HEADER RNA 09-APR-25 9QTJ TITLE STRUCTURE OF OCEANOBACILLUS IHEYENSIS GROUP II INTRON DOMAINS D1-D6 COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (461-MER); COMPND 3 CHAIN: 1; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: GROUP IIC INTRON SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: OCEANOBACILLUS IHEYENSIS; SOURCE 4 ORGANISM_TAXID: 182710 KEYWDS PROTEIN-FREE RNA CRYO-EM, RIBOZYME, METALLOENZYMES, SPLICING, RNA EXPDTA ELECTRON MICROSCOPY AUTHOR S.S.JADHAV,M.NIGRO,M.MARCIA REVDAT 1 18-FEB-26 9QTJ 0 JRNL AUTH R.C.KRETSCH,R.ALBRECHT,E.S.ANDERSEN,H.A.CHEN,W.CHIU,R.DAS, JRNL AUTH 2 J.G.GEZELLE,M.D.HARTMANN,C.HOBARTNER,Y.HU,S.JADHAV, JRNL AUTH 3 P.E.JOHNSON,C.P.JONES,D.KOIRALA,E.L.KRISTOFFERSEN,E.LARGY, JRNL AUTH 4 A.LEWICKA,C.D.MACKERETH,M.MARCIA,M.NIGRO,M.OJHA, JRNL AUTH 5 J.A.PICCIRILLI,P.A.RICE,H.SHIN,A.L.STECKELBERG,Z.SU, JRNL AUTH 6 Y.SRIVASTAVA,L.WANG,Y.WU,J.XIE,N.H.ZWERGIUS,J.MOULT, JRNL AUTH 7 A.KRYSHTAFOVYCH JRNL TITL FUNCTIONAL RELEVANCE OF CASP16 NUCLEIC ACID PREDICTIONS AS JRNL TITL 2 EVALUATED BY STRUCTURE PROVIDERS. JRNL REF PROTEINS V. 94 51 2026 JRNL REFN ESSN 1097-0134 JRNL PMID 40905273 JRNL DOI 10.1002/PROT.70043 REMARK 2 REMARK 2 RESOLUTION. 3.79 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, PHENIX, CRYOSPARC REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : NULL REMARK 3 REFINEMENT PROTOCOL : NULL REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : NULL REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 3.790 REMARK 3 NUMBER OF PARTICLES : 71128 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING AND AMPLITUDE REMARK 3 CORRECTION REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 9QTJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 09-APR-25. REMARK 100 THE DEPOSITION ID IS D_1292146748. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : SINGLE PARTICLE REMARK 245 SPECIMEN TYPE : NULL REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : PARTICLE REMARK 245 PARTICLE TYPE : POINT REMARK 245 NAME OF SAMPLE : GROUP IIC INTRON REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 6.50 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : TFS KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 800.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2400.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : NULL REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 3600.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : NULL REMARK 245 CALIBRATED MAGNIFICATION : NULL REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 300 REMARK 245 IMAGING DETAILS : NULL REMARK 247 REMARK 247 ELECTRON MICROSCOPY REMARK 247 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM ELECTRON REMARK 247 MICROSCOPY DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE REMARK 247 THAT CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES REMARK 247 ON THESE RECORDS ARE MEANINGLESS EXCEPT FOR THE CALCULATION REMARK 247 OF THE STRUCTURE FACTORS. 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: 1 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 G 1 1 REMARK 465 U 1 2 REMARK 465 U 1 84 REMARK 465 U 1 152 REMARK 465 C 1 289 REMARK 465 A 1 290 REMARK 465 C 1 291 REMARK 465 U 1 292 REMARK 465 C 1 451 REMARK 465 A 1 459 REMARK 465 U 1 472 REMARK 465 A 1 473 REMARK 465 C 1 474 REMARK 465 U 1 475 REMARK 465 C 1 476 REMARK 465 U 1 477 REMARK 465 A 1 478 REMARK 465 U 1 479 REMARK 465 U 1 480 REMARK 465 A 1 481 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 A 1 207 N9 C8 N7 C5 C6 N6 N1 REMARK 470 A 1 207 C2 N3 C4 REMARK 470 U 1 321 N1 C2 O2 N3 C4 O4 C5 REMARK 470 U 1 321 C6 REMARK 470 G 1 322 N9 C8 N7 C5 C6 O6 N1 REMARK 470 G 1 322 C2 N2 N3 C4 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 U 1 457 O6 G 1 463 1.98 REMARK 500 O4 U 1 168 O6 G 1 209 2.01 REMARK 500 O2 C 1 307 O6 G 1 314 2.02 REMARK 500 O2 U 1 348 O6 G 1 381 2.09 REMARK 500 O6 G 1 449 O4 U 1 470 2.12 REMARK 500 O2 U 1 276 N2 G 1 327 2.13 REMARK 500 N2 G 1 449 O2 U 1 470 2.14 REMARK 500 O4 U 1 306 O6 G 1 315 2.15 REMARK 500 N3 C 1 284 O2 U 1 298 2.19 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 1 107 C4 - N9 - C1' ANGL. DEV. = 8.0 DEGREES REMARK 500 U 1 351 N3 - C2 - O2 ANGL. DEV. = -4.4 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-53353 RELATED DB: EMDB REMARK 900 STRUCTURE OF OCEANOBACILLUS IHEYENSIS GROUP II INTRON DOMAINS D1-D6 DBREF 9QTJ 1 1 481 PDB 9QTJ 9QTJ 1 481 SEQRES 1 1 481 G U G U G C C C G G C A U SEQRES 2 1 481 G G G U G C A G U C U A U SEQRES 3 1 481 A G G G U G A G A G U C C SEQRES 4 1 481 C G A A C U G U G A A G G SEQRES 5 1 481 C A G A A G U A A C A G U SEQRES 6 1 481 U A G C C U A A C G C A A SEQRES 7 1 481 G G G U G U C C G U G G C SEQRES 8 1 481 G A C A U G G A A U C U G SEQRES 9 1 481 A A G G A A G C G G A C G SEQRES 10 1 481 G C A A A C C U U C G G U SEQRES 11 1 481 C U G A G G A A C A C G A SEQRES 12 1 481 A C U U C A U A U G A G G SEQRES 13 1 481 C U A G G U A U C A A U G SEQRES 14 1 481 G A U G A G U U U G C A U SEQRES 15 1 481 A A C A A A A C A A A G U SEQRES 16 1 481 C C U U U C U G C C A A A SEQRES 17 1 481 G U U G G U A C A G A G U SEQRES 18 1 481 A A A U G A A G C A G A U SEQRES 19 1 481 U G A U G A A G G G A A A SEQRES 20 1 481 G A C U G C A U U C U U A SEQRES 21 1 481 C C C G G G G A G G U C U SEQRES 22 1 481 G A U C G A A A C G C C A SEQRES 23 1 481 A G C A C U C U U G G U A SEQRES 24 1 481 A C C C A U U C A G C A A SEQRES 25 1 481 U G G A U G G C U G A A C SEQRES 26 1 481 G G U C A G A A G U C A G SEQRES 27 1 481 C A G A A G U C A U A G U SEQRES 28 1 481 A C C C U G C A U A C U C SEQRES 29 1 481 G A G A A U G U A A G G G SEQRES 30 1 481 G A A G G A C G G A A C A SEQRES 31 1 481 A U U A A G U U C G C U U SEQRES 32 1 481 A A U U G A A C C G C C G SEQRES 33 1 481 U A U A C C G A A C G G U SEQRES 34 1 481 A C G U A C G G U G G U G SEQRES 35 1 481 U G A G A G G A C G G G G SEQRES 36 1 481 G U U A G U C G C U C C C SEQRES 37 1 481 U U C U A C U C U A U U A CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MASTER 176 0 0 0 0 0 0 6 9878 1 0 37 END