCP*DGP*DCP*DCP*DCP*DGP*DGP*DCP*DTP*DTP*DCP*DC)-3'); COMPND 9 CHAIN: T; COMPND 10 ENGINEERED: YES; COMPND 11 OTHER_DETAILS: TEMPLATE; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: DNA POLYMERASE IV; COMPND 14 CHAIN: A; COMPND 15 SYNONYM: POL IV, DBH; COMPND 16 EC: 2.7.7.7; COMPND 17 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: SULFOLOBUS ACIDOCALDARIUS; SOURCE 11 ORGANISM_TAXID: 2285; SOURCE 12 GENE: DBH; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 15 EXPRESSION_SYSTEM_STRAIN: BLR(DE3)PLYSS; SOURCE 16 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 17 EXPRESSION_SYSTEM_PLASMID: PKKT7 KEYWDS DNA POLYMERASE, Y-FAMILY, LESION BYPASS, SINGLE-BASE DELETION, -1 KEYWDS 2 FRAMESHIFT, DNA DAMAGE, DNA REPAIR, DNA REPLICATION, DNA-BINDING, KEYWDS 3 DNA-DIRECTED DNA POLYMERASE, MAGNESIUM, METAL-BINDING, MUTATOR KEYWDS 4 PROTEIN, NUCLEOTIDYLTRANSFERASE, TRANSFERASE, TRANSFERASE-DNA KEYWDS 5 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.D.PATA,R.C.WILSON REVDAT 5 30-AUG-23 3BQ2 1 REMARK LINK REVDAT 4 25-OCT-17 3BQ2 1 SOURCE REMARK REVDAT 3 13-JUL-11 3BQ2 1 VERSN REVDAT 2 24-FEB-09 3BQ2 1 VERSN REVDAT 1 08-APR-08 3BQ2 0 JRNL AUTH R.C.WILSON,J.D.PATA JRNL TITL STRUCTURAL INSIGHTS INTO THE GENERATION OF SINGLE-BASE JRNL TITL 2 DELETIONS BY THE Y FAMILY DNA POLYMERASE DBH. JRNL REF MOL.CELL V. 29 767 2008 JRNL REFN ISSN 1097-2765 JRNL PMID 18374650 JRNL DOI 10.1016/J.MOLCEL.2008.01.014 REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 94.6 REMARK 3 NUMBER OF REFLECTIONS : 12802 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) : 0.237 REMARK 3 R VALUE (WORKING SET) : 0.234 REMARK 3 FREE R VALUE : 0.289 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 659 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) : 2.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.77 REMARK 3 REFLECTION IN BIN (WORKING SET) : 865 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.57 REMARK 3 BIN R VALUE (WORKING SET) : 0.3690 REMARK 3 BIN FREE R VALUE SET COUNT : 47 REMARK 3 BIN FREE R VALUE : 0.4310 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2704 REMARK 3 NUCLEIC ACID ATOMS : 466 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 33 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 47.48 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.34000 REMARK 3 B22 (A**2) : 2.34000 REMARK 3 B33 (A**2) : -4.67000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.404 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.366 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 38.190 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.916 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.861 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3265 ; 0.011 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4498 ; 1.328 ; 2.173 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 339 ; 6.083 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 115 ;39.994 ;24.783 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 542 ;19.592 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 17 ;10.217 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 522 ; 0.077 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2223 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1520 ; 0.221 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2142 ; 0.310 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 145 ; 0.161 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 1 ; 0.125 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 46 ; 0.188 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 6 ; 0.137 ; 0.200 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): 1754 ; 0.397 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2760 ; 0.681 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1867 ; 0.832 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1738 ; 1.422 ; 4.500 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 : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 240 REMARK 3 ORIGIN FOR THE GROUP (A): 30.6328 17.3286 -42.4320 REMARK 3 T TENSOR REMARK 3 T11: -0.2245 T22: -0.1677 REMARK 3 T33: -0.1067 T12: 0.1351 REMARK 3 T13: 0.0037 T23: -0.0651 REMARK 3 L TENSOR REMARK 3 L11: 1.8002 L22: 1.4560 REMARK 3 L33: 4.9782 L12: -0.3832 REMARK 3 L13: 1.3976 L23: -0.2416 REMARK 3 S TENSOR REMARK 3 S11: 0.0060 S12: -0.0124 S13: -0.2935 REMARK 3 S21: 0.2329 S22: 0.1338 S23: 0.1256 REMARK 3 S31: 0.3672 S32: -0.2820 S33: -0.1397 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 241 A 344 REMARK 3 ORIGIN FOR THE GROUP (A): 44.4239 -4.1753 -59.9517 REMARK 3 T TENSOR REMARK 3 T11: 0.1281 T22: 0.1400 REMARK 3 T33: 0.2328 T12: 0.0048 REMARK 3 T13: 0.0015 T23: -0.0897 REMARK 3 L TENSOR REMARK 3 L11: 2.9074 L22: 7.3030 REMARK 3 L33: 9.2970 L12: 2.4181 REMARK 3 L13: 1.3945 L23: 7.3410 REMARK 3 S TENSOR REMARK 3 S11: -0.1126 S12: 0.0845 S13: -0.3693 REMARK 3 S21: -0.0095 S22: 0.4947 S23: -0.7982 REMARK 3 S31: 0.5984 S32: 0.2678 S33: -0.3821 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : P 1 P 11 REMARK 3 RESIDUE RANGE : T 3 T 14 REMARK 3 ORIGIN FOR THE GROUP (A): 27.2828 -4.2077 -48.5620 REMARK 3 T TENSOR REMARK 3 T11: 0.6382 T22: 0.0676 REMARK 3 T33: 0.4815 T12: 0.1235 REMARK 3 T13: -0.2403 T23: 0.0352 REMARK 3 L TENSOR REMARK 3 L11: 0.5203 L22: 8.9903 REMARK 3 L33: 0.0780 L12: -2.1629 REMARK 3 L13: 0.2015 L23: -0.8375 REMARK 3 S TENSOR REMARK 3 S11: -0.2218 S12: 0.4282 S13: 0.7622 REMARK 3 S21: -0.8961 S22: -0.1172 S23: 0.6141 REMARK 3 S31: -0.3505 S32: -0.4016 S33: 0.3390 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK 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 3BQ2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-JAN-08. REMARK 100 THE DEPOSITION ID IS D_1000045825. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-JUL-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X25 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13596 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -0.500 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.0 REMARK 200 DATA REDUNDANCY : 5.300 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.75 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 0.44400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.000 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: PDB ENTRIES 1IM4 AND 1K1Q REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.31 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.58 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG-3350, CALCIUM ACETATE, GLYCEROL, REMARK 280 HEPES, PH 7, 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 34.16250 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 60.16900 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 60.16900 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 17.08125 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 60.16900 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 60.16900 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 51.24375 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 60.16900 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 60.16900 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 17.08125 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 60.16900 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 60.16900 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 51.24375 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 34.16250 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: 2930 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20450 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -32.5 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: P, T, A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 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 DT T 1 REMARK 465 DT T 2 REMARK 465 DC T 15 REMARK 465 ARG A 36 REMARK 465 THR A 37 REMARK 465 LYS A 38 REMARK 465 LYS A 345 REMARK 465 THR A 346 REMARK 465 ASN A 347 REMARK 465 LEU A 348 REMARK 465 SER A 349 REMARK 465 ASP A 350 REMARK 465 PHE A 351 REMARK 465 PHE A 352 REMARK 465 ASP A 353 REMARK 465 ILE A 354 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 DC T 14 O3' 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 DC P 9 C4 DC P 9 N4 -0.067 REMARK 500 DC P 9 N1 DC P 9 C6 0.042 REMARK 500 DC P 9 N3 DC P 9 C4 0.073 REMARK 500 DC P 9 C4 DC P 9 C5 0.054 REMARK 500 DG P 10 C2 DG P 10 N3 -0.052 REMARK 500 DG P 10 C6 DG P 10 O6 0.061 REMARK 500 DC T 3 C4 DC T 3 N4 0.098 REMARK 500 DC T 3 N1 DC T 3 C2 0.091 REMARK 500 DC T 3 C2 DC T 3 N3 0.065 REMARK 500 DC T 3 C4 DC T 3 C5 0.124 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 DA P 2 C3' - C2' - C1' ANGL. DEV. = -7.0 DEGREES REMARK 500 DA P 2 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 DG P 7 O4' - C1' - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 DC P 9 C6 - N1 - C2 ANGL. DEV. = 5.2 DEGREES REMARK 500 DC P 9 C2 - N3 - C4 ANGL. DEV. = 4.3 DEGREES REMARK 500 DC P 9 N3 - C4 - C5 ANGL. DEV. = -3.3 DEGREES REMARK 500 DG P 10 N3 - C4 - C5 ANGL. DEV. = 3.2 DEGREES REMARK 500 DC T 3 O4' - C4' - C3' ANGL. DEV. = -2.4 DEGREES REMARK 500 DC T 3 O4' - C1' - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 DC T 3 C4 - C5 - C6 ANGL. DEV. = 4.0 DEGREES REMARK 500 DG T 9 C3' - C2' - C1' ANGL. DEV. = -5.4 DEGREES REMARK 500 DG T 9 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 DG T 10 C3' - O3' - P ANGL. DEV. = 8.3 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 10 61.27 35.97 REMARK 500 SER A 34 -158.31 -80.04 REMARK 500 ALA A 44 -75.35 -67.77 REMARK 500 ASP A 205 -39.32 -38.15 REMARK 500 LYS A 216 -7.38 -59.56 REMARK 500 THR A 218 -51.19 -123.14 REMARK 500 ASN A 232 33.43 72.60 REMARK 500 SER A 235 -75.46 -112.02 REMARK 500 GLU A 236 95.33 52.92 REMARK 500 ARG A 257 -4.07 -141.52 REMARK 500 PRO A 264 -4.38 -55.22 REMARK 500 ALA A 273 -57.30 -132.24 REMARK 500 LYS A 276 37.58 -83.59 REMARK 500 LEU A 293 -11.92 65.75 REMARK 500 HIS A 304 -149.79 -86.79 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 355 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 105 OD1 REMARK 620 2 HOH A 356 O 120.2 REMARK 620 3 HOH A 357 O 67.4 110.1 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 355 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3BQ0 RELATED DB: PDB REMARK 900 PRE-INSERTION BINARY COMPLEX OF DBH REMARK 900 RELATED ID: 3BQ1 RELATED DB: PDB REMARK 900 INSERTION TERNARY COMPLEX OF DBH DBREF 3BQ2 A 1 354 UNP Q4JB80 DPO4_SULAC 1 354 DBREF 3BQ2 P 1 11 PDB 3BQ2 3BQ2 1 11 DBREF 3BQ2 T 1 15 PDB 3BQ2 3BQ2 1 15 SEQRES 1 P 11 DG DA DA DG DC DC DG DG DC DG DG SEQRES 1 T 15 DT DT DC DC DG DC DC DC DG DG DC DT DT SEQRES 2 T 15 DC DC SEQRES 1 A 354 MET ILE VAL ILE PHE VAL ASP PHE ASP TYR PHE PHE ALA SEQRES 2 A 354 GLN VAL GLU GLU VAL LEU ASN PRO GLN TYR LYS GLY LYS SEQRES 3 A 354 PRO LEU VAL VAL CYS VAL TYR SER GLY ARG THR LYS THR SEQRES 4 A 354 SER GLY ALA VAL ALA THR ALA ASN TYR GLU ALA ARG LYS SEQRES 5 A 354 LEU GLY VAL LYS ALA GLY MET PRO ILE ILE LYS ALA MET SEQRES 6 A 354 GLN ILE ALA PRO SER ALA ILE TYR VAL PRO MET ARG LYS SEQRES 7 A 354 PRO ILE TYR GLU ALA PHE SER ASN ARG ILE MET ASN LEU SEQRES 8 A 354 LEU ASN LYS HIS ALA ASP LYS ILE GLU VAL ALA SER ILE SEQRES 9 A 354 ASP GLU ALA TYR LEU ASP VAL THR ASN LYS VAL GLU GLY SEQRES 10 A 354 ASN PHE GLU ASN GLY ILE GLU LEU ALA ARG LYS ILE LYS SEQRES 11 A 354 GLN GLU ILE LEU GLU LYS GLU LYS ILE THR VAL THR VAL SEQRES 12 A 354 GLY VAL ALA PRO ASN LYS ILE LEU ALA LYS ILE ILE ALA SEQRES 13 A 354 ASP LYS SER LYS PRO ASN GLY LEU GLY VAL ILE ARG PRO SEQRES 14 A 354 THR GLU VAL GLN ASP PHE LEU ASN GLU LEU ASP ILE ASP SEQRES 15 A 354 GLU ILE PRO GLY ILE GLY SER VAL LEU ALA ARG ARG LEU SEQRES 16 A 354 ASN GLU LEU GLY ILE GLN LYS LEU ARG ASP ILE LEU SER SEQRES 17 A 354 LYS ASN TYR ASN GLU LEU GLU LYS ILE THR GLY LYS ALA SEQRES 18 A 354 LYS ALA LEU TYR LEU LEU LYS LEU ALA GLN ASN LYS TYR SEQRES 19 A 354 SER GLU PRO VAL GLU ASN LYS SER LYS ILE PRO HIS GLY SEQRES 20 A 354 ARG TYR LEU THR LEU PRO TYR ASN THR ARG ASP VAL LYS SEQRES 21 A 354 VAL ILE LEU PRO TYR LEU LYS LYS ALA ILE ASN GLU ALA SEQRES 22 A 354 TYR ASN LYS VAL ASN GLY ILE PRO MET ARG ILE THR VAL SEQRES 23 A 354 ILE ALA ILE MET GLU ASP LEU ASP ILE LEU SER LYS GLY SEQRES 24 A 354 LYS LYS PHE LYS HIS GLY ILE SER ILE ASP ASN ALA TYR SEQRES 25 A 354 LYS VAL ALA GLU ASP LEU LEU ARG GLU LEU LEU VAL ARG SEQRES 26 A 354 ASP LYS ARG ARG ASN VAL ARG ARG ILE GLY VAL LYS LEU SEQRES 27 A 354 ASP ASN ILE ILE ILE ASN LYS THR ASN LEU SER ASP PHE SEQRES 28 A 354 PHE ASP ILE HET CA A 355 1 HETNAM CA CALCIUM ION FORMUL 4 CA CA 2+ FORMUL 5 HOH *33(H2 O) HELIX 1 1 TYR A 10 ASN A 20 1 11 HELIX 2 2 PRO A 21 LYS A 24 5 4 HELIX 3 3 ASN A 47 LEU A 53 1 7 HELIX 4 4 PRO A 60 ALA A 68 1 9 HELIX 5 5 ARG A 77 ALA A 96 1 20 HELIX 6 6 ASN A 118 LYS A 138 1 21 HELIX 7 7 ASN A 148 LYS A 158 1 11 HELIX 8 8 GLU A 171 LEU A 179 1 9 HELIX 9 9 ASP A 180 ILE A 184 5 5 HELIX 10 10 GLY A 188 ASN A 196 1 9 HELIX 11 11 GLU A 197 GLY A 199 5 3 HELIX 12 12 LEU A 203 SER A 208 5 6 HELIX 13 13 TYR A 211 GLY A 219 1 9 HELIX 14 15 ASP A 258 GLU A 272 1 15 HELIX 15 16 SER A 307 ASP A 326 1 20 SHEET 1 A 8 LEU A 164 VAL A 166 0 SHEET 2 A 8 VAL A 141 ALA A 146 1 N VAL A 143 O GLY A 165 SHEET 3 A 8 VAL A 3 PHE A 8 -1 N ASP A 7 O THR A 142 SHEET 4 A 8 GLU A 106 ASP A 110 -1 O ALA A 107 N VAL A 6 SHEET 5 A 8 LYS A 98 SER A 103 -1 N GLU A 100 O TYR A 108 SHEET 6 A 8 LYS A 241 SER A 242 1 O LYS A 241 N VAL A 101 SHEET 7 A 8 VAL A 331 ILE A 342 -1 O ILE A 341 N SER A 242 SHEET 8 A 8 HIS A 246 THR A 256 -1 N HIS A 246 O LEU A 338 SHEET 1 B 8 LEU A 164 VAL A 166 0 SHEET 2 B 8 VAL A 141 ALA A 146 1 N VAL A 143 O GLY A 165 SHEET 3 B 8 VAL A 3 PHE A 8 -1 N ASP A 7 O THR A 142 SHEET 4 B 8 GLU A 106 ASP A 110 -1 O ALA A 107 N VAL A 6 SHEET 5 B 8 LYS A 98 SER A 103 -1 N GLU A 100 O TYR A 108 SHEET 6 B 8 LYS A 241 SER A 242 1 O LYS A 241 N VAL A 101 SHEET 7 B 8 VAL A 331 ILE A 342 -1 O ILE A 341 N SER A 242 SHEET 8 B 8 ILE A 280 MET A 290 -1 N ILE A 287 O GLY A 335 SHEET 1 C 3 GLY A 41 ALA A 46 0 SHEET 2 C 3 LEU A 28 TYR A 33 -1 N VAL A 32 O ALA A 42 SHEET 3 C 3 ILE A 72 PRO A 75 1 O ILE A 72 N VAL A 29 LINK OD1 ASP A 105 CA CA A 355 1555 1555 2.68 LINK CA CA A 355 O HOH A 356 1555 1555 2.30 LINK CA CA A 355 O HOH A 357 1555 1555 2.95 CISPEP 1 LYS A 160 PRO A 161 0 3.46 SITE 1 AC1 1 ASP A 105 CRYST1 120.338 120.338 68.325 90.00 90.00 90.00 P 41 21 2 8 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 0.008310 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008310 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014636 0.00000