HEADER RNA 22-APR-21 7EOP TITLE CRYSTAL STRUCTURE OF THE PEPPER APTAMER IN COMPLEX WITH HBC620 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPPER (49-MER); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 3 ORGANISM_TAXID: 32630; SOURCE 4 EXPRESSION_SYSTEM: IN VITRO TRANSCRIPTION VECTOR PT7-TP(DELTAI); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 905931 KEYWDS FLUORESCENT RNA, APTAMER, HBC620, RNA EXPDTA X-RAY DIFFRACTION AUTHOR K.Y.HUANG,A.M.REN REVDAT 3 29-NOV-23 7EOP 1 REMARK REVDAT 2 16-FEB-22 7EOP 1 JRNL REVDAT 1 24-NOV-21 7EOP 0 JRNL AUTH K.HUANG,X.CHEN,C.LI,Q.SONG,H.LI,L.ZHU,Y.YANG,A.REN JRNL TITL STRUCTURE-BASED INVESTIGATION OF FLUOROGENIC PEPPER APTAMER. JRNL REF NAT.CHEM.BIOL. V. 17 1289 2021 JRNL REFN ESSN 1552-4469 JRNL PMID 34725509 JRNL DOI 10.1038/S41589-021-00884-6 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14_3260 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.91 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 13691 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.190 REMARK 3 FREE R VALUE : 0.211 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.790 REMARK 3 FREE R VALUE TEST SET COUNT : 656 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 28.9140 - 3.0770 0.99 2675 136 0.1690 0.1736 REMARK 3 2 3.0770 - 2.4427 1.00 2632 133 0.2039 0.2396 REMARK 3 3 2.4427 - 2.1341 0.98 2580 128 0.2059 0.2446 REMARK 3 4 2.1341 - 1.9390 1.00 2558 153 0.2059 0.2403 REMARK 3 5 1.9390 - 1.8000 0.98 2590 106 0.2304 0.2937 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) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.590 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.59 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 : 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 7EOP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 23-APR-21. REMARK 100 THE DEPOSITION ID IS D_1300021893. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-MAY-19 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 : 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) : 1.102 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 : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13710 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 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 (%) : 99.1 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : 0.08800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 3.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.4 REMARK 200 DATA REDUNDANCY IN SHELL : 5.80 REMARK 200 R MERGE FOR SHELL (I) : 0.64000 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: 7EOG REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M AMMONIUM CHLORIDE, 0.005 M REMARK 280 MAGNESIUM CHLORIDE, 0.025 M HEPES, PH 7.0, 1.25 M 1,6-HEXANEDIOL, REMARK 280 40% MPD, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K 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 46.22350 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 17.49150 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 46.22350 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 17.49150 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 440 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8300 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 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 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 HOH A 210 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 295 LIES ON A SPECIAL POSITION. 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 O2' C A 49 O HOH A 201 2.02 REMARK 500 O3' C A 49 O HOH A 201 2.06 REMARK 500 O4 U A 20 O HOH A 202 2.11 REMARK 500 O HOH A 333 O HOH A 334 2.13 REMARK 500 OP2 C A 43 O HOH A 203 2.16 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 G A 9 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 MG A 105 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 C A 7 OP2 REMARK 620 2 U A 8 OP2 89.2 REMARK 620 3 HOH A 275 O 170.8 87.9 REMARK 620 4 HOH A 280 O 88.6 82.6 82.3 REMARK 620 5 HOH A 290 O 89.6 170.3 91.8 87.8 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 104 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A 30 OP2 REMARK 620 2 HOH A 224 O 177.0 REMARK 620 3 HOH A 266 O 92.8 90.0 REMARK 620 4 HOH A 274 O 88.8 88.4 176.5 REMARK 620 5 HOH A 277 O 92.6 86.7 87.2 95.9 REMARK 620 6 HOH A 328 O 91.2 89.8 87.2 89.7 173.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 102 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U A 32 OP2 REMARK 620 2 HOH A 225 O 90.7 REMARK 620 3 HOH A 231 O 94.3 175.0 REMARK 620 4 HOH A 273 O 178.4 89.3 85.7 REMARK 620 5 HOH A 317 O 93.3 90.9 88.3 85.1 REMARK 620 6 HOH A 331 O 94.2 89.0 91.1 87.3 172.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 103 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U A 42 OP2 REMARK 620 2 HOH A 263 O 176.2 REMARK 620 3 HOH A 292 O 88.3 89.2 REMARK 620 4 HOH A 305 O 92.6 90.1 87.1 REMARK 620 5 HOH A 322 O 94.3 83.0 92.1 173.1 REMARK 620 6 HOH A 332 O 95.8 86.8 175.1 90.1 90.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 106 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 208 O REMARK 620 2 HOH A 216 O 86.7 REMARK 620 3 HOH A 253 O 85.0 88.0 REMARK 620 4 HOH A 268 O 172.6 99.9 98.5 REMARK 620 5 HOH A 301 O 95.3 91.5 179.4 81.2 REMARK 620 6 HOH A 351 O 87.5 173.9 93.5 85.8 87.1 REMARK 620 N 1 2 3 4 5 DBREF 7EOP A 2 49 PDB 7EOP 7EOP 2 49 SEQRES 1 A 48 G C G C A C U G G C G C U SEQRES 2 A 48 G C G C C U U C G G G C G SEQRES 3 A 48 C C A A U C G U A G C G U SEQRES 4 A 48 G U C G G C G C C HET GTP A 101 32 HET MG A 102 1 HET MG A 103 1 HET MG A 104 1 HET MG A 105 1 HET MG A 106 1 HET J93 A 107 25 HETNAM GTP GUANOSINE-5'-TRIPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM J93 4-[(~{Z})-1-CYANO-2-[5-[2-HYDROXYETHYL(METHYL) HETNAM 2 J93 AMINO]THIENO[3,2-B]THIOPHEN-2- HETNAM 3 J93 YL]ETHENYL]BENZENECARBONITRILE FORMUL 2 GTP C10 H16 N5 O14 P3 FORMUL 3 MG 5(MG 2+) FORMUL 8 J93 C19 H15 N3 O S2 FORMUL 9 HOH *151(H2 O) LINK P G A 2 O3' GTP A 101 1555 1555 1.57 LINK OP2 C A 7 MG MG A 105 1555 1555 2.03 LINK OP2 U A 8 MG MG A 105 1555 1555 1.97 LINK OP2 A A 30 MG MG A 104 1555 1555 1.99 LINK OP2 U A 32 MG MG A 102 1555 1555 1.99 LINK OP2 U A 42 MG MG A 103 1555 1555 2.01 LINK MG MG A 102 O HOH A 225 1555 1555 2.11 LINK MG MG A 102 O HOH A 231 1555 1555 2.15 LINK MG MG A 102 O HOH A 273 1555 1555 2.15 LINK MG MG A 102 O HOH A 317 1555 1555 2.05 LINK MG MG A 102 O HOH A 331 1555 1555 2.15 LINK MG MG A 103 O HOH A 263 1555 1555 1.99 LINK MG MG A 103 O HOH A 292 1555 1555 2.16 LINK MG MG A 103 O HOH A 305 1555 1555 2.15 LINK MG MG A 103 O HOH A 322 1555 1555 2.03 LINK MG MG A 103 O HOH A 332 1555 1555 2.09 LINK MG MG A 104 O HOH A 224 1555 1555 2.13 LINK MG MG A 104 O HOH A 266 1555 1555 2.16 LINK MG MG A 104 O HOH A 274 1555 1555 2.06 LINK MG MG A 104 O HOH A 277 1555 1555 2.08 LINK MG MG A 104 O HOH A 328 1555 1555 2.23 LINK MG MG A 105 O HOH A 275 1555 1555 2.02 LINK MG MG A 105 O HOH A 280 1555 1555 2.23 LINK MG MG A 105 O HOH A 290 1555 1555 2.09 LINK MG MG A 106 O HOH A 208 1555 2656 2.24 LINK MG MG A 106 O HOH A 216 1555 2656 2.16 LINK MG MG A 106 O HOH A 253 1555 2656 1.95 LINK MG MG A 106 O HOH A 268 1555 1555 2.08 LINK MG MG A 106 O HOH A 301 1555 1555 1.90 LINK MG MG A 106 O HOH A 351 1555 1555 2.08 CRYST1 92.447 34.983 57.839 90.00 127.57 90.00 C 1 2 1 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 0.010817 0.000000 0.008320 0.00000 SCALE2 0.000000 0.028585 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021812 0.00000