HEADER RNA 18-DEC-13 4O41 TITLE AMIDE LINKED RNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: AMIDE LINKED RNA; COMPND 3 CHAIN: A, B, C, D; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: SHORT NA STRANDS UGAGC(URU)CGGCUC, WHERE URU COMPND 6 REPRESENTS THE AMIDE LINKED RESIDUE SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: CHEMICALLY SYNTHESIZED MODIFIED RIBO NUCLEIC ACID KEYWDS MODIFIED RNA, RNA STRUCTURE, AMIDE RNA, AMIDE INTERNUCLEOSIDE KEYWDS 2 LINKAGE, MODIFIED NUCLEOSIDE, RNA EXPDTA X-RAY DIFFRACTION AUTHOR P.S.PALLAN,M.EGLI REVDAT 2 03-SEP-14 4O41 1 REMARK REVDAT 1 09-JUL-14 4O41 0 JRNL AUTH D.MUTISYA,C.SELVAM,B.D.LUNSTAD,P.S.PALLAN,A.HAAS,D.LEAKE, JRNL AUTH 2 M.EGLI,E.ROZNERS JRNL TITL AMIDES ARE EXCELLENT MIMICS OF PHOSPHATE INTERNUCLEOSIDE JRNL TITL 2 LINKAGES AND ARE WELL TOLERATED IN SHORT INTERFERING RNAS. JRNL REF NUCLEIC ACIDS RES. V. 42 6542 2014 JRNL REFN ISSN 0305-1048 JRNL PMID 24813446 JRNL DOI 10.1093/NAR/GKU235 REMARK 2 REMARK 2 RESOLUTION. 1.20 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) : 1.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 3.000 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) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.147 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.212 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 1795 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 37491 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 : 1029 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 284 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) : 0.018 REMARK 3 ANGLE DISTANCES (A) : 0.033 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: NULL REMARK 4 REMARK 4 4O41 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-JAN-14. REMARK 100 THE RCSB ID CODE IS RCSB084014. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-AUG-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.7686 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 300 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35934 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.200 REMARK 200 RESOLUTION RANGE LOW (A) : 28.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 5.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.8 REMARK 200 DATA REDUNDANCY : 7.700 REMARK 200 R MERGE (I) : 0.07600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.6600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.40 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.8 REMARK 200 DATA REDUNDANCY IN SHELL : 7.80 REMARK 200 R MERGE FOR SHELL (I) : 0.29600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 6.210 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SINGLE WAVELENGTH ANOMALOUS DISPERSION REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.89 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20 MM SODIUM CACODYLATE, 45 MM REMARK 280 STRONTIUM CHLORIDE, 10 MM MAGNESIUM CHLORIDE, 6 MM SPERMINE REMARK 280 TETRAHYDROCHLORIDE AND 5% 2-METHYL-2,4-PENTANEDIOL [MPD (V/V)], REMARK 280 PH 6.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1510 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4880 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -59.0 KCAL/MOL 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1100 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4620 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -6.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D 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 400 REMARK 400 COMPOUND REMARK 400 URU represents the amide linked residue REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 U A 101 REMARK 465 U C 301 REMARK 465 U D 401 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 SR SR A 702 O HOH A 835 2.10 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 G B 204 C2' G B 204 O2' -0.204 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 U B 201 C3' - C2' - C1' ANGL. DEV. = -4.5 DEGREES REMARK 500 U B 201 C2 - N3 - C4 ANGL. DEV. = -4.0 DEGREES REMARK 500 U B 201 N3 - C4 - O4 ANGL. DEV. = 4.8 DEGREES REMARK 500 U B 201 C5 - C4 - O4 ANGL. DEV. = -5.6 DEGREES REMARK 500 G B 204 C3' - C2' - C1' ANGL. DEV. = -7.2 DEGREES REMARK 500 G B 209 C2 - N3 - C4 ANGL. DEV. = 3.8 DEGREES REMARK 500 G C 302 N1 - C6 - O6 ANGL. DEV. = -3.9 DEGREES REMARK 500 G D 409 C6 - N1 - C2 ANGL. DEV. = -4.5 DEGREES REMARK 500 G D 409 C2 - N3 - C4 ANGL. DEV. = 4.2 DEGREES REMARK 500 G D 409 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 G D 409 C5 - N7 - C8 ANGL. DEV. = 3.4 DEGREES REMARK 500 U D 412 C2 - N3 - C4 ANGL. DEV. = 3.8 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 SR A 702 SR REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 805 O REMARK 620 2 HOH A 814 O 129.5 REMARK 620 3 HOH A 811 O 71.1 73.6 REMARK 620 4 HOH A 821 O 149.8 78.1 136.6 REMARK 620 5 G A 110 O6 71.1 140.0 141.4 79.3 REMARK 620 6 G A 110 N7 99.6 75.4 127.9 73.4 66.6 REMARK 620 7 HOH A 838 O 133.9 72.2 81.1 59.0 121.4 126.4 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SR A 701 SR REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 840 O REMARK 620 2 C A 113 O3' 126.7 REMARK 620 3 HOH A 866 O 134.2 72.2 REMARK 620 4 HOH A 817 O 78.6 145.1 72.9 REMARK 620 5 C A 113 O2' 76.0 62.2 134.2 152.1 REMARK 620 6 HOH A 815 O 73.0 77.9 71.8 89.8 93.7 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 SR A 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SR A 702 DBREF 4O41 A 101 113 PDB 4O41 4O41 101 113 DBREF 4O41 B 201 213 PDB 4O41 4O41 201 213 DBREF 4O41 C 301 313 PDB 4O41 4O41 301 313 DBREF 4O41 D 401 413 PDB 4O41 4O41 401 413 SEQRES 1 A 12 U G A G C URU C G G C U C SEQRES 1 B 12 U G A G C URU C G G C U C SEQRES 1 C 12 U G A G C URU C G G C U C SEQRES 1 D 12 U G A G C URU C G G C U C HET URU A 106 39 HET URU B 206 46 HET URU C 306 39 HET URU D 406 39 HET SR A 701 1 HET SR A 702 1 HETNAM URU ((2S,3S,4R,5R)-5-(2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)- HETNAM 2 URU YL)-3-(2- ((((2R,5R)-5-(2,4-DIOXO-3,4- HETNAM 3 URU DIHYDROPYRIMIDIN-1(2H)-YL)- 3,4- HETNAM 4 URU DIHYDROXYTETRAHYDROFURAN-2-YL)METHYL)AMINO)-2- HETNAM 5 URU OXOETHYL)-4- HYDROXYTETRAHYDROFURAN-2-YL)METHYL HETNAM 6 URU PHOSPHATE HETNAM SR STRONTIUM ION FORMUL 1 URU 4(C20 H26 N5 O14 P) FORMUL 5 SR 2(SR 2+) FORMUL 7 HOH *284(H2 O) LINK O3' C A 105 P URU A 106 1555 1555 1.60 LINK OX' URU A 106 P C A 108 1555 1555 1.58 LINK O3'A C B 205 P AURU B 206 1555 1555 1.60 LINK O3'B C B 205 P BURU B 206 1555 1555 1.63 LINK OX' URU B 206 P C B 208 1555 1555 1.56 LINK O3' C C 305 P URU C 306 1555 1555 1.60 LINK OX' URU C 306 P C C 308 1555 1555 1.55 LINK O3' C D 405 P URU D 406 1555 1555 1.59 LINK OX' URU D 406 P C D 408 1555 1555 1.56 LINK SR SR A 702 O HOH A 805 1555 1555 2.42 LINK SR SR A 702 O HOH A 814 1555 1555 2.52 LINK SR SR A 701 O HOH A 840 1555 1555 2.52 LINK SR SR A 702 O HOH A 811 1555 1555 2.56 LINK O3' C A 113 SR SR A 701 1555 1555 2.57 LINK SR SR A 701 O HOH A 866 1555 1555 2.58 LINK SR SR A 701 O HOH A 817 1555 1555 2.58 LINK O2' C A 113 SR SR A 701 1555 1555 2.60 LINK SR SR A 701 O HOH A 815 1555 1555 2.62 LINK SR SR A 702 O HOH A 821 1555 1555 2.63 LINK O6 G A 110 SR SR A 702 1555 1555 2.76 LINK N7 G A 110 SR SR A 702 1555 1555 2.76 LINK SR SR A 702 O HOH A 838 1555 1555 2.77 SITE 1 AC1 5 C A 113 HOH A 815 HOH A 817 HOH A 840 SITE 2 AC1 5 HOH A 866 SITE 1 AC2 8 G A 109 G A 110 HOH A 805 HOH A 811 SITE 2 AC2 8 HOH A 814 HOH A 821 HOH A 835 HOH A 838 CRYST1 22.360 34.330 43.300 110.03 94.24 95.83 P 1 4 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 0.044723 0.004566 0.005265 0.00000 SCALE2 0.000000 0.029280 0.011040 0.00000 SCALE3 0.000000 0.000000 0.024750 0.00000 MASTER 290 0 6 0 0 0 4 6 0 0 0 4 END