PDB Short entry for 2XY5 HEADER TRANSFERASE/DNA 15-NOV-10 2XY5 TITLE CRYSTAL STRUCTURE OF AN ARTIFICIAL SALEN-COPPER BASEPAIR IN COMPLEX TITLE 2 WITH FRAGMENT DNA POLYMERASE I FROM BACILLUS STEAROTHERMOPHILUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE I; COMPND 3 CHAIN: A; COMPND 4 EC: 2.7.7.7; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: 5'-D(*GP*AP*CP*CP*SAYP*TP*CP*CP*CP*TP)-3'; COMPND 8 CHAIN: B; COMPND 9 SYNONYM: POLYDESOXYRIBONUCLEOTIDE; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: 5'-D(*AP*GP*GP*GP*AP*SAYP*GP*GP*TP*CP)-3'; COMPND 13 CHAIN: C; COMPND 14 SYNONYM: POLYDESOXYRIBONUCLEOTIDE; COMPND 15 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GEOBACILLUS STEAROTHERMOPHILUS; SOURCE 3 ORGANISM_TAXID: 1422; SOURCE 4 STRAIN: DSM 22; SOURCE 5 ATCC: 12980; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 OTHER_DETAILS: GERMAN COLLECTION OF MICROORGANISMS (DSM); SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 13 ORGANISM_TAXID: 32630; SOURCE 14 MOL_ID: 3; SOURCE 15 SYNTHETIC: YES; SOURCE 16 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 17 ORGANISM_TAXID: 32630 KEYWDS TRANSFERASE-DNA COMPLEX, SYNTHETIC BIOLOGY, METAL BASEPAIR, KEYWDS 2 REPLICATION, SALEN COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR C.KAUL,M.MUELLER,M.WAGNER,S.SCHNEIDER,T.CARELL REVDAT 5 20-DEC-23 2XY5 1 HETSYN LINK REVDAT 4 29-JUL-20 2XY5 1 COMPND REMARK HET HETNAM REVDAT 4 2 1 HETSYN FORMUL LINK SITE REVDAT 4 3 1 ATOM REVDAT 3 30-MAY-12 2XY5 1 JRNL REVDAT 2 05-OCT-11 2XY5 1 JRNL REMARK REVDAT 1 27-JUL-11 2XY5 0 JRNL AUTH C.KAUL,M.MUELLER,M.WAGNER,S.SCHNEIDER,T.CARELL JRNL TITL REVERSIBLE BOND FORMATION ENABLES THE REPLICATION AND JRNL TITL 2 AMPLIFICATION OF A CROSSLINKING SALEN COMPLEX AS AN JRNL TITL 3 ORTHOGONAL BASE PAIR. JRNL REF NATURE CHEM. V. 3 794 2011 JRNL REFN ISSN 1755-4330 JRNL PMID 21941252 JRNL DOI 10.1038/NCHEM.1117 REMARK 2 REMARK 2 RESOLUTION. 2.22 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 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) : 2.22 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 67.68 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 41587 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) : 0.195 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2189 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) : 2.22 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.28 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2985 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2320 REMARK 3 BIN FREE R VALUE SET COUNT : 157 REMARK 3 BIN FREE R VALUE : 0.2930 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4572 REMARK 3 NUCLEIC ACID ATOMS : 404 REMARK 3 HETEROGEN ATOMS : 56 REMARK 3 SOLVENT ATOMS : 183 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.68 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.20000 REMARK 3 B22 (A**2) : -1.26000 REMARK 3 B33 (A**2) : -0.95000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.219 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.188 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.126 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.938 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.941 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.915 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5169 ; 0.013 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 3371 ; 0.006 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7093 ; 1.469 ; 2.082 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8204 ; 0.904 ; 3.001 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 584 ; 5.434 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 222 ;36.037 ;24.279 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 822 ;14.113 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 36 ;21.697 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 810 ; 0.079 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5423 ; 0.005 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 963 ; 0.001 ; 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): 2910 ; 0.685 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1164 ; 0.145 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4676 ; 1.327 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2259 ; 2.063 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2415 ; 3.316 ; 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 2XY5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 15-NOV-10. REMARK 100 THE DEPOSITION ID IS D_1290046206. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-DEC-09 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 : SLS REMARK 200 BEAMLINE : X10SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.3785 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 43840 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.220 REMARK 200 RESOLUTION RANGE LOW (A) : 93.470 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 4.800 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.22 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.34 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.80 REMARK 200 R MERGE FOR SHELL (I) : 0.43000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.500 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 ENTRY 1U45 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 44.08550 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 52.79550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 46.73450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 52.79550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 44.08550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 46.73450 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: 4970 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27440 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -80.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 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 ARG A 306 CD NE CZ NH1 NH2 REMARK 470 GLU A 364 CD OE1 OE2 REMARK 470 LYS A 431 CE NZ REMARK 470 LYS A 434 CG CD CE NZ REMARK 470 ARG A 459 NE CZ NH1 NH2 REMARK 470 LYS A 498 CG CD CE NZ REMARK 470 ARG A 512 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 516 CG CD OE1 NE2 REMARK 470 GLU A 520 CG CD OE1 OE2 REMARK 470 GLU A 525 CG CD OE1 OE2 REMARK 470 LYS A 532 CG CD CE NZ REMARK 470 LYS A 548 CG CD CE NZ REMARK 470 LYS A 549 CG CD CE NZ REMARK 470 LYS A 551 CG CD CE NZ REMARK 470 THR A 552 OG1 CG2 REMARK 470 GLN A 579 CG CD OE1 NE2 REMARK 470 LYS A 593 CG CD CE NZ REMARK 470 LYS A 600 CG CD CE NZ REMARK 470 TYR A 719 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ARG A 729 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 730 CG CD CE NZ REMARK 470 GLU A 737 CD OE1 OE2 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 OD2 ASP A 598 O HOH A 2079 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 DG B 20 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 DT B 25 O4' - C1' - N1 ANGL. DEV. = 7.8 DEGREES REMARK 500 DC B 26 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 DC B 27 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 DC B 28 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 DG C 5 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 DG C 6 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 DA C 8 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 DT C 12 C5 - C4 - O4 ANGL. DEV. = -4.2 DEGREES REMARK 500 DC C 13 O4' - C1' - N1 ANGL. DEV. = 2.8 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 ALA A 421 41.70 -84.97 REMARK 500 GLU A 540 -63.47 -121.53 REMARK 500 ILE A 588 -70.75 -107.29 REMARK 500 LEU A 610 -59.50 -121.44 REMARK 500 ILE A 628 -31.48 -145.15 REMARK 500 HIS A 768 19.16 85.85 REMARK 500 HIS A 829 -54.82 71.37 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 EDN: REACTS WITH SAY AND CU1 TO YIELD A CROSSLINK OF TWO DNA REMARK 600 STRANDS. 2 H2O ARE RELEASED. REMARK 600 MRD: 2-METHYL-2,4-PENTANEDIOL ALSO KNOWN AS HEXYLENE GLYCOL REMARK 600 SAY: 2'-DEOXY-1'-(3-HYDROXY-4-FORMYLPHENYL)RIBOSE-5'-MONOPHOSPHATE 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 CU1 C1014 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SAY B 24 OAR REMARK 620 2 SAY C 9 OAR 89.9 REMARK 620 3 EDN C1015 NAA 103.9 165.4 REMARK 620 4 EDN C1015 NAD 162.6 98.4 66.9 REMARK 620 N 1 2 3 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2XY6 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A SALICYLIC ALDEHYDE BASEPAIR IN COMPLEX WITH REMARK 900 FRAGMENT DNA POLYMERASE I FROM BACILLUS STEAROTHERMOPHILUS REMARK 900 RELATED ID: 2XO7 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A DA:O- ALLYLHYDROXYLAMINE-DC BASEPAIR IN REMARK 900 COMPLEX WITH FRAGMENT DNA POLYMERASE I FROM BACILLUS REMARK 900 STEAROTHERMOPHILUS REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE ENTRY ABOVE IS NOT FROM STRAIN DSM22, BUT HAS MAXIMUM REMARK 999 IDENTITY. ONLY THR 550 IS SER IN OUR SEQUENCE. DBREF 2XY5 A 297 876 UNP E1C9K5 E1C9K5_BACST 1 580 DBREF 2XY5 B 20 29 PDB 2XY5 2XY5 20 29 DBREF 2XY5 C 4 13 PDB 2XY5 2XY5 4 13 SEQADV 2XY5 ALA A 296 UNP E1C9K5 EXPRESSION TAG SEQRES 1 A 581 ALA ALA LYS MET ALA PHE THR LEU ALA ASP ARG VAL THR SEQRES 2 A 581 GLU GLU MET LEU ALA ASP LYS ALA ALA LEU VAL VAL GLU SEQRES 3 A 581 VAL VAL GLU GLU ASN TYR HIS ASP ALA PRO ILE VAL GLY SEQRES 4 A 581 ILE ALA VAL VAL ASN GLU HIS GLY ARG PHE PHE LEU ARG SEQRES 5 A 581 PRO GLU THR ALA LEU ALA ASP PRO GLN PHE VAL ALA TRP SEQRES 6 A 581 LEU GLY ASP GLU THR LYS LYS LYS SER MET PHE ASP SER SEQRES 7 A 581 LYS ARG ALA ALA VAL ALA LEU LYS TRP LYS GLY ILE GLU SEQRES 8 A 581 LEU CYS GLY VAL SER PHE ASP LEU LEU LEU ALA ALA TYR SEQRES 9 A 581 LEU LEU ASP PRO ALA GLN GLY VAL ASP ASP VAL ALA ALA SEQRES 10 A 581 ALA ALA LYS MET LYS GLN TYR GLU ALA VAL ARG PRO ASP SEQRES 11 A 581 GLU ALA VAL TYR GLY LYS GLY ALA LYS ARG ALA VAL PRO SEQRES 12 A 581 ASP GLU PRO VAL LEU ALA GLU HIS LEU VAL ARG LYS ALA SEQRES 13 A 581 ALA ALA ILE TRP ALA LEU GLU ARG PRO PHE LEU ASP GLU SEQRES 14 A 581 LEU ARG ARG ASN GLU GLN ASP ARG LEU LEU VAL GLU LEU SEQRES 15 A 581 GLU GLN PRO LEU SER SER ILE LEU ALA GLU MET GLU PHE SEQRES 16 A 581 ALA GLY VAL LYS VAL ASP THR LYS ARG LEU GLU GLN MET SEQRES 17 A 581 GLY GLU GLU LEU ALA GLU GLN LEU ARG THR VAL GLU GLN SEQRES 18 A 581 ARG ILE TYR GLU LEU ALA GLY GLN GLU PHE ASN ILE ASN SEQRES 19 A 581 SER PRO LYS GLN LEU GLY VAL ILE LEU PHE GLU LYS LEU SEQRES 20 A 581 GLN LEU PRO VAL LEU LYS LYS SER LYS THR GLY TYR SER SEQRES 21 A 581 THR SER ALA ASP VAL LEU GLU LYS LEU ALA PRO TYR HIS SEQRES 22 A 581 GLU ILE VAL GLU ASN ILE LEU HIS TYR ARG GLN LEU GLY SEQRES 23 A 581 LYS LEU GLN SER THR TYR ILE GLU GLY LEU LEU LYS VAL SEQRES 24 A 581 VAL ARG PRO ASP THR LYS LYS VAL HIS THR ILE PHE ASN SEQRES 25 A 581 GLN ALA LEU THR GLN THR GLY ARG LEU SER SER THR GLU SEQRES 26 A 581 PRO ASN LEU GLN ASN ILE PRO ILE ARG LEU GLU GLU GLY SEQRES 27 A 581 ARG LYS ILE ARG GLN ALA PHE VAL PRO SER GLU SER ASP SEQRES 28 A 581 TRP LEU ILE PHE ALA ALA ASP TYR SER GLN ILE GLU LEU SEQRES 29 A 581 ARG VAL LEU ALA HIS ILE ALA GLU ASP ASP ASN LEU MET SEQRES 30 A 581 GLU ALA PHE ARG ARG ASP LEU ASP ILE HIS THR LYS THR SEQRES 31 A 581 ALA MET ASP ILE PHE GLN VAL SER GLU ASP GLU VAL THR SEQRES 32 A 581 PRO ASN MET ARG ARG GLN ALA LYS ALA VAL ASN PHE GLY SEQRES 33 A 581 ILE VAL TYR GLY ILE SER ASP TYR GLY LEU ALA GLN ASN SEQRES 34 A 581 LEU ASN ILE SER ARG LYS GLU ALA ALA GLU PHE ILE GLU SEQRES 35 A 581 ARG TYR PHE GLU SER PHE PRO GLY VAL LYS ARG TYR MET SEQRES 36 A 581 GLU ASN ILE VAL GLN GLU ALA LYS GLN LYS GLY TYR VAL SEQRES 37 A 581 THR THR LEU LEU HIS ARG ARG ARG TYR LEU PRO ASP ILE SEQRES 38 A 581 THR SER ARG ASN PHE ASN VAL ARG SER PHE ALA GLU ARG SEQRES 39 A 581 MET ALA MET ASN THR PRO ILE GLN GLY SER ALA ALA ASP SEQRES 40 A 581 ILE ILE LYS LYS ALA MET ILE ASP LEU ASN ALA ARG LEU SEQRES 41 A 581 LYS GLU GLU ARG LEU GLN ALA ARG LEU LEU LEU GLN VAL SEQRES 42 A 581 HIS ASP GLU LEU ILE LEU GLU ALA PRO LYS GLU GLU MET SEQRES 43 A 581 GLU ARG LEU CYS ARG LEU VAL PRO GLU VAL MET GLU GLN SEQRES 44 A 581 ALA VAL THR LEU ARG VAL PRO LEU LYS VAL ASP TYR HIS SEQRES 45 A 581 TYR GLY SER THR TRP TYR ASP ALA LYS SEQRES 1 B 10 DG DA DC DC SAY DT DC DC DC DT SEQRES 1 C 10 DA DG DG DG DA SAY DG DG DT DC HET SAY B 24 19 HET SAY C 9 19 HET GLC D 1 11 HET Z9N D 2 12 HET SO4 A1877 5 HET SO4 A1878 5 HET SO4 A1879 5 HET SO4 A1880 5 HET MRD A1881 8 HET CU1 C1014 1 HET EDN C1015 4 HETNAM SAY [(2R,3S,5R)-3-HYDROXY-5-(3-HYDROXY-4-METHANOYL-PHENYL) HETNAM 2 SAY OXOLAN-2-YL]METHYL DIHYDROGEN PHOSPHATE HETNAM GLC ALPHA-D-GLUCOPYRANOSE HETNAM Z9N ALPHA-D-FRUCTOFURANOSE HETNAM SO4 SULFATE ION HETNAM MRD (4R)-2-METHYLPENTANE-2,4-DIOL HETNAM CU1 COPPER (I) ION HETNAM EDN ETHANE-1,2-DIAMINE HETSYN SAY 2'-DEOXY-1'-(3-HYDROXY-4-FORMYLPHENYL)RIBOSE-5'- HETSYN 2 SAY MONOPHOSPHATE HETSYN GLC ALPHA-D-GLUCOSE; D-GLUCOSE; GLUCOSE HETSYN Z9N ALPHA-D-FRUCTOSE; D-FRUCTOSE; FRUCTOSE HETSYN EDN ETHYLENEDIAMINE FORMUL 2 SAY 2(C12 H15 O8 P) FORMUL 4 GLC C6 H12 O6 FORMUL 4 Z9N C6 H12 O6 FORMUL 5 SO4 4(O4 S 2-) FORMUL 9 MRD C6 H14 O2 FORMUL 10 CU1 CU 1+ FORMUL 11 EDN C2 H8 N2 FORMUL 12 HOH *183(H2 O) HELIX 1 1 THR A 308 ALA A 313 5 6 HELIX 2 2 ARG A 347 LEU A 352 1 6 HELIX 3 3 ASP A 354 ASP A 363 1 10 HELIX 4 4 ASP A 372 TRP A 382 1 11 HELIX 5 5 LEU A 394 ASP A 402 1 9 HELIX 6 6 PRO A 403 GLY A 406 5 4 HELIX 7 7 ASP A 409 MET A 416 1 8 HELIX 8 8 PRO A 424 GLY A 430 1 7 HELIX 9 9 LYS A 431 ARG A 435 5 5 HELIX 10 10 ASP A 439 ASN A 468 1 30 HELIX 11 11 GLN A 470 LEU A 477 1 8 HELIX 12 12 LEU A 477 GLY A 492 1 16 HELIX 13 13 ASP A 496 GLY A 523 1 28 HELIX 14 14 SER A 530 GLU A 540 1 11 HELIX 15 15 SER A 557 ALA A 565 1 9 HELIX 16 16 PRO A 566 HIS A 568 5 3 HELIX 17 17 GLU A 569 ILE A 588 1 20 HELIX 18 18 ILE A 588 VAL A 595 1 8 HELIX 19 19 LEU A 630 LYS A 635 1 6 HELIX 20 20 ILE A 636 GLN A 638 5 3 HELIX 21 21 GLN A 656 GLU A 667 1 12 HELIX 22 22 ASP A 668 ARG A 677 1 10 HELIX 23 23 ASP A 680 PHE A 690 1 11 HELIX 24 24 SER A 693 VAL A 697 5 5 HELIX 25 25 THR A 698 TYR A 714 1 17 HELIX 26 26 SER A 717 ASN A 726 1 10 HELIX 27 27 SER A 728 PHE A 743 1 16 HELIX 28 28 PHE A 743 GLY A 761 1 19 HELIX 29 29 PRO A 774 SER A 778 5 5 HELIX 30 30 ASN A 780 GLU A 818 1 39 HELIX 31 31 GLU A 840 ALA A 855 1 16 SHEET 1 AA 6 THR A 302 LEU A 303 0 SHEET 2 AA 6 GLY A 342 LEU A 346 1 O ARG A 343 N THR A 302 SHEET 3 AA 6 GLY A 334 ASN A 339 -1 O ILE A 335 N LEU A 346 SHEET 4 AA 6 LYS A 315 GLU A 321 -1 O ALA A 317 N VAL A 338 SHEET 5 AA 6 LYS A 367 MET A 370 1 O LYS A 367 N ALA A 316 SHEET 6 AA 6 VAL A 390 ASP A 393 1 N SER A 391 O LYS A 368 SHEET 1 AB 3 LYS A 601 VAL A 602 0 SHEET 2 AB 3 VAL A 493 VAL A 495 -1 O VAL A 493 N VAL A 602 SHEET 3 AB 3 PHE A 640 VAL A 641 -1 O VAL A 641 N LYS A 494 SHEET 1 AC 2 ILE A 605 ASN A 607 0 SHEET 2 AC 2 SER A 617 THR A 619 -1 O SER A 617 N ASN A 607 SHEET 1 AD 4 ARG A 823 GLN A 827 0 SHEET 2 AD 4 GLU A 831 PRO A 837 -1 O ILE A 833 N LEU A 825 SHEET 3 AD 4 TRP A 647 TYR A 654 -1 O LEU A 648 N ALA A 836 SHEET 4 AD 4 VAL A 864 GLY A 869 -1 O ASP A 865 N ASP A 653 SHEET 1 AE 2 TYR A 762 THR A 764 0 SHEET 2 AE 2 ARG A 770 TYR A 772 -1 O ARG A 771 N VAL A 763 LINK O3' DC B 23 P SAY B 24 1555 1555 1.60 LINK O3' SAY B 24 P DT B 25 1555 1555 1.59 LINK CAG SAY B 24 NAA EDN C1015 1555 1555 1.60 LINK O3' DA C 8 P SAY C 9 1555 1555 1.59 LINK O3' SAY C 9 P DG C 10 1555 1555 1.61 LINK CAG SAY C 9 NAD EDN C1015 1555 1555 1.36 LINK C1 GLC D 1 O2 Z9N D 2 1555 1555 1.41 LINK OAR SAY B 24 CU CU1 C1014 1555 1555 2.01 LINK OAR SAY C 9 CU CU1 C1014 1555 1555 1.82 LINK CU CU1 C1014 NAA EDN C1015 1555 1555 1.99 LINK CU CU1 C1014 NAD EDN C1015 1555 1555 2.27 CISPEP 1 GLU A 620 PRO A 621 0 0.54 CRYST1 88.171 93.469 105.591 90.00 90.00 90.00 P 21 21 21 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 0.011342 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010699 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009471 0.00000