10 20 30 40 50 60 70 80 1XUW - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER DNA 26-OCT-04 1XUW
TITLE STRUCTURAL RATIONALIZATION OF A LARGE DIFFERENCE IN RNA TITLE 2 AFFINITY DESPITE A SMALL DIFFERENCE IN CHEMISTRY BETWEEN TITLE 3 TWO 2'-O-MODIFIED 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, AUTHOR 2 M.MANOHARAN,M.EGLI
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, JRNL AUTH 2 T.P.PRAKASH,M.MANOHARAN,M.EGLI JRNL TITL STRUCTURAL RATIONALIZATION OF A LARGE DIFFERENCE JRNL TITL 2 IN RNA AFFINITY DESPITE A SMALL DIFFERENCE IN JRNL TITL 3 CHEMISTRY BETWEEN TWO 2'-O-MODIFIED NUCLEIC ACID JRNL TITL 4 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 1
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 : 416 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. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-NOV-04. REMARK 100 THE RCSB ID CODE IS RCSB030790.
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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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, REMARK 280 12 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