HEADER DNA 20-MAY-22 8CXF TITLE CRYSTAL STRUCTURE OF AN I-MOTIF FROM THE HRAS PROMOTER REGION COMPND MOL_ID: 1; COMPND 2 MOLECULE: HRAS DNA; COMPND 3 CHAIN: B, 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 HRAS, I-MOTIF, DNA EXPDTA X-RAY DIFFRACTION AUTHOR L.A.YATSUNYK,K.S.LI REVDAT 3 22-MAY-24 8CXF 1 REMARK REVDAT 2 28-JUN-23 8CXF 1 JRNL REVDAT 1 10-MAY-23 8CXF 0 JRNL AUTH K.S.LI,D.JORDAN,L.Y.LIN,S.E.MCCARTHY,J.S.SCHNEEKLOTH JR., JRNL AUTH 2 L.A.YATSUNYK JRNL TITL CRYSTAL STRUCTURE OF AN I-MOTIF FROM THE HRAS ONCOGENE JRNL TITL 2 PROMOTER. JRNL REF ANGEW.CHEM.INT.ED.ENGL. V. 62 01666 2023 JRNL REFN ESSN 1521-3773 JRNL PMID 36995904 JRNL DOI 10.1002/ANIE.202301666 REMARK 2 REMARK 2 RESOLUTION. 1.77 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) : 1.77 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.01 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.280 REMARK 3 COMPLETENESS FOR RANGE (%) : 88.3 REMARK 3 NUMBER OF REFLECTIONS : 17568 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.223 REMARK 3 R VALUE (WORKING SET) : 0.221 REMARK 3 FREE R VALUE : 0.237 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.040 REMARK 3 FREE R VALUE TEST SET COUNT : 1763 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 41.0100 - 4.1500 0.99 1437 160 0.1526 0.1380 REMARK 3 2 4.1500 - 3.3000 0.98 1390 144 0.2057 0.2371 REMARK 3 3 3.2900 - 2.8800 0.96 1328 147 0.2531 0.2877 REMARK 3 4 2.8800 - 2.6200 0.98 1346 156 0.2700 0.3245 REMARK 3 5 2.6200 - 2.4300 0.96 1325 143 0.2513 0.3090 REMARK 3 6 2.4300 - 2.2900 0.95 1303 148 0.2702 0.3356 REMARK 3 7 2.2900 - 2.1700 0.91 1233 137 0.2823 0.2687 REMARK 3 8 2.1700 - 2.0800 0.90 1246 133 0.3012 0.3414 REMARK 3 9 2.0800 - 2.0000 0.87 1191 143 0.3467 0.3368 REMARK 3 10 2.0000 - 1.9300 0.87 1192 125 0.3529 0.3448 REMARK 3 11 1.9300 - 1.8700 0.80 1085 133 0.4021 0.4228 REMARK 3 12 1.8700 - 1.8100 0.70 939 99 0.4446 0.3949 REMARK 3 13 1.8100 - 1.7700 0.59 790 95 0.4858 0.5453 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) : 0.251 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 40.521 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 38.58 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 58.95 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 : 0.008 1175 REMARK 3 ANGLE : 0.943 1800 REMARK 3 CHIRALITY : 0.040 206 REMARK 3 PLANARITY : 0.006 52 REMARK 3 DIHEDRAL : 31.901 508 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): 58.7398 12.7545 14.9303 REMARK 3 T TENSOR REMARK 3 T11: 0.5119 T22: 0.5341 REMARK 3 T33: 0.4489 T12: 0.1769 REMARK 3 T13: 0.0112 T23: 0.0019 REMARK 3 L TENSOR REMARK 3 L11: 0.3174 L22: 0.6068 REMARK 3 L33: 0.2545 L12: -0.4105 REMARK 3 L13: -0.1091 L23: 0.0113 REMARK 3 S TENSOR REMARK 3 S11: -0.6139 S12: -0.7075 S13: 0.0398 REMARK 3 S21: 0.1309 S22: 0.4412 S23: 0.0086 REMARK 3 S31: -0.0226 S32: 0.0442 S33: -0.0029 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 8CXF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-MAY-22. REMARK 100 THE DEPOSITION ID IS D_1000264740. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-JUL-21 REMARK 200 TEMPERATURE (KELVIN) : 196 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 : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9196 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 : 19101 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.770 REMARK 200 RESOLUTION RANGE LOW (A) : 41.010 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.9 REMARK 200 DATA REDUNDANCY : 9.600 REMARK 200 R MERGE (I) : 0.05900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.77 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 68.5 REMARK 200 DATA REDUNDANCY IN SHELL : 6.10 REMARK 200 R MERGE FOR SHELL (I) : 1.46200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: PHENIX 1.18.2_3874 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: RECTANGULAR PRISM REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.99 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.05 M MES, 17% W/V PEG 4000, X M REMARK 280 SPERMINE TETRAHYDROCHLORIDE (ADD SPERMINE CONCENTRATION), PH 6.0, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-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 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 59.19600 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 15.63550 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 59.19600 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 15.63550 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 APPLY THE FOLLOWING TO CHAINS: B, 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 DC B 1 O5' REMARK 470 DA B 27 C5' C4' O4' C3' O3' C2' C1' REMARK 470 DA B 27 N9 C8 N7 C5 C6 N6 N1 REMARK 470 DA B 27 C2 N3 C4 REMARK 470 DC A 1 O5' REMARK 470 DA A 27 C5' C4' O4' C3' O3' C2' C1' REMARK 470 DA A 27 N9 C8 N7 C5 C6 N6 N1 REMARK 470 DA A 27 C2 N3 C4 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 DG B 26 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 DC A 25 O4' - C1' - N1 ANGL. DEV. = 2.2 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 B 241 DISTANCE = 6.48 ANGSTROMS REMARK 525 HOH B 242 DISTANCE = 8.82 ANGSTROMS DBREF 8CXF B 1 27 PDB 8CXF 8CXF 1 27 DBREF 8CXF A 1 27 PDB 8CXF 8CXF 1 27 SEQRES 1 B 27 DC DG DC CBR DC DG DT DG DC DC DC DT DG SEQRES 2 B 27 DC DG DC DC DC DG DC DA DA DC DC DC DG SEQRES 3 B 27 DA SEQRES 1 A 27 DC DG DC CBR DC DG DT DG DC DC DC DT DG SEQRES 2 A 27 DC DG DC DC DC DG DC DA DA DC DC DC DG SEQRES 3 A 27 DA HET CBR B 4 20 HET CBR A 4 20 HET PG5 B 101 12 HETNAM CBR 5-BROMO-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE HETNAM PG5 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE FORMUL 1 CBR 2(C9 H13 BR N3 O7 P) FORMUL 3 PG5 C8 H18 O4 FORMUL 4 HOH *73(H2 O) LINK O3' DC B 3 P CBR B 4 1555 1555 1.61 LINK O3' CBR B 4 P DC B 5 1555 1555 1.61 LINK O3' DC A 3 P CBR A 4 1555 1555 1.61 LINK O3' CBR A 4 P DC A 5 1555 1555 1.61 CRYST1 118.392 31.271 54.279 90.00 92.93 90.00 C 1 2 1 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 0.008447 0.000000 0.000432 0.00000 SCALE2 0.000000 0.031979 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018447 0.00000