HEADER RNA 28-DEC-16 5MRX TITLE 27-NT SRL WITH A 5-HYDROXYMETHYL CYTIDINE MODIFICATION COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (27-MER); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: MRC=5HYDROXYMETHYL-CYTOSINE SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 4 ORGANISM_TAXID: 562 KEYWDS RNA, MODIFICATION, TETRALOOP EXPDTA X-RAY DIFFRACTION AUTHOR E.ENNIFAR,R.MICURA REVDAT 4 17-JAN-24 5MRX 1 REMARK REVDAT 3 30-MAR-22 5MRX 1 JRNL REVDAT 2 16-OCT-19 5MRX 1 REMARK REVDAT 1 17-JAN-18 5MRX 0 JRNL AUTH C.RIML,A.LUSSER,E.ENNIFAR,R.MICURA JRNL TITL SYNTHESIS, THERMODYNAMIC PROPERTIES, AND CRYSTAL STRUCTURE JRNL TITL 2 OF RNA OLIGONUCLEOTIDES CONTAINING 5-HYDROXYMETHYLCYTOSINE JRNL REF J.ORG.CHEM. 2017 JRNL REFN ISSN 0022-3263 JRNL DOI 10.1021/ACS.JOC.7B01171 REMARK 2 REMARK 2 RESOLUTION. 0.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 0.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.51 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 57106 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.159 REMARK 3 R VALUE (WORKING SET) : 0.145 REMARK 3 FREE R VALUE : 0.168 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.030 REMARK 3 FREE R VALUE TEST SET COUNT : 2870 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 27.5609 - 2.3092 0.95 2761 146 0.1034 0.1790 REMARK 3 2 2.3092 - 1.8330 0.95 2725 143 0.1365 0.1544 REMARK 3 3 1.8330 - 1.6013 0.95 2740 144 0.1350 0.1436 REMARK 3 4 1.6013 - 1.4549 0.95 2740 145 0.1621 0.1583 REMARK 3 5 1.4549 - 1.3506 0.95 2695 141 0.1706 0.1821 REMARK 3 6 1.3506 - 1.2710 0.95 2736 145 0.1724 0.1740 REMARK 3 7 1.2710 - 1.2073 0.95 2740 144 0.1767 0.1628 REMARK 3 8 1.2073 - 1.1548 0.95 2722 143 0.1767 0.1958 REMARK 3 9 1.1548 - 1.1103 0.95 2721 143 0.1770 0.1693 REMARK 3 10 1.1103 - 1.0720 0.95 2725 144 0.1803 0.1878 REMARK 3 11 1.0720 - 1.0385 0.95 2699 142 0.1776 0.1845 REMARK 3 12 1.0385 - 1.0088 0.95 2732 143 0.1894 0.1919 REMARK 3 13 1.0088 - 0.9822 0.95 2687 142 0.2074 0.2014 REMARK 3 14 0.9822 - 0.9583 0.95 2721 143 0.2282 0.2390 REMARK 3 15 0.9583 - 0.9365 0.95 2751 145 0.2649 0.2613 REMARK 3 16 0.9365 - 0.9166 0.95 2694 142 0.2824 0.2962 REMARK 3 17 0.9166 - 0.8982 0.95 2720 143 0.3180 0.3180 REMARK 3 18 0.8982 - 0.8813 0.95 2711 143 0.3392 0.3515 REMARK 3 19 0.8813 - 0.8655 0.93 2649 139 0.3646 0.4058 REMARK 3 20 0.8655 - 0.8509 0.89 2577 136 0.4112 0.4468 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.780 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.006 707 REMARK 3 ANGLE : 1.123 1107 REMARK 3 CHIRALITY : 0.047 147 REMARK 3 PLANARITY : 0.013 30 REMARK 3 DIHEDRAL : 12.481 347 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5MRX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 29-DEC-16. REMARK 100 THE DEPOSITION ID IS D_1200002914. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-NOV-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06DA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.77 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 57106 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.850 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 22.36 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 30.3200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: MOLREP REMARK 200 STARTING MODEL: 3DVZ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.91 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: WELL: 3.0M (NH4)2SO4 DROP: 50MM KMOPS REMARK 280 PH7.0, 10MM MNCL2, 10MM MGCL2, 1.0MM NA-EDTA PH 8.0, 10MM TRIS REMARK 280 PH 8.0, RNA 2.5MG/ML 2VOL DROP + 1VOL WELL, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+3/4 REMARK 290 4555 Y,-X,Z+1/4 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 38.40000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 57.60000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 19.20000 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4820 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 A 2709 O HOH A 2741 1.99 REMARK 500 O HOH A 2814 O HOH A 2871 2.04 REMARK 500 O HOH A 2791 O HOH A 2873 2.05 REMARK 500 O HOH A 2834 O HOH A 2873 2.07 REMARK 500 O HOH A 2774 O HOH A 2811 2.08 REMARK 500 O HOH A 2844 O HOH A 2858 2.10 REMARK 500 O HOH A 2896 O HOH A 2901 2.11 REMARK 500 O HOH A 2842 O HOH A 2847 2.12 REMARK 500 O HOH A 2823 O HOH A 2830 2.12 REMARK 500 O HOH A 2797 O HOH A 2823 2.12 REMARK 500 O HOH A 2709 O HOH A 2856 2.13 REMARK 500 O HOH A 2843 O HOH A 2863 2.13 REMARK 500 O HOH A 2802 O HOH A 2846 2.13 REMARK 500 O HOH A 2833 O HOH A 2861 2.14 REMARK 500 O HOH A 2821 O HOH A 2884 2.14 REMARK 500 O HOH A 2805 O HOH A 2875 2.14 REMARK 500 O HOH A 2838 O HOH A 2862 2.15 REMARK 500 O HOH A 2830 O HOH A 2888 2.15 REMARK 500 O HOH A 2755 O HOH A 2775 2.16 REMARK 500 O HOH A 2829 O HOH A 2839 2.17 REMARK 500 O HOH A 2776 O HOH A 2816 2.17 REMARK 500 O HOH A 2728 O HOH A 2840 2.18 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 HO2' U A 2653 H22 G A 2661 1565 1.33 REMARK 500 O HOH A 2782 O HOH A 2791 3674 2.08 REMARK 500 O HOH A 2703 O HOH A 2776 3684 2.08 REMARK 500 O HOH A 2848 O HOH A 2903 4465 2.15 REMARK 500 O HOH A 2893 O HOH A 2906 1645 2.16 REMARK 500 O HOH A 2900 O HOH A 2909 3664 2.16 REMARK 500 O HOH A 2902 O HOH A 2904 1465 2.16 REMARK 500 O HOH A 2782 O HOH A 2873 3674 2.18 REMARK 500 O HOH A 2890 O HOH A 2901 1545 2.19 REMARK 500 O HOH A 2763 O HOH A 2800 4365 2.19 REMARK 500 O HOH A 2797 O HOH A 2836 4365 2.19 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 5HM A2651 O3' - P - OP1 ANGL. DEV. = -16.9 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A2895 DISTANCE = 5.83 ANGSTROMS REMARK 525 HOH A2896 DISTANCE = 5.86 ANGSTROMS REMARK 525 HOH A2897 DISTANCE = 5.91 ANGSTROMS REMARK 525 HOH A2898 DISTANCE = 5.94 ANGSTROMS REMARK 525 HOH A2899 DISTANCE = 6.02 ANGSTROMS REMARK 525 HOH A2900 DISTANCE = 6.17 ANGSTROMS REMARK 525 HOH A2901 DISTANCE = 6.31 ANGSTROMS REMARK 525 HOH A2902 DISTANCE = 6.32 ANGSTROMS REMARK 525 HOH A2903 DISTANCE = 6.38 ANGSTROMS REMARK 525 HOH A2904 DISTANCE = 6.70 ANGSTROMS REMARK 525 HOH A2905 DISTANCE = 6.74 ANGSTROMS REMARK 525 HOH A2906 DISTANCE = 6.83 ANGSTROMS REMARK 525 HOH A2907 DISTANCE = 7.14 ANGSTROMS REMARK 525 HOH A2908 DISTANCE = 8.24 ANGSTROMS REMARK 525 HOH A2909 DISTANCE = 8.93 ANGSTROMS REMARK 525 HOH A2910 DISTANCE = 9.38 ANGSTROMS REMARK 525 HOH A2911 DISTANCE = 10.42 ANGSTROMS DBREF 5MRX A 2647 2673 PDB 5MRX 5MRX 2647 2673 SEQRES 1 A 27 U G C U 5HM C U A G U A C G SEQRES 2 A 27 A G A G G A C C G G A G U SEQRES 3 A 27 G HET 5HM A2651 34 HETNAM 5HM 5-(HYDROXYMETHYL)CYTIDINE 5'-(DIHYDROGEN PHOSPHATE) HETSYN 5HM 5-HYDROXYMETHYLCYTIDINE 5'-MONOPHOSPHATE FORMUL 1 5HM C10 H16 N3 O9 P FORMUL 2 HOH *211(H2 O) LINK O3' U A2650 P 5HM A2651 1555 1555 1.60 LINK O3' 5HM A2651 P C A2652 1555 1555 1.60 CRYST1 29.510 29.510 76.800 90.00 90.00 90.00 P 43 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 0.033887 0.000000 0.000000 0.00000 SCALE2 0.000000 0.033887 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013021 0.00000