2B2B - Header Asymmetric Unit

HEADER DNA 19-SEP-05 2B2B

TITLE STRUCTURAL DISTORTIONS IN PSORALEN CROSS-LINKED DNA

COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*CP*GP*CP*TP*AP*GP*CP*GP*G)-3'; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES

SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THE D(CCGCTAGCGG) DECAMER DNA SEQUENCE WAS SOURCE 4 SYNTHESIZED USING- CYANOETHYL PHOSPHORAMIDITE CHEMISTRY ON SOURCE 5 AN APPLIED BIOSYSTEMS DNA SYNTHESIZER IN THE CENTER FOR SOURCE 6 GENE RESEARCH AND BIOTECHNOLOGY AT OREGON STATE SOURCE 7 UNIVERSITY. THE 5-O-DIMETHOXYTRITYL GROUP WAS LEFT SOURCE 8 ATTACHED TO FACILITATE SEPARATION FROM FAILURE SEQUENCES SOURCE 9 USING REVERSE-PHASE HPLC. THE TARGET FRACTION WAS THEN SOURCE 10 DRIED OVERNIGHT, DETRITYLATED USING 3% ACETIC ACID, SOURCE 11 DESALTED ON A SEPHADEX (SIGMA) G-25 SIZE EXCLUSION COLUMN SOURCE 12 AND DRIED OVERNIGHT.

KEYWDS RECOMBINATION, PSORALEN, NUCLEIC ACID STRUCTURE, DNA

EXPDTA X-RAY DIFFRACTION

AUTHOR F.A.HAYS,H.YONGGANG,B.F.EICHMAN,W.KONG,J.HEARST,P.S.HO

REVDAT 2 24-FEB-09 2B2B 1 VERSN REVDAT 1 03-OCT-06 2B2B 0

JRNL AUTH F.A.HAYS,H.YONGGANG,B.F.EICHMAN,W.KONG,J.HEARST, JRNL AUTH 2 P.S.HO JRNL TITL STRUCTURAL DISTORTIONS IN PSORALEN CROSS-LINKED DNA JRNL REF TO BE PUBLISHED JRNL REFN

REMARK 1

REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS.

REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.89 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 6518 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) : 0.215 REMARK 3 R VALUE (WORKING SET) : 0.210 REMARK 3 FREE R VALUE : 0.262 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.800 REMARK 3 FREE R VALUE TEST SET COUNT : 788 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) : 1.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.54 REMARK 3 REFLECTION IN BIN (WORKING SET) : 238 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.00 REMARK 3 BIN R VALUE (WORKING SET) : 0.2650 REMARK 3 BIN FREE R VALUE SET COUNT : 26 REMARK 3 BIN FREE R VALUE : 0.2540 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 404 REMARK 3 HETEROGEN ATOMS : 30 REMARK 3 SOLVENT ATOMS : 194 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.59 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.79000 REMARK 3 B22 (A**2) : 0.80000 REMARK 3 B33 (A**2) : -0.50000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.40000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.130 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.127 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.093 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.492 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.909 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.886 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 480 ; 0.016 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 714 ; 3.111 ; 3.000 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 81 ; 0.137 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 223 ; 0.016 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 279 ; 0.366 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 269 ; 0.326 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 175 ; 0.290 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 5 ; 0.314 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 58 ; 0.275 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 54 ; 0.219 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): 2 ; 0.188 ; 0.200 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): 1 ; 0.054 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 580 ; 2.500 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 714 ; 3.041 ; 4.500 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 : 1.20 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 REMARK 3 RIDING POSITIONS. RESIDUE (B C 14 ) AND RESIDUE (B T 15 ) ARE REMARK 3 NOT LINKED. DISTANCE OF O3*-P BOND IS 1.91

REMARK 4 REMARK 4 2B2B COMPLIES WITH FORMAT V. 3.15, 01-DEC-08

REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-SEP-05. REMARK 100 THE RCSB ID CODE IS RCSB034587.

REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-MAR-03 REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7306 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 26.890 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 83.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.08100 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 18.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 50.2 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.62800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: EPMR REMARK 200 STARTING MODEL: PDB ENTRY 1FHY REMARK 200 REMARK 200 REMARK: NULL

REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.92 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.12 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.5 MM HMT-D(CCGCTAGCGG), 30 MM REMARK 280 NACACODYLATE (PH = 7.0), 25 MM CALCIUM CHLORIDE AND 5% 2- REMARK 280 METHYL-2,4-PENTANEDIOL (MPD) AGAINST A 30 ML RESERVOIR REMARK 280 SOLUTION OF 15% MPD (BOOSTED TO 20% TWO WEEKS LATER), VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298K

REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 34.50350 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 11.24800 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 34.50350 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 11.24800 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 BIOMT1 2 -1.000000 0.000000 0.000000 41.01661 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 34.81303

REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 173 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 181 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 155 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 189 LIES ON A SPECIAL POSITION.

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 C5 DT A 5 C3 PSO A 21 1.52 REMARK 500 O HOH A 53 O HOH A 142 2.00 REMARK 500 C7 DT A 5 C4 PSO A 21 2.03 REMARK 500 O HOH B 130 O HOH B 131 2.07 REMARK 500 O2 DC B 12 O HOH B 63 2.08 REMARK 500 OP1 DC B 14 O HOH B 150 2.09 REMARK 500 OP2 DG B 19 O HOH B 51 2.11 REMARK 500 O HOH A 52 O HOH A 177 2.12 REMARK 500 O HOH A 120 O HOH A 174 2.13 REMARK 500 C5 DT B 15 C5' PSO A 21 2.14 REMARK 500 O HOH A 70 O HOH A 166 2.15 REMARK 500 O HOH B 28 O HOH B 38 2.16 REMARK 500 O HOH B 49 O HOH B 105 2.16 REMARK 500 N1 DG B 13 O HOH B 168 2.16 REMARK 500 C6 DT B 15 C4' PSO A 21 2.18 REMARK 500 N3 DC B 12 O HOH B 168 2.19 REMARK 500 OP1 DG B 13 O HOH B 159 2.19 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 HOH A 127 O HOH B 98 2666 2.15 REMARK 500 REMARK 500 REMARK: NULL 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 DT A 5 C5 DT A 5 C6 0.175 REMARK 500 DT A 5 O3' DA A 6 P 0.077 REMARK 500 DC A 8 O3' DC A 8 C3' -0.044 REMARK 500 DG B 13 N7 DG B 13 C8 -0.038 REMARK 500 DT B 15 C5 DT B 15 C6 0.207 REMARK 500 DC B 14 O3' DT B 15 P 0.300 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 DC A 1 O4' - C4' - C3' ANGL. DEV. = -2.5 DEGREES REMARK 500 DC A 1 C1' - O4' - C4' ANGL. DEV. = 4.9 DEGREES REMARK 500 DC A 1 N1 - C1' - C2' ANGL. DEV. = 8.4 DEGREES REMARK 500 DC A 1 C6 - N1 - C2 ANGL. DEV. = -3.4 DEGREES REMARK 500 DC A 2 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 DG A 3 C3' - C2' - C1' ANGL. DEV. = -6.2 DEGREES REMARK 500 DG A 3 C5 - C6 - O6 ANGL. DEV. = -3.8 DEGREES REMARK 500 DC A 4 O4' - C4' - C3' ANGL. DEV. = 4.8 DEGREES REMARK 500 DC A 4 C1' - O4' - C4' ANGL. DEV. = -6.8 DEGREES REMARK 500 DC A 4 O4' - C1' - C2' ANGL. DEV. = 4.2 DEGREES REMARK 500 DC A 4 O4' - C1' - N1 ANGL. DEV. = -4.6 DEGREES REMARK 500 DC A 4 N1 - C2 - O2 ANGL. DEV. = 4.9 DEGREES REMARK 500 DT A 5 O4' - C1' - N1 ANGL. DEV. = -6.7 DEGREES REMARK 500 DT A 5 C2 - N3 - C4 ANGL. DEV. = 3.9 DEGREES REMARK 500 DT A 5 C4 - C5 - C6 ANGL. DEV. = -6.4 DEGREES REMARK 500 DT A 5 C4 - C5 - C7 ANGL. DEV. = -7.3 DEGREES REMARK 500 DT A 5 C6 - C5 - C7 ANGL. DEV. = -8.7 DEGREES REMARK 500 DA A 6 O4' - C1' - N9 ANGL. DEV. = -5.5 DEGREES REMARK 500 DA A 6 N1 - C2 - N3 ANGL. DEV. = -4.1 DEGREES REMARK 500 DA A 6 C2 - N3 - C4 ANGL. DEV. = 3.6 DEGREES REMARK 500 DA A 6 N9 - C4 - C5 ANGL. DEV. = -3.8 DEGREES REMARK 500 DA A 6 N3 - C4 - N9 ANGL. DEV. = 4.9 DEGREES REMARK 500 DT A 5 C3' - O3' - P ANGL. DEV. = 7.8 DEGREES REMARK 500 DG A 7 O4' - C1' - N9 ANGL. DEV. = 4.9 DEGREES REMARK 500 DG A 7 C2 - N3 - C4 ANGL. DEV. = 4.1 DEGREES REMARK 500 DC A 8 O4' - C1' - N1 ANGL. DEV. = -7.1 DEGREES REMARK 500 DC A 8 O3' - P - OP1 ANGL. DEV. = 6.7 DEGREES REMARK 500 DG A 9 O4' - C1' - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 DG A 10 C4 - C5 - N7 ANGL. DEV. = -2.5 DEGREES REMARK 500 DC B 12 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 DC B 11 C3' - O3' - P ANGL. DEV. = 8.1 DEGREES REMARK 500 DG B 13 C6 - N1 - C2 ANGL. DEV. = -3.9 DEGREES REMARK 500 DG B 13 N3 - C2 - N2 ANGL. DEV. = -4.6 DEGREES REMARK 500 DC B 14 O4' - C1' - N1 ANGL. DEV. = -7.1 DEGREES REMARK 500 DT B 15 N1 - C1' - C2' ANGL. DEV. = 10.3 DEGREES REMARK 500 DT B 15 O4' - C1' - N1 ANGL. DEV. = -6.1 DEGREES REMARK 500 DT B 15 C4 - C5 - C6 ANGL. DEV. = -4.4 DEGREES REMARK 500 DT B 15 C4 - C5 - C7 ANGL. DEV. = -5.0 DEGREES REMARK 500 DT B 15 C6 - C5 - C7 ANGL. DEV. = -11.6 DEGREES REMARK 500 DA B 16 O4' - C1' - C2' ANGL. DEV. = 3.1 DEGREES REMARK 500 DG B 17 O4' - C1' - N9 ANGL. DEV. = -5.4 DEGREES REMARK 500 DG B 17 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 DC B 18 O4' - C1' - N1 ANGL. DEV. = -5.8 DEGREES REMARK 500 DG B 19 O4' - C1' - C2' ANGL. DEV. = 3.4 DEGREES REMARK 500 DG B 20 N9 - C1' - C2' ANGL. DEV. = 10.0 DEGREES REMARK 500 DG B 20 C2 - N3 - C4 ANGL. DEV. = 3.1 DEGREES REMARK 500 DG B 20 C8 - N9 - C4 ANGL. DEV. = -3.0 DEGREES REMARK 500 REMARK 500 REMARK: NULL

REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 56 DISTANCE = 5.49 ANGSTROMS REMARK 525 HOH B 184 DISTANCE = 5.26 ANGSTROMS

REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 SPM A 22

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 NA A 27 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DC A 4 OP1 REMARK 620 2 DT B 15 O4 110.0 REMARK 620 3 HOH A 29 O 52.5 106.7 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 23 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG B 17 OP2 REMARK 620 2 HOH B 97 O 78.2 REMARK 620 3 HOH B 223 O 81.0 73.5 REMARK 620 4 HOH B 50 O 101.0 179.1 105.8 REMARK 620 5 HOH B 93 O 166.2 110.8 111.1 70.0 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 24 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 180 O REMARK 620 2 HOH A 166 O 93.0 REMARK 620 3 HOH A 33 O 78.4 150.9 REMARK 620 4 HOH A 70 O 58.5 54.4 98.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 25 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 90 O REMARK 620 2 HOH A 42 O 81.1 REMARK 620 3 HOH A 224 O 135.5 69.0 REMARK 620 4 HOH B 75 O 152.2 124.7 70.2 REMARK 620 N 1 2 3

REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SPM A 22 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 23 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 24 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 25 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 26 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 27 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PSO A 21

REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1FHY RELATED DB: PDB REMARK 900 PSORALEN CROSS-LINKED D(CCGCTAGCGG) FORMS HOLLIDAY JUNCTION

DBREF 2B2B A 1 10 PDB 2B2B 2B2B 1 10 DBREF 2B2B B 11 20 PDB 2B2B 2B2B 11 20

SEQRES 1 A 10 DC DC DG DC DT DA DG DC DG DG SEQRES 1 B 10 DC DC DG DC DT DA DG DC DG DG

HET SPM A 22 6 HET CA B 23 1 HET NA A 24 1 HET CA A 25 1 HET NA B 26 1 HET NA A 27 1 HET PSO A 21 19

HETNAM SPM SPERMINE HETNAM CA CALCIUM ION HETNAM NA SODIUM ION HETNAM PSO 4'-HYDROXYMETHYL-4,5',8-TRIMETHYLPSORALEN

FORMUL 3 SPM C10 H26 N4 FORMUL 4 CA 2(CA 2+) FORMUL 5 NA 3(NA 1+) FORMUL 9 PSO C15 H14 O4 FORMUL 10 HOH *194(H2 O)

LINK C5 DT A 5 C4 PSO A 21 1555 1555 1.47 LINK C6 DT A 5 C3 PSO A 21 1555 1555 1.46 LINK C5 DT B 15 C4' PSO A 21 1555 1555 1.53 LINK C6 DT B 15 C5' PSO A 21 1555 1555 1.49 LINK OP1 DC A 4 NA NA A 27 1555 1555 2.60 LINK O4 DT B 15 NA NA A 27 1555 1555 2.80 LINK OP2 DG B 17 CA CA B 23 1555 1555 2.30 LINK CA CA B 23 O HOH B 97 1555 1555 2.70 LINK CA CA B 23 O HOH B 223 1555 1555 2.24 LINK CA CA B 23 O HOH B 50 1555 1555 2.57 LINK CA CA B 23 O HOH B 93 1555 1555 2.94 LINK NA NA A 24 O HOH A 180 1555 1555 2.57 LINK NA NA A 24 O HOH A 166 1555 1555 2.03 LINK NA NA A 24 O HOH A 33 1555 1555 2.66 LINK NA NA A 24 O HOH A 70 1555 1555 2.56 LINK CA CA A 25 O HOH A 90 1555 1555 2.78 LINK CA CA A 25 O HOH A 42 1555 1555 2.54 LINK CA CA A 25 O HOH A 224 1555 1555 2.29 LINK CA CA A 25 O HOH B 75 1555 1555 2.39 LINK NA NA A 27 O HOH A 29 1555 1555 2.48

SITE 1 AC1 6 DC A 1 DG A 10 HOH A 177 DG B 19 SITE 2 AC1 6 HOH B 111 HOH B 204 SITE 1 AC2 6 DG A 9 DG B 17 HOH B 50 HOH B 93 SITE 2 AC2 6 HOH B 97 HOH B 223 SITE 1 AC3 6 HOH A 33 HOH A 57 HOH A 70 HOH A 151 SITE 2 AC3 6 HOH A 166 HOH A 180 SITE 1 AC4 4 HOH A 42 HOH A 90 HOH A 224 HOH B 75 SITE 1 AC5 5 HOH A 36 HOH A 53 HOH A 126 HOH A 142 SITE 2 AC5 5 HOH B 48 SITE 1 AC6 4 DC A 4 HOH A 29 HOH A 141 DT B 15 SITE 1 AC7 5 DC A 4 DT A 5 DA A 6 DT B 15 SITE 2 AC7 5 DA B 16

CRYST1 69.007 22.496 44.670 90.00 128.80 90.00 C 1 2 1 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 0.014491 0.000000 0.011653 0.00000

SCALE2 0.000000 0.044452 0.000000 0.00000

SCALE3 0.000000 0.000000 0.028726 0.00000