HEADER RNA 25-FEB-19 6JJI TITLE CRYSTAL STRUCTURE OF A TWO-QUARTET RNA PARALLEL G-QUADRUPLEX COMPLEXED TITLE 2 WITH THE PORPHYRIN TMPYP4 (1:1) COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (5'-R(*GP*GP*CP*UP*CP*GP*GP*CP*GP*GP*CP*GP*GP*A)-3'); COMPND 3 CHAIN: B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: PSEUDORABIES VIRUS EA; SOURCE 4 ORGANISM_TAXID: 101947 KEYWDS G-QUADRUPLEX, TWO-QUARTET, COMPLEX, RNA EXPDTA X-RAY DIFFRACTION AUTHOR Y.S.ZHANG,G.N.PARKINSON,D.G.WEI REVDAT 4 22-NOV-23 6JJI 1 REMARK REVDAT 3 07-OCT-20 6JJI 1 JRNL REVDAT 2 09-SEP-20 6JJI 1 JRNL REMARK LINK REVDAT 1 26-FEB-20 6JJI 0 JRNL AUTH Y.ZHANG,K.EL OMARI,R.DUMAN,S.LIU,S.HAIDER,A.WAGNER, JRNL AUTH 2 G.N.PARKINSON,D.WEI JRNL TITL NATIVE DE NOVO STRUCTURAL DETERMINATIONS OF NON-CANONICAL JRNL TITL 2 NUCLEIC ACID MOTIFS BY X-RAY CRYSTALLOGRAPHY AT LONG JRNL TITL 3 WAVELENGTHS. JRNL REF NUCLEIC ACIDS RES. V. 48 9886 2020 JRNL REFN ESSN 1362-4962 JRNL PMID 32453431 JRNL DOI 10.1093/NAR/GKAA439 REMARK 2 REMARK 2 RESOLUTION. 3.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.13_2998 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 : LS_WUNIT_K1 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 16.04 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.170 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 3 NUMBER OF REFLECTIONS : 817 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.195 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.410 REMARK 3 FREE R VALUE TEST SET COUNT : 36 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 3.2100 - 3.1000 0.97 781 36 0.1927 0.2497 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.120 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.950 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 71.08 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 8.0762 2.9584 4.4843 REMARK 3 T TENSOR REMARK 3 T11: 0.4487 T22: 0.5065 REMARK 3 T33: 0.5806 T12: 0.1394 REMARK 3 T13: 0.0071 T23: 0.0850 REMARK 3 L TENSOR REMARK 3 L11: 3.7420 L22: 9.3281 REMARK 3 L33: 2.8320 L12: 0.3343 REMARK 3 L13: 0.0303 L23: -0.9756 REMARK 3 S TENSOR REMARK 3 S11: 0.1476 S12: -0.0432 S13: 0.3778 REMARK 3 S21: 1.5600 S22: -0.2791 S23: 0.2917 REMARK 3 S31: -0.3647 S32: -0.1161 S33: 0.2184 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 6JJI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-FEB-19. REMARK 100 THE DEPOSITION ID IS D_1300011193. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-MAY-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97900 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 825 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.100 REMARK 200 RESOLUTION RANGE LOW (A) : 16.042 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.6 REMARK 200 DATA REDUNDANCY : 9.600 REMARK 200 R MERGE (I) : 0.10800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.21 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.40300 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: PHASER REMARK 200 STARTING MODEL: 6JJH REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.14 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: POTASSIUM CACODYLATE, SODIUM REMARK 280 CACODYLATE, POTASSIUM CHLORIDE, MPD, PH 6, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 283K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 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 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 28.77850 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 28.77850 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 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 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: 900 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5440 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -4.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 K K B 101 LIES ON A SPECIAL POSITION. REMARK 375 K K B 102 LIES ON A SPECIAL POSITION. 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 K B 103 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G B 1 O6 REMARK 620 2 G B 1 O6 0.0 REMARK 620 3 G B 2 O6 79.9 79.9 REMARK 620 4 G B 2 O6 79.9 79.9 0.0 REMARK 620 5 G B 6 O6 78.1 78.1 94.3 94.3 REMARK 620 6 G B 6 O6 78.1 78.1 94.3 94.3 0.0 REMARK 620 7 G B 7 O6 145.3 145.3 70.0 70.0 87.1 87.1 REMARK 620 8 G B 7 O6 145.3 145.3 70.0 70.0 87.1 87.1 0.0 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K B 102 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G B 2 O6 REMARK 620 2 G B 2 O6 0.0 REMARK 620 3 G B 7 O6 69.5 69.5 REMARK 620 4 G B 7 O6 69.5 69.5 0.0 REMARK 620 5 G B 9 O6 130.1 130.1 77.1 77.1 REMARK 620 6 G B 9 O6 130.1 130.1 77.1 77.1 0.0 REMARK 620 7 G B 12 O6 82.0 82.0 87.5 87.5 60.2 60.2 REMARK 620 8 G B 12 O6 82.0 82.0 87.5 87.5 60.2 60.2 0.0 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K B 101 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G B 9 O6 REMARK 620 2 G B 9 O6 0.0 REMARK 620 3 G B 10 O6 79.8 79.8 REMARK 620 4 G B 10 O6 79.8 79.8 0.0 REMARK 620 5 G B 12 O6 53.9 53.9 93.7 93.7 REMARK 620 6 G B 12 O6 53.9 53.9 93.7 93.7 0.0 REMARK 620 7 G B 13 O6 121.1 121.1 85.3 85.3 71.0 71.0 REMARK 620 8 G B 13 O6 121.1 121.1 85.3 85.3 71.0 71.0 0.0 REMARK 620 N 1 2 3 4 5 6 7 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K B 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K B 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K B 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue POH B 104 DBREF 6JJI B 1 14 PDB 6JJI 6JJI 1 14 SEQRES 1 B 14 G G C U C G G C G G C G G SEQRES 2 B 14 A HET K B 101 1 HET K B 102 1 HET K B 103 1 HET POH B 104 52 HETNAM K POTASSIUM ION HETNAM POH (1Z,4Z,9Z,15Z)-5,10,15,20-TETRAKIS(1-METHYLPYRIDIN-1- HETNAM 2 POH IUM-4-YL)-21,23-DIHYDROPORPHYRIN HETSYN POH TMPYP4 FORMUL 2 K 3(K 1+) FORMUL 5 POH C44 H38 N8 4+ LINK O6 G B 1 K K B 103 1555 1555 2.49 LINK O6 G B 1 K K B 103 1555 4555 2.70 LINK O6 G B 2 K K B 102 1555 1555 2.66 LINK O6 G B 2 K K B 102 1555 4555 2.76 LINK O6 G B 2 K K B 103 1555 1555 2.61 LINK O6 G B 2 K K B 103 1555 4555 2.92 LINK O6 G B 6 K K B 103 1555 1555 2.47 LINK O6 G B 6 K K B 103 1555 4555 2.73 LINK O6 G B 7 K K B 102 1555 1555 2.70 LINK O6 G B 7 K K B 102 1555 4555 2.83 LINK O6 G B 7 K K B 103 1555 1555 2.71 LINK O6 G B 7 K K B 103 1555 4555 2.80 LINK O6 G B 9 K K B 101 1555 1555 2.94 LINK O6 G B 9 K K B 101 1555 4555 2.99 LINK O6 G B 9 K K B 102 1555 1555 2.65 LINK O6 G B 9 K K B 102 1555 4555 2.73 LINK O6 G B 10 K K B 101 1555 1555 2.73 LINK O6 G B 10 K K B 101 1555 4555 2.82 LINK O6 G B 12 K K B 101 1555 1555 2.95 LINK O6 G B 12 K K B 101 1555 4555 3.05 LINK O6 G B 12 K K B 102 1555 1555 2.67 LINK O6 G B 12 K K B 102 1555 4555 2.83 LINK O6 G B 13 K K B 101 1555 1555 2.82 LINK O6 G B 13 K K B 101 1555 4555 2.90 SITE 1 AC1 5 G B 9 G B 10 G B 12 G B 13 SITE 2 AC1 5 K B 102 SITE 1 AC2 6 G B 2 G B 7 G B 9 G B 12 SITE 2 AC2 6 K B 101 K B 103 SITE 1 AC3 5 G B 1 G B 2 G B 6 G B 7 SITE 2 AC3 5 K B 102 SITE 1 AC4 4 C B 5 G B 10 G B 13 A B 14 CRYST1 23.509 29.244 57.557 90.00 90.00 90.00 P 2 2 21 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 0.042537 0.000000 0.000000 0.00000 SCALE2 0.000000 0.034195 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017374 0.00000