HEADER RNA 18-AUG-16 5LR5 TITLE N6-METHYLADENINE IS ACCOMMODATED IN A CONVENTIONAL A-U BASEPAIR COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (5'-R(*GP*GP*(6MZ)P*CP*UP*AP*GP*UP*(CBV)P*C)-3'); COMPND 3 CHAIN: A, B, C, D; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_TAXID: 9606 KEYWDS N6-METHYLADENINE, RNA FOLDING, WATSON-CRICK BASEPAIRS, RNA EXPDTA X-RAY DIFFRACTION AUTHOR L.HUANG,D.M.J.LILLEY REVDAT 5 10-JUL-19 5LR5 1 REMARK REVDAT 4 20-FEB-19 5LR5 1 REMARK SEQRES REVDAT 3 13-SEP-17 5LR5 1 JRNL REVDAT 2 28-JUN-17 5LR5 1 JRNL REVDAT 1 21-JUN-17 5LR5 0 JRNL AUTH L.HUANG,S.ASHRAF,J.WANG,D.M.LILLEY JRNL TITL CONTROL OF BOX C/D SNORNP ASSEMBLY BY N(6)-METHYLATION OF JRNL TITL 2 ADENINE. JRNL REF EMBO REP. V. 18 1631 2017 JRNL REFN ESSN 1469-3178 JRNL PMID 28623187 JRNL DOI 10.15252/EMBR.201743967 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (DEV_2481: ???) 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.71 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.3 REMARK 3 NUMBER OF REFLECTIONS : 5910 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.249 REMARK 3 R VALUE (WORKING SET) : 0.247 REMARK 3 FREE R VALUE : 0.287 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.540 REMARK 3 FREE R VALUE TEST SET COUNT : 528 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 43.7155 - 3.8093 0.99 2865 121 0.1720 0.2177 REMARK 3 2 3.8093 - 3.0237 0.92 2677 105 0.2847 0.2830 REMARK 3 3 3.0237 - 2.6416 0.98 2765 182 0.3858 0.4142 REMARK 3 4 2.6416 - 2.4001 0.96 2802 120 0.4235 0.4358 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) : 0.440 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 38.710 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 : 0.020 956 REMARK 3 ANGLE : 4.691 1494 REMARK 3 CHIRALITY : 0.053 188 REMARK 3 PLANARITY : 0.003 40 REMARK 3 DIHEDRAL : 10.504 404 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 5LR5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 18-AUG-16. REMARK 100 THE DEPOSITION ID IS D_1200001234. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-JUN-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 : DIAMOND REMARK 200 BEAMLINE : I02 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9193 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5911 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.270 REMARK 200 RESOLUTION RANGE LOW (A) : 43.710 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.400 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 200 DATA REDUNDANCY : 41.70 REMARK 200 R MERGE (I) : 0.14300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.27 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.31 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.6 REMARK 200 DATA REDUNDANCY IN SHELL : 38.70 REMARK 200 R MERGE FOR SHELL (I) : 2.70000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.72 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.05 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM SULFATE 0.1 M SODIUM REMARK 280 ACETATE TRIHYDRATE PH 4.6 25% W/V POLYETHYLENE GLYCOL 4000, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 72.41667 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 36.20833 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 54.31250 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 18.10417 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 90.52083 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3470 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 3230 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 5.0 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3700 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 3220 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 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 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 O3' C A 4 O HOH A 101 1.86 REMARK 500 O2' G B 2 O HOH B 101 1.88 REMARK 500 O5' G B 7 O HOH B 102 1.91 REMARK 500 C3' G B 7 O HOH B 102 1.92 REMARK 500 O1P 6MZ B 3 O HOH B 103 1.93 REMARK 500 O2' CBV A 9 O HOH A 102 1.99 REMARK 500 O4' 6MZ A 3 O HOH A 103 2.10 REMARK 500 C1' G B 2 O HOH B 101 2.14 REMARK 500 C2' G B 2 O HOH B 101 2.18 REMARK 500 O3' A B 6 O HOH B 104 2.19 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 A 2 O3' 6MZ A 3 P 0.091 REMARK 500 G B 2 O3' 6MZ B 3 P 0.091 REMARK 500 U D 8 O3' CBV D 9 P 0.095 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 C 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-nucleotide G B 2 and 6MZ B 3 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-nucleotide 6MZ B 3 and C B 4 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-nucleotide CBV B 9 and C B REMARK 800 10 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-nucleotide G C 2 and 6MZ C 3 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-nucleotide 6MZ C 3 and C C 4 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-nucleotide CBV C 9 and C C REMARK 800 10 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-nucleotide G D 2 and 6MZ D 3 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-nucleotide 6MZ D 3 and C D 4 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-nucleotide CBV D 9 and C D REMARK 800 10 DBREF 5LR5 A 1 10 PDB 5LR5 5LR5 1 10 DBREF 5LR5 B 1 10 PDB 5LR5 5LR5 1 10 DBREF 5LR5 C 1 10 PDB 5LR5 5LR5 1 10 DBREF 5LR5 D 1 10 PDB 5LR5 5LR5 1 10 SEQRES 1 A 10 G G 6MZ C U A G U CBV C SEQRES 1 B 10 G G 6MZ C U A G U CBV C SEQRES 1 C 10 G G 6MZ C U A G U CBV C SEQRES 1 D 10 G G 6MZ C U A G U CBV C HET 6MZ A 3 24 HET CBV A 9 22 HET 6MZ B 3 24 HET CBV B 9 22 HET 6MZ C 3 24 HET CBV C 9 22 HET 6MZ D 3 24 HET CBV D 9 22 HET SO4 C 101 5 HETNAM 6MZ N6-METHYLADENOSINE-5'-MONOPHOSPHATE HETNAM CBV 5-BROMOCYTIDINE 5'-(DIHYDROGEN PHOSPHATE) HETNAM SO4 SULFATE ION FORMUL 1 6MZ 4(C11 H16 N5 O7 P) FORMUL 1 CBV 4(C9 H13 BR N3 O8 P) FORMUL 5 SO4 O4 S 2- FORMUL 6 HOH *10(H2 O) LINK O3' G A 2 P 6MZ A 3 1555 1555 1.70 LINK O3' 6MZ A 3 P C A 4 1555 1555 1.60 LINK O3' U A 8 P CBV A 9 1555 1555 1.61 LINK O3' CBV A 9 P C A 10 1555 1555 1.60 LINK O3' G B 2 P 6MZ B 3 1555 1555 1.70 LINK O3' 6MZ B 3 P C B 4 1555 1555 1.60 LINK O3' U B 8 P CBV B 9 1555 1555 1.61 LINK O3' CBV B 9 P C B 10 1555 1555 1.60 LINK O3' G C 2 P 6MZ C 3 1555 1555 1.61 LINK O3' 6MZ C 3 P C C 4 1555 1555 1.61 LINK O3' U C 8 P CBV C 9 1555 1555 1.61 LINK O3' CBV C 9 P C C 10 1555 1555 1.60 LINK O3' G D 2 P 6MZ D 3 1555 1555 1.61 LINK O3' 6MZ D 3 P C D 4 1555 1555 1.60 LINK O3' U D 8 P CBV D 9 1555 1555 1.70 LINK O3' CBV D 9 P C D 10 1555 1555 1.60 SITE 1 AC1 3 G C 7 U C 8 U D 5 SITE 1 AC2 7 U A 8 CBV A 9 C A 10 G B 1 SITE 2 AC2 7 C B 4 HOH B 101 HOH B 103 SITE 1 AC3 6 G A 7 U A 8 CBV A 9 G B 2 SITE 2 AC3 6 U B 5 HOH B 103 SITE 1 AC4 5 G A 1 G A 2 6MZ A 3 U B 8 SITE 2 AC4 5 G C 1 SITE 1 AC5 6 U A 5 G C 1 C C 4 U D 8 SITE 2 AC5 6 CBV D 9 C D 10 SITE 1 AC6 7 U A 5 U B 8 G C 2 U C 5 SITE 2 AC6 7 G D 7 U D 8 CBV D 9 SITE 1 AC7 9 G B 1 U C 5 U C 8 HOH C 201 SITE 2 AC7 9 G D 1 G D 2 6MZ D 3 G D 7 SITE 3 AC7 9 U D 8 SITE 1 AC8 6 A B 6 U C 8 CBV C 9 C C 10 SITE 2 AC8 6 G D 1 C D 4 SITE 1 AC9 7 G C 7 U C 8 CBV C 9 G D 2 SITE 2 AC9 7 U D 5 CBV D 9 C D 10 SITE 1 AD1 7 G A 1 A A 6 G C 1 G C 2 SITE 2 AD1 7 6MZ C 3 C D 4 U D 8 CRYST1 50.470 50.470 108.625 90.00 90.00 120.00 P 65 24 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 0.019814 0.011439 0.000000 0.00000 SCALE2 0.000000 0.022879 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009206 0.00000