HEADER DNA 26-OCT-04 1XUW TITLE STRUCTURAL RATIONALIZATION OF A LARGE DIFFERENCE IN RNA AFFINITY TITLE 2 DESPITE A SMALL DIFFERENCE IN CHEMISTRY BETWEEN TWO 2'-O-MODIFIED TITLE 3 NUCLEIC ACID ANALOGS COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*GP*CP*GP*TP*AP*(NMT)P*AP*CP*GP*C)-3'); COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: SYNTHETICALLY CREATED KEYWDS RNA MIMETIC METHYLCARBAMATE AMIDE ANALOG, DNA EXPDTA X-RAY DIFFRACTION AUTHOR R.PATTANAYEK,L.SETHAPHONG,C.PAN,M.PRHAVC,T.P.PRAKASH,M.MANOHARAN, AUTHOR 2 M.EGLI REVDAT 5 24-JUL-19 1XUW 1 REMARK LINK REVDAT 4 11-OCT-17 1XUW 1 REMARK REVDAT 3 24-FEB-09 1XUW 1 VERSN REVDAT 2 16-JAN-07 1XUW 1 JRNL REMARK MODRES REVDAT 1 14-DEC-04 1XUW 0 JRNL AUTH R.PATTANAYEK,L.SETHAPHONG,C.PAN,M.PRHAVC,T.P.PRAKASH, JRNL AUTH 2 M.MANOHARAN,M.EGLI JRNL TITL STRUCTURAL RATIONALIZATION OF A LARGE DIFFERENCE IN RNA JRNL TITL 2 AFFINITY DESPITE A SMALL DIFFERENCE IN CHEMISTRY BETWEEN TWO JRNL TITL 3 2'-O-MODIFIED NUCLEIC ACID ANALOGUES. JRNL REF J.AM.CHEM.SOC. V. 126 15006 2004 JRNL REFN ISSN 0002-7863 JRNL PMID 15547979 JRNL DOI 10.1021/JA044637K REMARK 2 REMARK 2 RESOLUTION. 1.25 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) : 1.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT 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) : 0.153 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.153 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.221 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 711 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 13637 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 : 414 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 153 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) : 0.011 REMARK 3 ANGLE DISTANCES (A) : 0.020 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 1XUW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-NOV-04. REMARK 100 THE DEPOSITION ID IS D_1000030790. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-NOV-02 REMARK 200 TEMPERATURE (KELVIN) : 110 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) : 0.96297 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 : MAR REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14402 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.250 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 200 DATA REDUNDANCY : 2.600 REMARK 200 R MERGE (I) : 0.07700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.29 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.20 REMARK 200 R MERGE FOR SHELL (I) : 0.25400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: 1DPL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1MM 10MER, 40MM SODIUM CACODYLATE, 12 REMARK 280 MM SPERMINE 4HCL, 80MM POTASSIUM CHLORIDE, 10% MPD, PH 7.0, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K 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 12.29950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 23.15250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.43800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 23.15250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 12.29950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 22.43800 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 300 REMARK: DECAMER DUPLEX 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 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 1032 O HOH B 1066 4565 1.99 REMARK 500 O HOH A 1086 O HOH A 1095 3655 2.18 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 DC A 2 C2' DC A 2 C1' -0.067 REMARK 500 DG A 3 C2' DG A 3 C1' -0.101 REMARK 500 DT A 4 C2' DT A 4 C1' -0.093 REMARK 500 DT A 4 O4' DT A 4 C1' 0.097 REMARK 500 DG A 9 C2' DG A 9 C1' -0.085 REMARK 500 DC A 10 C2' DC A 10 C1' -0.081 REMARK 500 DG B 111 C2' DG B 111 C1' -0.075 REMARK 500 DG B 119 C2' DG B 119 C1' -0.109 REMARK 500 DC B 120 C2' DC B 120 C1' -0.094 REMARK 500 DC B 120 O4' DC B 120 C1' 0.067 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 C5 - C6 - O6 ANGL. DEV. = 4.1 DEGREES REMARK 500 DC A 2 C6 - N1 - C2 ANGL. DEV. = -2.8 DEGREES REMARK 500 DC A 2 C5 - C6 - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 DG A 3 O4' - C1' - N9 ANGL. DEV. = -6.0 DEGREES REMARK 500 DG A 3 N1 - C6 - O6 ANGL. DEV. = -4.5 DEGREES REMARK 500 DT A 4 O4' - C1' - N1 ANGL. DEV. = -4.3 DEGREES REMARK 500 DA A 5 O4' - C4' - C3' ANGL. DEV. = -3.7 DEGREES REMARK 500 DC A 8 O4' - C4' - C3' ANGL. DEV. = -2.5 DEGREES REMARK 500 DC A 8 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 DC A 8 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 DG A 9 O4' - C1' - N9 ANGL. DEV. = -5.3 DEGREES REMARK 500 DC A 10 C4 - C5 - C6 ANGL. DEV. = -3.0 DEGREES REMARK 500 DG B 113 O4' - C4' - C3' ANGL. DEV. = -2.9 DEGREES REMARK 500 DA B 117 P - O5' - C5' ANGL. DEV. = -11.9 DEGREES REMARK 500 DC B 118 O4' - C4' - C3' ANGL. DEV. = -3.2 DEGREES REMARK 500 DG B 119 O4' - C1' - C2' ANGL. DEV. = 3.2 DEGREES REMARK 500 DG B 119 O4' - C1' - N9 ANGL. DEV. = -8.4 DEGREES REMARK 500 DG B 119 N3 - C4 - C5 ANGL. DEV. = 3.2 DEGREES REMARK 500 DG B 119 C5 - N7 - C8 ANGL. DEV. = 3.1 DEGREES REMARK 500 DG B 119 N7 - C8 - N9 ANGL. DEV. = -3.3 DEGREES REMARK 500 DG B 119 C5 - C6 - O6 ANGL. DEV. = 4.2 DEGREES REMARK 500 DC B 120 O4' - C1' - N1 ANGL. DEV. = -6.1 DEGREES REMARK 500 REMARK 500 REMARK: NULL DBREF 1XUW A 1 10 PDB 1XUW 1XUW 1 10 DBREF 1XUW B 111 120 PDB 1XUW 1XUW 111 120 SEQRES 1 A 10 DG DC DG DT DA NMT DA DC DG DC SEQRES 1 B 10 DG DC DG DT DA NMT DA DC DG DC MODRES 1XUW NMT A 6 DT MODRES 1XUW NMT B 116 DT HET NMT A 6 27 HET NMT B 116 25 HETNAM NMT 1-(O2-(METHYLCARBAMOYL)-O5-HYDROXYPHOSPHINYL-BETA-D- HETNAM 2 NMT RIBOFURANOSYL)THYMINE FORMUL 1 NMT 2(C12 H20 N3 O10 P) FORMUL 3 HOH *153(H2 O) LINK O3' DA A 5 P NMT A 6 1555 1555 1.62 LINK O3' NMT A 6 P DA A 7 1555 1555 1.63 LINK O3' DA B 115 P NMT B 116 1555 1555 1.58 LINK O3' NMT B 116 P DA B 117 1555 1555 1.58 CRYST1 24.599 44.876 46.305 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 0.040652 0.000000 0.000000 0.00000 SCALE2 0.000000 0.022284 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021596 0.00000 MASTER 265 0 2 0 0 0 0 6 0 0 0 2 END