HEADER TRANSFERASE/DNA 19-DEC-07 3BQ1
TITLE INSERTION TERNARY COMPLEX OF DBH DNA POLYMERASE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: DNA (5'-D(*DGP*DAP*DAP*DGP*DCP*DCP*DGP*DGP*DCP*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(*DT*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 MOL_ID: 2;
SOURCE 4 SYNTHETIC: YES;
SOURCE 5 MOL_ID: 3;
SOURCE 6 ORGANISM_SCIENTIFIC: SULFOLOBUS ACIDOCALDARIUS;
SOURCE 7 ORGANISM_TAXID: 2285;
SOURCE 8 GENE: DBH;
SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 10 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 11 EXPRESSION_SYSTEM_STRAIN: BLR(DE3)PLYSS;
SOURCE 12 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 13 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 4 30-AUG-23 3BQ1 1 REMARK LINK
REVDAT 3 13-JUL-11 3BQ1 1 VERSN
REVDAT 2 24-FEB-09 3BQ1 1 VERSN
REVDAT 1 08-APR-08 3BQ1 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)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6
REMARK 3 NUMBER OF REFLECTIONS : 14437
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) : 0.207
REMARK 3 R VALUE (WORKING SET) : 0.204
REMARK 3 FREE R VALUE : 0.267
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900
REMARK 3 FREE R VALUE TEST SET COUNT : 711
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) : 2.79
REMARK 3 REFLECTION IN BIN (WORKING SET) : 257
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.13
REMARK 3 BIN R VALUE (WORKING SET) : 0.3170
REMARK 3 BIN FREE R VALUE SET COUNT : 6
REMARK 3 BIN FREE R VALUE : 0.3970
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 2719
REMARK 3 NUCLEIC ACID ATOMS : 466
REMARK 3 HETEROGEN ATOMS : 31
REMARK 3 SOLVENT ATOMS : 41
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) : 42.58
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 0.66000
REMARK 3 B22 (A**2) : 0.66000
REMARK 3 B33 (A**2) : -1.32000
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): 1.225
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.359
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.301
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 30.757
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.935
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.879
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3316 ; 0.008 ; 0.022
REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4572 ; 1.242 ; 2.181
REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 343 ; 4.720 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 115 ;39.030 ;24.783
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 542 ;17.946 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 17 ;13.984 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 527 ; 0.071 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2253 ; 0.003 ; 0.020
REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1356 ; 0.207 ; 0.200
REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2209 ; 0.301 ; 0.200
REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 113 ; 0.127 ; 0.200
REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 1 ; 0.019 ; 0.200
REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 44 ; 0.178 ; 0.200
REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 5 ; 0.117 ; 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): 1766 ; 0.339 ; 1.500
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2786 ; 0.593 ; 2.000
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1901 ; 0.823 ; 3.000
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1786 ; 1.411 ; 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 : 4
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 168
REMARK 3 ORIGIN FOR THE GROUP (A): 36.4731 23.7167 -16.2550
REMARK 3 T TENSOR
REMARK 3 T11: -0.1364 T22: -0.2609
REMARK 3 T33: -0.1699 T12: 0.1040
REMARK 3 T13: 0.0034 T23: 0.0108
REMARK 3 L TENSOR
REMARK 3 L11: 3.7732 L22: 2.9560
REMARK 3 L33: 8.4046 L12: -1.7225
REMARK 3 L13: 2.8887 L23: -2.2423
REMARK 3 S TENSOR
REMARK 3 S11: -0.1278 S12: -0.1759 S13: 0.0944
REMARK 3 S21: 0.5939 S22: 0.2680 S23: 0.0603
REMARK 3 S31: -0.1606 S32: 0.0261 S33: -0.1402
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 169 A 232
REMARK 3 ORIGIN FOR THE GROUP (A): 25.4967 8.0272 3.1778
REMARK 3 T TENSOR
REMARK 3 T11: 0.7697 T22: 0.3022
REMARK 3 T33: 0.5936 T12: 0.1921
REMARK 3 T13: 0.3154 T23: 0.0561
REMARK 3 L TENSOR
REMARK 3 L11: 6.2892 L22: 5.1271
REMARK 3 L33: 4.4685 L12: 3.2636
REMARK 3 L13: 0.5072 L23: -0.1177
REMARK 3 S TENSOR
REMARK 3 S11: -0.1621 S12: -0.5781 S13: -0.6095
REMARK 3 S21: 1.5075 S22: -0.1418 S23: 1.5165
REMARK 3 S31: 0.6813 S32: -0.7497 S33: 0.3039
REMARK 3
REMARK 3 TLS GROUP : 3
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : A 233 A 344
REMARK 3 ORIGIN FOR THE GROUP (A): 46.0571 -2.7752 -25.8630
REMARK 3 T TENSOR
REMARK 3 T11: 0.1066 T22: 0.0167
REMARK 3 T33: -0.0451 T12: 0.0255
REMARK 3 T13: 0.0388 T23: 0.0347
REMARK 3 L TENSOR
REMARK 3 L11: 3.8478 L22: 7.4374
REMARK 3 L33: 9.3826 L12: 0.3578
REMARK 3 L13: 0.3188 L23: 3.7325
REMARK 3 S TENSOR
REMARK 3 S11: -0.3965 S12: 0.3756 S13: -0.4833
REMARK 3 S21: -0.3564 S22: 0.2454 S23: -0.3253
REMARK 3 S31: 0.7984 S32: 0.1979 S33: 0.1511
REMARK 3
REMARK 3 TLS GROUP : 4
REMARK 3 NUMBER OF COMPONENTS GROUP : 2
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : P 1 P 10
REMARK 3 RESIDUE RANGE : T 2 T 15
REMARK 3 ORIGIN FOR THE GROUP (A): 29.0816 -2.6905 -16.7683
REMARK 3 T TENSOR
REMARK 3 T11: 0.3642 T22: -0.0767
REMARK 3 T33: 0.5107 T12: 0.1741
REMARK 3 T13: -0.1298 T23: 0.2685
REMARK 3 L TENSOR
REMARK 3 L11: 2.3760 L22: 10.4653
REMARK 3 L33: 2.6938 L12: 0.3269
REMARK 3 L13: 0.5364 L23: -0.7635
REMARK 3 S TENSOR
REMARK 3 S11: -0.0688 S12: 0.7358 S13: 0.6858
REMARK 3 S21: -0.3183 S22: 0.0520 S23: 1.8674
REMARK 3 S31: -0.4840 S32: -0.2952 S33: 0.0169
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: NULL
REMARK 4
REMARK 4 3BQ1 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_1000045824.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 28-MAR-07
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 : X29A
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL
REMARK 200 WAVELENGTH OR RANGE (A) : 1.0809
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 : HKL-2000
REMARK 200 DATA SCALING SOFTWARE : HKL-2000
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15669
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 (%) : 99.6
REMARK 200 DATA REDUNDANCY : 6.500
REMARK 200 R MERGE (I) : 0.06600
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 24.4000
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 (%) : 99.1
REMARK 200 DATA REDUNDANCY IN SHELL : 5.10
REMARK 200 R MERGE FOR SHELL (I) : 0.52300
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.100
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 (%): 57.26
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.88
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 35.10500
REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 62.48000
REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 62.48000
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 17.55250
REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 62.48000
REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 62.48000
REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 52.65750
REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 62.48000
REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 62.48000
REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 17.55250
REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 62.48000
REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 62.48000
REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 52.65750
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 35.10500
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: 3800 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 20580 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -34.8 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 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 DT T 2 P OP1 OP2
REMARK 470 DC T 15 C5' C4' O4' C3' O3' C2' C1'
REMARK 470 DC T 15 N1 C2 O2 N3 C4 N4 C5
REMARK 470 DC T 15 C6
REMARK 470 ARG A 36 CG CD NE CZ NH1 NH2
REMARK 470 THR A 37 OG1 CG2
REMARK 470 LYS A 38 CG CD CE NZ
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. = -6.3 DEGREES
REMARK 500 DG P 4 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES
REMARK 500 DG P 4 C3' - O3' - P ANGL. DEV. = 8.4 DEGREES
REMARK 500 DC P 6 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES
REMARK 500 DT T 2 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES
REMARK 500 DT T 2 C3' - O3' - P ANGL. DEV. = 8.9 DEGREES
REMARK 500 DC T 7 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES
REMARK 500 DC T 8 C3' - C2' - C1' ANGL. DEV. = -4.8 DEGREES
REMARK 500 DC T 8 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES
REMARK 500 DC T 11 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES
REMARK 500 DT T 12 O4' - C1' - N1 ANGL. DEV. = 2.4 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 60.16 28.61
REMARK 500 ARG A 36 -162.98 -68.58
REMARK 500 LYS A 220 -64.64 -146.06
REMARK 500 SER A 235 36.67 -166.88
REMARK 500 LEU A 293 -11.52 71.07
REMARK 500 LYS A 298 135.31 -174.06
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 A4001 CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 DG3 P 11 O2B
REMARK 620 2 DG3 P 11 O2G 77.7
REMARK 620 3 ASP A 7 OD2 161.2 102.9
REMARK 620 4 PHE A 8 O 84.8 98.4 76.5
REMARK 620 5 ASP A 105 OD2 88.4 162.0 93.9 91.7
REMARK 620 6 HOH A4018 O 112.0 109.9 85.7 149.3 64.5
REMARK 620 N 1 2 3 4 5
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 4001
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DG3 P 11
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: 3BQ2 RELATED DB: PDB
REMARK 900 POST-INSERTION BINARY COMPLEX OF DBH
DBREF 3BQ1 A 1 354 UNP Q4JB80 DPO4_SULAC 1 354
DBREF 3BQ1 P 1 10 PDB 3BQ1 3BQ1 1 10
DBREF 3BQ1 T 1 15 PDB 3BQ1 3BQ1 1 15
SEQRES 1 P 10 DG DA DA DG DC DC DG DG DC 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 DG3 P 11 30
HET CA A4001 1
HETNAM DG3 2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE
HETNAM CA CALCIUM ION
FORMUL 4 DG3 C10 H16 N5 O12 P3
FORMUL 5 CA CA 2+
FORMUL 6 HOH *41(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 LYS A 94 1 18
HELIX 6 6 ASN A 118 LYS A 138 1 21
HELIX 7 7 ASN A 148 SER A 159 1 12
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 GLU A 197 1 10
HELIX 11 11 LYS A 202 ILE A 206 5 5
HELIX 12 12 ASN A 210 GLY A 219 1 10
HELIX 13 13 LYS A 220 GLN A 231 1 12
HELIX 14 14 ASP A 258 VAL A 277 1 20
HELIX 15 15 SER A 307 ASP A 326 1 20
SHEET 1 A 5 LYS A 98 SER A 103 0
SHEET 2 A 5 GLU A 106 ASP A 110 -1 O TYR A 108 N GLU A 100
SHEET 3 A 5 VAL A 3 PHE A 8 -1 N VAL A 6 O ALA A 107
SHEET 4 A 5 VAL A 141 ALA A 146 -1 O ALA A 146 N VAL A 3
SHEET 5 A 5 LEU A 164 VAL A 166 1 O GLY A 165 N VAL A 143
SHEET 1 B 3 ALA A 42 ALA A 46 0
SHEET 2 B 3 LEU A 28 VAL A 32 -1 N VAL A 30 O THR A 45
SHEET 3 B 3 ILE A 72 PRO A 75 1 O VAL A 74 N CYS A 31
SHEET 1 C 2 LYS A 241 SER A 242 0
SHEET 2 C 2 ILE A 341 ILE A 342 -1 O ILE A 341 N SER A 242
SHEET 1 D 4 HIS A 246 THR A 256 0
SHEET 2 D 4 VAL A 331 ASP A 339 -1 O ILE A 334 N LEU A 250
SHEET 3 D 4 ARG A 283 MET A 290 -1 N ILE A 289 O ARG A 333
SHEET 4 D 4 ILE A 295 LYS A 301 -1 O LEU A 296 N ALA A 288
LINK O2B DG3 P 11 CA CA A4001 1555 1555 2.40
LINK O2G DG3 P 11 CA CA A4001 1555 1555 2.32
LINK OD2 ASP A 7 CA CA A4001 1555 1555 2.30
LINK O PHE A 8 CA CA A4001 1555 1555 2.32
LINK OD2 ASP A 105 CA CA A4001 1555 1555 2.30
LINK CA CA A4001 O HOH A4018 1555 1555 2.98
CISPEP 1 LYS A 160 PRO A 161 0 -5.17
SITE 1 AC1 4 ASP A 7 PHE A 8 ASP A 105 HOH A4018
SITE 1 AC2 16 ASP A 7 PHE A 8 TYR A 10 PHE A 11
SITE 2 AC2 16 PHE A 12 ALA A 44 THR A 45 ARG A 51
SITE 3 AC2 16 GLY A 58 ASP A 105 LYS A 160 HOH A4018
SITE 4 AC2 16 DG P 10 HOH P 29 DC T 3 DC T 4
CRYST1 124.960 124.960 70.210 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 0.008003 0.000000 0.000000 0.00000
SCALE2 0.000000 0.008003 0.000000 0.00000
SCALE3 0.000000 0.000000 0.014243 0.00000
(ATOM LINES ARE NOT SHOWN.)
END