HEADER DNA 14-APR-05 1VRO TITLE SELENIUM-ASSISTED NUCLEIC ACID CRYSTALLOGRAPHY: USE OF TITLE 2 PHOSPHOROSELENOATES FOR MAD PHASING OF A DNA STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*(GMS)P*CP*GP*CP*G)-3'; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: SYNTHESIZED WITH A SOLID-PHASE OLIGONUCLEOTIDE SOURCE 4 SYNTHESIZER USING DNA PHOSPHORAMIDITES AND POTASSIUM SELENOCYANIDE SOURCE 5 FOR INTRODUCING THE PHOSPHOROSELENOATE LINKAGE KEYWDS LEFT-HANDED Z-DNA, PHOSPHOROSELENOATE, MULTIWAVELENGTH ANOMALOUS KEYWDS 2 DISPERSION (MAD), COVALENT MODIFICATION OF OLIGONUCLEOTIDES, KEYWDS 3 OLIGONUCLEOTIDE ANALOGUE, PHASING STRATEGY, SYNCHROTRON, DNA EXPDTA X-RAY DIFFRACTION AUTHOR C.J.WILDS,R.PATTANAYEK,C.PAN,Z.WAWRZAK,M.EGLI REVDAT 4 27-DEC-23 1VRO 1 REMARK LINK REVDAT 3 24-JUL-19 1VRO 1 REMARK LINK REVDAT 2 24-FEB-09 1VRO 1 VERSN REVDAT 1 19-APR-05 1VRO 0 SPRSDE 19-APR-05 1VRO 1N6S JRNL AUTH C.J.WILDS,R.PATTANAYEK,C.PAN,Z.WAWRZAK,M.EGLI JRNL TITL SELENIUM-ASSISTED NUCLEIC ACID CRYSTALLOGRAPHY: USE OF JRNL TITL 2 PHOSPHOROSELENOATES FOR MAD PHASING OF A DNA STRUCTURE JRNL REF J.AM.CHEM.SOC. V. 124 14910 2002 JRNL REFN ISSN 0002-7863 JRNL PMID 12475332 JRNL DOI 10.1021/JA021058B REMARK 2 REMARK 2 RESOLUTION. 1.10 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) : 1.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.7 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) : 0.097 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.129 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 508 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 9718 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)) : 0.096 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.129 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 508 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 9692 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 240 REMARK 3 HETEROGEN ATOMS : 15 REMARK 3 SOLVENT ATOMS : 73 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 : 3005 REMARK 3 NUMBER OF RESTRAINTS : 5144 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.028 REMARK 3 ANGLE DISTANCES (A) : 0.022 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 : ENGH & HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: SHELX-97 REMARK 4 REMARK 4 1VRO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-APR-05. REMARK 100 THE DEPOSITION ID IS D_1000002092. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-JAN-02 REMARK 200 TEMPERATURE (KELVIN) : 120 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) : 0.9561, 0.9787, 0.9784 REMARK 200 MONOCHROMATOR : GRAPHITE 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 : 9718 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.100 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 200 DATA REDUNDANCY : 7.470 REMARK 200 R MERGE (I) : 0.04100 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 22.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.14 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.4 REMARK 200 DATA REDUNDANCY IN SHELL : 7.47 REMARK 200 R MERGE FOR SHELL (I) : 0.07500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 15.85 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 (%): 5.98 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.5MM DNA, 4MM-15MM MAGNESIUM REMARK 280 CHLORIDE, 50MM SODIUM CACODYLATE, 2MM-8MM SPERMINE REMARK 280 TETRAHYDROCHLORIDE AND RESERVOIR 30% 2-METHYL-2,4-PENTANEDIOL, REMARK 280 PH 7.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291.0K 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 8.88900 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 22.05800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 15.67400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 22.05800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 8.88900 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 15.67400 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 425 O HOH B 468 2.08 REMARK 500 O HOH A 459 O HOH A 463 2.16 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' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 DC A 1 C5 - C6 - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 DC A 1 C3' - O3' - P ANGL. DEV. = 8.8 DEGREES 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 MG B 301 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG B 112 N7 REMARK 620 2 HOH B 418 O 89.2 REMARK 620 3 HOH B 420 O 90.0 96.0 REMARK 620 4 HOH B 431 O 85.5 174.6 83.3 REMARK 620 5 HOH B 437 O 178.8 92.0 89.8 93.3 REMARK 620 6 HOH B 439 O 92.3 88.6 174.9 92.3 87.9 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 SPM A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 301 DBREF 1VRO A 1 6 PDB 1VRO 1VRO 1 6 DBREF 1VRO B 107 112 PDB 1VRO 1VRO 107 112 SEQRES 1 A 6 DC GMS DC DG DC DG SEQRES 1 B 6 DC GMS DC DG DC DG MODRES 1VRO GMS A 2 DG MODRES 1VRO GMS B 108 DG HET GMS A 2 26 HET GMS B 108 22 HET SPM A 201 14 HET MG B 301 1 HETNAM GMS 2'-DEOXYGUANOSINE-5'-MONOSELENOPHOSPHATE HETNAM SPM SPERMINE HETNAM MG MAGNESIUM ION FORMUL 1 GMS 2(C10 H14 N5 O6 P SE) FORMUL 3 SPM C10 H26 N4 FORMUL 4 MG MG 2+ FORMUL 5 HOH *73(H2 O) LINK O3'A DC A 1 P AGMS A 2 1555 1555 1.60 LINK O3'B DC A 1 P BGMS A 2 1555 1555 1.59 LINK O3' GMS A 2 P DC A 3 1555 1555 1.60 LINK O3' DC B 107 P GMS B 108 1555 1555 1.59 LINK O3' GMS B 108 P DC B 109 1555 1555 1.64 LINK N7 DG B 112 MG MG B 301 1555 1555 2.29 LINK MG MG B 301 O HOH B 418 1555 1555 2.21 LINK MG MG B 301 O HOH B 420 1555 1555 2.02 LINK MG MG B 301 O HOH B 431 1555 1555 2.03 LINK MG MG B 301 O HOH B 437 1555 1555 2.02 LINK MG MG B 301 O HOH B 439 1555 1555 1.99 SITE 1 AC1 13 GMS A 2 DC A 3 DG A 6 HOH A 401 SITE 2 AC1 13 HOH A 408 HOH A 438 HOH A 458 GMS B 108 SITE 3 AC1 13 DG B 110 DC B 111 DG B 112 HOH B 414 SITE 4 AC1 13 HOH B 444 SITE 1 AC2 6 DG B 112 HOH B 418 HOH B 420 HOH B 431 SITE 2 AC2 6 HOH B 437 HOH B 439 CRYST1 17.778 31.348 44.116 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 0.056249 0.000000 0.000000 0.00000 SCALE2 0.000000 0.031900 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022668 0.00000