HEADER RNA 08-NOV-24 9KGG TITLE CRYO-EM STRUCTURE OF LINEAR INTRON OF THYMIDYLATE SYNTHASE (TD) GENE TITLE 2 OF BACTERIOPHAGE T4 COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (267-MER); COMPND 3 CHAIN: U; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA PHAGE T4; SOURCE 3 ORGANISM_TAXID: 2681598; SOURCE 4 EXPRESSION_SYSTEM: IN VITRO TRANSCRIPTION VECTOR PT7-FLUC(DELTAI); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 905932 KEYWDS T4 TD, GROUP I INTRON, CRYO-EM, CIRCULAR RNA, RNA EXPDTA ELECTRON MICROSCOPY AUTHOR L.AN,S.LI,K.ZHANG REVDAT 1 12-NOV-25 9KGG 0 JRNL AUTH L.AN,S.LI,K.ZHANG JRNL TITL MECHANISTIC INSIGHTS INTO CYCLIZATION OF THE T4 TD GROUP I JRNL TITL 2 INTRON JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.12 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : 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) : 3.120 REMARK 3 NUMBER OF PARTICLES : 425460 REMARK 3 CTF CORRECTION METHOD : NONE REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 9KGG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 13-NOV-24. REMARK 100 THE DEPOSITION ID IS D_1300053496. 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 : CRYO-EM STRUCTURE OF LINEAR REMARK 245 INTRON OF THYMIDYLATE SYNTHASE REMARK 245 (TD) GENE OF BACTERIOPHAGE T4 REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 1.00 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.50 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) : 1300.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2700.00 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) : 6500.00 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 APPLY THE FOLLOWING TO CHAINS: U 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: 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 U 63 N2 G U 66 1.99 REMARK 500 O2' A U 85 O2' U U 163 2.06 REMARK 500 OP1 U U 41 O2' G U 186 2.11 REMARK 500 REMARK 500 REMARK: NULL 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 G U 1 P G U 1 OP3 -0.124 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 C U 97 N1 - C2 - O2 ANGL. DEV. = 4.1 DEGREES REMARK 500 C U 97 C2 - N1 - C1' ANGL. DEV. = 7.5 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 U 301 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U U 3 O3' REMARK 620 2 A U 4 OP1 62.0 REMARK 620 3 U U 74 OP1 81.8 83.0 REMARK 620 4 A U 190 OP1 108.6 170.3 98.8 REMARK 620 5 A U 192 OP1 170.3 109.1 93.4 80.4 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG U 302 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A U 73 OP1 REMARK 620 2 A U 120 OP2 113.8 REMARK 620 N 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-62318 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF LINEAR INTRON OF THYMIDYLATE SYNTHASE (TD) REMARK 900 GENE OF BACTERIOPHAGE T4 DBREF 9KGG U 1 267 PDB 9KGG 9KGG 1 267 SEQRES 1 U 267 G G U A A U U G A G G C C SEQRES 2 U 267 U G A G U A U A A G G U G SEQRES 3 U 267 A C U U A U A C U U G U A SEQRES 4 U 267 A U C U A U C U A A A C G SEQRES 5 U 267 G G G A A C C U C U C U A SEQRES 6 U 267 G U A G A C A A U C C C G SEQRES 7 U 267 U G C U A A A U U G U A G SEQRES 8 U 267 G A C U G C C C G G G U U SEQRES 9 U 267 C U A C A U A A A U G C C SEQRES 10 U 267 U A A C G A C U A U C C C SEQRES 11 U 267 U U U G G G G A G U A G G SEQRES 12 U 267 G U C A A G U G A C U C G SEQRES 13 U 267 A A A C G A U A G A C A A SEQRES 14 U 267 C U U G C U U U A A C A A SEQRES 15 U 267 G U U G G A G A U A U A G SEQRES 16 U 267 U C U G C U C U G C A U G SEQRES 17 U 267 G U G A C A U G C A G C U SEQRES 18 U 267 G G A U A U A A U U C C G SEQRES 19 U 267 G G G U A A G A U U A A C SEQRES 20 U 267 G A C C U U A U C U G A A SEQRES 21 U 267 C A U A A U G HET MG U 301 1 HET MG U 302 1 HET MG U 303 1 HETNAM MG MAGNESIUM ION FORMUL 2 MG 3(MG 2+) LINK O3' U U 3 MG MG U 301 1555 1555 2.14 LINK OP1 A U 4 MG MG U 301 1555 1555 2.63 LINK OP1 A U 73 MG MG U 302 1555 1555 2.00 LINK OP1 U U 74 MG MG U 301 1555 1555 1.84 LINK OP2 A U 120 MG MG U 302 1555 1555 1.84 LINK OP1 A U 190 MG MG U 301 1555 1555 1.85 LINK OP1 A U 192 MG MG U 301 1555 1555 2.68 LINK OP2 A U 194 MG MG U 303 1555 1555 2.39 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 TER 5690 G U 267 HETATM 5691 MG MG U 301 133.644 127.923 139.514 1.00 30.00 MG HETATM 5692 MG MG U 302 139.286 125.910 133.713 1.00 30.00 MG HETATM 5693 MG MG U 303 130.435 135.255 135.375 1.00 30.00 MG CONECT 56 5691 CONECT 69 5691 CONECT 1538 5692 CONECT 1560 5691 CONECT 2533 5692 CONECT 4031 5691 CONECT 4073 5691 CONECT 4116 5693 CONECT 5691 56 69 1560 4031 CONECT 5691 4073 CONECT 5692 1538 2533 CONECT 5693 4116 MASTER 171 0 3 0 0 0 0 6 5692 1 12 21 END