HEADER DNA 27-JUN-23 8TAA TITLE RIGHT-LEFT HYBRID PARALLEL G-QUADRUPLEX IN COMPLEX WITH N-METHYL TITLE 2 MESOPORPHYRIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (25-MER); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_TAXID: 9606 KEYWDS G-QUADRUPLEX, RIGHT-LEFT-HANDED, PARALLEL, NMM, DNA EXPDTA X-RAY DIFFRACTION AUTHOR P.C.SETH,L.A.YATSUNYK REVDAT 1 03-JUL-24 8TAA 0 JRNL AUTH P.C.SETH,L.A.YATSUNYK JRNL TITL RIGHT-LEFT HYBRID PARALLEL G-QUADRUPLEX IN COMPLEX WITH JRNL TITL 2 N-METHYL MESOPORPHYRIN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.39 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 13049 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.213 REMARK 3 R VALUE (WORKING SET) : 0.212 REMARK 3 FREE R VALUE : 0.231 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.380 REMARK 3 FREE R VALUE TEST SET COUNT : 702 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 35.3900 - 2.4800 1.00 2654 154 0.1907 0.2229 REMARK 3 2 2.4800 - 1.9700 1.00 2471 142 0.2663 0.2385 REMARK 3 3 1.9700 - 1.7200 1.00 2408 137 0.2421 0.2567 REMARK 3 4 1.7200 - 1.5600 1.00 2414 127 0.2215 0.2128 REMARK 3 5 1.5600 - 1.4500 1.00 2400 142 0.3083 0.3306 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.194 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.531 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.44 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.70 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 : 0.013 651 REMARK 3 ANGLE : 1.728 1001 REMARK 3 CHIRALITY : 0.078 100 REMARK 3 PLANARITY : 0.018 29 REMARK 3 DIHEDRAL : 36.769 258 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): -3.8766 4.0402 -9.6821 REMARK 3 T TENSOR REMARK 3 T11: 0.3350 T22: 0.1626 REMARK 3 T33: 0.2311 T12: -0.0146 REMARK 3 T13: -0.0230 T23: 0.0339 REMARK 3 L TENSOR REMARK 3 L11: 3.3606 L22: 8.4572 REMARK 3 L33: 4.8337 L12: -2.4257 REMARK 3 L13: -1.6932 L23: 2.7076 REMARK 3 S TENSOR REMARK 3 S11: 0.2165 S12: 0.0416 S13: 0.0938 REMARK 3 S21: -0.7123 S22: -0.0564 S23: 0.1551 REMARK 3 S31: -0.2390 S32: 0.0900 S33: -0.1545 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 8TAA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-JUN-23. REMARK 100 THE DEPOSITION ID IS D_1000274691. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-OCT-22 REMARK 200 TEMPERATURE (KELVIN) : 196 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97918 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13141 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.450 REMARK 200 RESOLUTION RANGE LOW (A) : 141.540 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 12.20 REMARK 200 R MERGE (I) : 0.04900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.47 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 1.78900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX 1.20.1_4487 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: AMORPHOUS CUBES REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2MM SPERMINE, 45% MPD, 0.08M NACL, REMARK 280 0.04M NACACO PH 6.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 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+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 70.77150 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 15.44850 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 15.44850 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 35.38575 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 15.44850 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 15.44850 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 106.15725 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 15.44850 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 15.44850 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 35.38575 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 15.44850 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 15.44850 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 106.15725 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 70.77150 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 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: 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 DT A 14 O3' DT A 14 C3' -0.042 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 DT A 11 O5' - P - OP2 ANGL. DEV. = -6.0 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 MMP A 101 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 A 104 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG A 1 O6 REMARK 620 2 DG A 3 O6 89.4 REMARK 620 3 DG A 4 O6 66.0 79.6 REMARK 620 4 DG A 6 O6 158.2 76.1 95.0 REMARK 620 5 DG A 7 O6 101.6 134.4 65.7 78.4 REMARK 620 6 DG A 9 O6 132.5 109.4 157.7 68.6 95.3 REMARK 620 7 DG A 10 O6 68.3 153.8 102.1 129.2 66.5 79.0 REMARK 620 8 DG A 12 O6 75.2 67.5 128.7 112.7 158.1 73.1 92.7 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 106 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG A 1 O6 REMARK 620 2 DG A 4 O6 68.6 REMARK 620 3 DG A 7 O6 107.1 69.0 REMARK 620 4 DG A 10 O6 70.0 106.3 68.8 REMARK 620 5 DG A 15 O6 88.6 150.0 139.1 82.5 REMARK 620 6 DG A 18 O6 150.7 139.5 83.5 89.6 67.3 REMARK 620 7 DG A 21 O6 136.0 81.3 90.0 152.1 104.6 69.3 REMARK 620 8 DG A 24 O6 80.2 87.8 149.9 138.8 68.6 104.5 66.9 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 105 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG A 15 O6 REMARK 620 2 DG A 16 O6 73.7 REMARK 620 3 DG A 18 O6 66.9 88.3 REMARK 620 4 DG A 19 O6 131.8 76.1 75.6 REMARK 620 5 DG A 21 O6 103.7 154.3 67.8 88.3 REMARK 620 6 DG A 22 O6 154.1 118.6 132.1 74.1 75.1 REMARK 620 7 DG A 24 O6 69.1 131.7 103.7 152.1 66.5 87.4 REMARK 620 8 DG A 25 O6 89.0 73.2 153.2 116.8 132.5 74.6 76.5 REMARK 620 N 1 2 3 4 5 6 7 DBREF 8TAA A 1 25 PDB 8TAA 8TAA 1 25 SEQRES 1 A 25 DG DT DG DG DT DG DG DT DG DG DT DG DA SEQRES 2 A 25 DT DG DG DT DG DG DT DG DG DT DG DG HET MMP A 101 31 HET SPM A 102 14 HET MPD A 103 8 HET K A 104 1 HET K A 105 1 HET K A 106 1 HETNAM MMP N-METHYLMESOPORPHYRIN HETNAM SPM SPERMINE HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL HETNAM K POTASSIUM ION FORMUL 2 MMP C35 H40 N4 O4 FORMUL 3 SPM C10 H26 N4 FORMUL 4 MPD C6 H14 O2 FORMUL 5 K 3(K 1+) FORMUL 8 HOH *38(H2 O) LINK O6 DG A 1 K K A 104 1555 1555 2.88 LINK O6 DG A 1 K K A 106 1555 1555 2.80 LINK O6 DG A 3 K K A 104 1555 1555 2.75 LINK O6 DG A 4 K K A 104 1555 1555 2.91 LINK O6 DG A 4 K K A 106 1555 1555 2.79 LINK O6 DG A 6 K K A 104 1555 1555 2.70 LINK O6 DG A 7 K K A 104 1555 1555 2.91 LINK O6 DG A 7 K K A 106 1555 1555 2.78 LINK O6 DG A 9 K K A 104 1555 1555 2.80 LINK O6 DG A 10 K K A 104 1555 1555 2.85 LINK O6 DG A 10 K K A 106 1555 1555 2.81 LINK O6 DG A 12 K K A 104 1555 1555 2.79 LINK O6 DG A 15 K K A 105 1555 1555 2.84 LINK O6 DG A 15 K K A 106 1555 1555 2.86 LINK O6 DG A 16 K K A 105 1555 1555 2.73 LINK O6 DG A 18 K K A 105 1555 1555 2.89 LINK O6 DG A 18 K K A 106 1555 1555 2.84 LINK O6 DG A 19 K K A 105 1555 1555 2.74 LINK O6 DG A 21 K K A 105 1555 1555 2.88 LINK O6 DG A 21 K K A 106 1555 1555 2.82 LINK O6 DG A 22 K K A 105 1555 1555 2.70 LINK O6 DG A 24 K K A 105 1555 1555 2.83 LINK O6 DG A 24 K K A 106 1555 1555 2.85 LINK O6 DG A 25 K K A 105 1555 1555 2.71 CRYST1 30.897 30.897 141.543 90.00 90.00 90.00 P 41 21 2 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 0.032366 0.000000 0.000000 0.00000 SCALE2 0.000000 0.032366 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007065 0.00000