HEADER RNA 09-DEC-24 9MFH TITLE ENV2 COBALAMIN RIBOSWITCH APTAMER DOMAIN IN THE APO STATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (76-MER); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: MARINE METAGENOME; SOURCE 4 ORGANISM_TAXID: 408172 KEYWDS RIBOSWITCH, APTAMER, VITAMIN B12, COBALAMIN, RNA EXPDTA X-RAY DIFFRACTION AUTHOR L.T.OLENGINSKI,R.T.BATEY REVDAT 1 24-SEP-25 9MFH 0 JRNL AUTH L.T.OLENGINSKI,A.J.WIERZBA,S.P.LAURSEN,R.T.BATEY JRNL TITL DESIGNING SMALL MOLECULES TARGETING A CRYPTIC RNA BINDING JRNL TITL 2 SITE THROUGH BASE DISPLACEMENT. JRNL REF NAT.CHEM.BIOL. 2025 JRNL REFN ESSN 1552-4469 JRNL PMID 40883492 JRNL DOI 10.1038/S41589-025-02018-8 REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2_4158 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) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.65 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 3 NUMBER OF REFLECTIONS : 6433 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.247 REMARK 3 R VALUE (WORKING SET) : 0.242 REMARK 3 FREE R VALUE : 0.294 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.030 REMARK 3 FREE R VALUE TEST SET COUNT : 645 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 19.6500 - 4.6000 0.96 1173 132 0.2241 0.2688 REMARK 3 2 4.6000 - 3.6600 0.99 1168 128 0.2259 0.2483 REMARK 3 3 3.6600 - 3.2000 0.99 1161 125 0.2191 0.2768 REMARK 3 4 3.2000 - 2.9100 0.99 1154 136 0.2810 0.3591 REMARK 3 5 2.9100 - 2.7000 0.97 1132 124 0.3308 0.4285 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) : 0.480 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.830 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 : 0.002 1828 REMARK 3 ANGLE : 0.637 2848 REMARK 3 CHIRALITY : 0.033 380 REMARK 3 PLANARITY : 0.005 76 REMARK 3 DIHEDRAL : 14.570 909 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 9MFH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-DEC-24. REMARK 100 THE DEPOSITION ID IS D_1000290873. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-DEC-24 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : SEALED TUBE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-003 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54178 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 200K REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7804 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.2 REMARK 200 DATA REDUNDANCY : 2.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 70.9 REMARK 200 DATA REDUNDANCY IN SHELL : 1.80 REMARK 200 R MERGE FOR SHELL (I) : 0.25500 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.65 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.26 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% (V/V) (+/-)-2-METHYL-2,4 REMARK 280 -PENTANEDIOL, 40 MM SODIUM CACODYLATE TRIHYDRATE (PH 7.0), 12 MM REMARK 280 SPERMINE TETRAHYDROCHLORIDE, 80 MM POTASSIUM CHLORIDE, 20 MM REMARK 280 MAGNESIUM CHLORIDE HEXAHYDRATE. HANGING DROP. 303.15 K, VAPOR REMARK 280 DIFFUSION, HANGING DROP 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 54.66300 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.66000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 54.66300 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 19.66000 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 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 291 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 N3 C A 68 O HOH A 201 2.00 REMARK 500 N1 G A 15 O HOH A 201 2.03 REMARK 500 OP2 A A 7 O HOH A 202 2.05 REMARK 500 O HOH A 209 O HOH A 343 2.14 REMARK 500 OP2 G A 21 O HOH A 203 2.17 REMARK 500 OP1 U A 11 O HOH A 204 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O2' C A 54 O2 C A 54 2555 2.17 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 A 375 DISTANCE = 6.34 ANGSTROMS REMARK 525 HOH A 376 DISTANCE = 6.56 ANGSTROMS REMARK 525 HOH A 377 DISTANCE = 6.74 ANGSTROMS REMARK 525 HOH A 378 DISTANCE = 7.81 ANGSTROMS REMARK 525 HOH A 379 DISTANCE = 7.91 ANGSTROMS REMARK 525 HOH A 380 DISTANCE = 9.66 ANGSTROMS REMARK 525 HOH A 381 DISTANCE = 9.74 ANGSTROMS 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 101 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A 5 OP1 REMARK 620 2 A A 6 OP2 92.8 REMARK 620 3 HOH A 213 O 101.2 123.7 REMARK 620 4 HOH A 230 O 87.3 168.7 67.3 REMARK 620 5 HOH A 245 O 79.9 84.3 151.6 84.6 REMARK 620 N 1 2 3 4 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 U A 11 OP1 REMARK 620 2 A A 12 OP2 85.1 REMARK 620 3 HOH A 204 O 61.3 107.5 REMARK 620 4 HOH A 265 O 108.5 109.3 140.6 REMARK 620 N 1 2 3 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 A A 41 OP2 REMARK 620 2 A A 41 O5' 55.8 REMARK 620 3 C A 42 OP2 120.4 79.5 REMARK 620 N 1 2 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 A A 49 OP1 REMARK 620 2 G A 58 OP2 75.8 REMARK 620 3 HOH A 250 O 78.2 66.1 REMARK 620 4 HOH A 314 O 156.4 95.0 118.4 REMARK 620 N 1 2 3 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 G A 62 O6 REMARK 620 2 HOH A 298 O 157.6 REMARK 620 N 1 DBREF 9MFH A 1 76 PDB 9MFH 9MFH 1 76 SEQRES 1 A 76 G G U A A A A G C A U A G SEQRES 2 A 76 U G G G A A A G U G A C G SEQRES 3 A 76 U G A A A U U C G U C C A SEQRES 4 A 76 C A C G A A A G U A A G G SEQRES 5 A 76 U C A U A G U C C G A A U SEQRES 6 A 76 G C C A C C U A C C A HET MG A 101 1 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 MG A 107 1 HET MG A 108 1 HETNAM MG MAGNESIUM ION FORMUL 2 MG 8(MG 2+) FORMUL 10 HOH *181(H2 O) LINK OP1 G A 1 MG MG A 107 1555 1555 2.84 LINK OP1 A A 5 MG MG A 101 1555 1555 2.41 LINK OP2 A A 6 MG MG A 101 1555 1555 2.10 LINK OP1 U A 11 MG MG A 105 1555 1555 2.23 LINK OP2 A A 12 MG MG A 105 1555 1555 1.82 LINK OP2 A A 19 MG MG A 108 1555 1555 2.76 LINK OP2 A A 41 MG MG A 106 1555 1555 2.38 LINK O5' A A 41 MG MG A 106 1555 1555 2.86 LINK OP2 C A 42 MG MG A 106 1555 1555 3.00 LINK OP1 A A 49 MG MG A 102 1555 1555 2.24 LINK OP2 G A 58 MG MG A 102 1555 1555 2.37 LINK O6 G A 62 MG MG A 104 1555 1555 2.88 LINK MG MG A 101 O HOH A 213 1555 1555 2.04 LINK MG MG A 101 O HOH A 230 1555 1555 2.46 LINK MG MG A 101 O HOH A 245 1555 1555 2.45 LINK MG MG A 102 O HOH A 250 1555 1555 2.48 LINK MG MG A 102 O HOH A 314 1555 1555 2.36 LINK MG MG A 103 O HOH A 217 1555 1555 2.46 LINK MG MG A 104 O HOH A 298 1555 1555 2.79 LINK MG MG A 105 O HOH A 204 1555 1555 2.03 LINK MG MG A 105 O HOH A 265 1555 1555 2.10 CRYST1 109.326 39.320 64.189 90.00 121.18 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 0.009147 0.000000 0.005536 0.00000 SCALE2 0.000000 0.025432 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018210 0.00000 CONECT 2 1639 CONECT 90 1633 CONECT 113 1633 CONECT 221 1637 CONECT 242 1637 CONECT 398 1640 CONECT 867 1638 CONECT 868 1638 CONECT 889 1638 CONECT 1040 1634 CONECT 1235 1634 CONECT 1333 1636 CONECT 1633 90 113 1653 1670 CONECT 1633 1685 CONECT 1634 1040 1235 1690 1754 CONECT 1635 1657 CONECT 1636 1333 1738 CONECT 1637 221 242 1644 1705 CONECT 1638 867 868 889 CONECT 1639 2 CONECT 1640 398 CONECT 1644 1637 CONECT 1653 1633 CONECT 1657 1635 CONECT 1670 1633 CONECT 1685 1633 CONECT 1690 1634 CONECT 1705 1637 CONECT 1738 1636 CONECT 1754 1634 MASTER 304 0 8 0 0 0 0 6 1820 1 30 6 END