HEADER DNA 01-AUG-02 1MA8 TITLE A-DNA DECAMER GCGTA(UMS)ACGC WITH INCORPORATED 2'-METHYLSELENO-URIDINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*GP*CP*GP*TP*AP*UMSP*AP*CP*GP*C)-3'; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: U-SE-MODIFIED DNA DUPLEX SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS 2'-METHYLSELENO-URIDINE, DNA EXPDTA X-RAY DIFFRACTION AUTHOR M.TEPLOVA,C.J.WILDS,Z.WAWRZAK,V.TERESHKO,Q.DU,N.CARRASCO,Z.HUANG, AUTHOR 2 M.EGLI REVDAT 4 14-FEB-24 1MA8 1 REMARK REVDAT 3 24-JUL-19 1MA8 1 REMARK LINK REVDAT 2 24-FEB-09 1MA8 1 VERSN REVDAT 1 11-DEC-02 1MA8 0 JRNL AUTH M.TEPLOVA,C.J.WILDS,Z.WAWRZAK,V.TERESHKO,Q.DU,N.CARRASCO, JRNL AUTH 2 Z.HUANG,M.EGLI JRNL TITL COVALENT INCORPORATION OF SELENIUM INTO OLIGONUCLEOTIDES FOR JRNL TITL 2 X-RAY CRYSTAL STRUCTURE DETERMINATION VIA MAD: PROOF OF JRNL TITL 3 PRINCIPLE JRNL REF BIOCHIMIE V. 84 849 2002 JRNL REFN ISSN 0300-9084 JRNL PMID 12458077 JRNL DOI 10.1016/S0300-9084(02)01440-2 REMARK 2 REMARK 2 RESOLUTION. 1.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : 0.173 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 1048 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 406 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 141 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : NULL REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : NULL REMARK 3 NUMBER OF RESTRAINTS : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.015 REMARK 3 ANGLE DISTANCES (A) : 0.023 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : NULL REMARK 3 ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : NULL REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL REMARK 3 SIMILAR ADP COMPONENTS (A**2) : NULL REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : NULL REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1MA8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-AUG-02. REMARK 100 THE DEPOSITION ID IS D_1000016790. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-MAY-01 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 5ID-B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : NULL 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 : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23332 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04900 REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.35 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.26300 REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.63 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.88 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MPD, SPERMINE TETRAHYDROCHLORIDE, REMARK 280 POTASSIUM CHLORIDE, SODIUM CHLORIDE, SODIUM CACODYLATE, PH 7.0, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K 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 12.27750 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 22.67000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.98350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 22.67000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 12.27750 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 21.98350 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: DIMERIC 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH B 791 O HOH B 820 0.91 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 846 O HOH B 842 1455 1.95 REMARK 500 O HOH A 752 O HOH A 808 3655 2.02 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 DG A 1 N7 DG A 1 C8 0.040 REMARK 500 DC A 2 C2' DC A 2 C1' -0.070 REMARK 500 DC A 2 N1 DC A 2 C6 -0.046 REMARK 500 DG A 3 C2' DG A 3 C1' -0.074 REMARK 500 DT A 4 C2' DT A 4 C1' -0.082 REMARK 500 DA A 5 N3 DA A 5 C4 -0.037 REMARK 500 DC A 8 N1 DC A 8 C6 -0.039 REMARK 500 DG A 9 C2' DG A 9 C1' -0.062 REMARK 500 DG B 111 C2' DG B 111 C1' -0.073 REMARK 500 DC B 112 C5' DC B 112 C4' 0.045 REMARK 500 DC B 112 C2' DC B 112 C1' -0.062 REMARK 500 DC B 112 O4' DC B 112 C1' 0.074 REMARK 500 DC B 112 O4' DC B 112 C4' 0.065 REMARK 500 DC B 112 O3' DC B 112 C3' 0.081 REMARK 500 DG B 113 O4' DG B 113 C4' 0.056 REMARK 500 DA B 115 C2' DA B 115 C1' -0.080 REMARK 500 DA B 115 O4' DA B 115 C1' 0.072 REMARK 500 DG B 119 C3' DG B 119 C2' -0.060 REMARK 500 DG B 119 C2' DG B 119 C1' -0.100 REMARK 500 DG B 119 O4' DG B 119 C1' 0.086 REMARK 500 DC B 120 C2' DC B 120 C1' -0.083 REMARK 500 DC B 120 O4' DC B 120 C1' 0.084 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 A 1 O4' - C1' - N9 ANGL. DEV. = -5.3 DEGREES REMARK 500 DC A 2 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 DC A 2 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 DG A 3 O4' - C1' - N9 ANGL. DEV. = -6.5 DEGREES REMARK 500 DT A 4 O4' - C1' - N1 ANGL. DEV. = -4.3 DEGREES REMARK 500 DA A 7 O4' - C4' - C3' ANGL. DEV. = -2.8 DEGREES REMARK 500 DC A 8 O4' - C4' - C3' ANGL. DEV. = -2.6 DEGREES REMARK 500 DG A 9 O4' - C1' - N9 ANGL. DEV. = -5.4 DEGREES REMARK 500 DG A 9 N1 - C6 - O6 ANGL. DEV. = 3.8 DEGREES REMARK 500 DC A 10 N3 - C4 - N4 ANGL. DEV. = -4.8 DEGREES REMARK 500 DG B 111 O4' - C1' - N9 ANGL. DEV. = -5.1 DEGREES REMARK 500 DC B 112 C1' - O4' - C4' ANGL. DEV. = -7.6 DEGREES REMARK 500 DG B 113 C5 - N7 - C8 ANGL. DEV. = -3.2 DEGREES REMARK 500 DG B 113 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 DG B 113 N1 - C6 - O6 ANGL. DEV. = -3.8 DEGREES REMARK 500 DG B 113 C5 - C6 - O6 ANGL. DEV. = 3.9 DEGREES REMARK 500 DT B 114 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 DT B 114 C4 - C5 - C7 ANGL. DEV. = 3.8 DEGREES REMARK 500 DA B 115 O4' - C1' - N9 ANGL. DEV. = -5.7 DEGREES REMARK 500 DA B 115 C8 - N9 - C4 ANGL. DEV. = 2.5 DEGREES REMARK 500 DA B 117 P - O5' - C5' ANGL. DEV. = -10.1 DEGREES REMARK 500 DG B 119 O4' - C1' - N9 ANGL. DEV. = -5.2 DEGREES REMARK 500 DC B 120 O4' - C1' - N1 ANGL. DEV. = -5.9 DEGREES REMARK 500 REMARK 500 REMARK: NULL DBREF 1MA8 A 1 10 PDB 1MA8 1MA8 1 10 DBREF 1MA8 B 111 120 PDB 1MA8 1MA8 111 120 SEQRES 1 A 10 DG DC DG DT DA UMS DA DC DG DC SEQRES 1 B 10 DG DC DG DT DA UMS DA DC DG DC MODRES 1MA8 UMS A 6 DU MODRES 1MA8 UMS B 116 DU HET UMS A 6 33 HET UMS B 116 33 HETNAM UMS 2'-METHYLSELENYL-2'-DEOXYURIDINE-5'-PHOSPHATE FORMUL 1 UMS 2(C10 H15 N2 O8 P SE) FORMUL 3 HOH *141(H2 O) LINK O3' DA A 5 P UMS A 6 1555 1555 1.60 LINK O3' UMS A 6 P DA A 7 1555 1555 1.58 LINK O3' DA B 115 P UMS B 116 1555 1555 1.62 LINK O3' UMS B 116 P DA B 117 1555 1555 1.62 CRYST1 24.555 43.967 45.340 90.00 90.00 90.00 P 21 21 21 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 0.040725 0.000000 0.000000 0.00000 SCALE2 0.000000 0.022744 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022056 0.00000