HEADER RNA 10-JUL-23 8K0P TITLE THE ANOXYBACILLUS PUSHCHINOENSIS ORF-LESS GROUP IIC INTRON HYER1 AT TITLE 2 SYMMETRIC APO STATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (542-MER); COMPND 3 CHAIN: A, C; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ANOXYBACILLUS PUSHCHINOENSIS; SOURCE 3 ORGANISM_TAXID: 150248; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ORF-LESS GROUP IIC INTRON, RIBOZYMES, RNA EXPDTA ELECTRON MICROSCOPY AUTHOR H.Z.ZHU,J.J.G.LIU REVDAT 1 15-MAY-24 8K0P 0 JRNL AUTH Z.X.LIU,S.ZHANG,H.Z.ZHU,Z.H.CHEN,Y.YANG,L.Q.LI,Y.LEI,Y.LIU, JRNL AUTH 2 D.Y.LI,A.SUN,C.P.LI,S.Q.TAN,G.L.WANG,J.Y.SHEN,S.JIN,C.GAO, JRNL AUTH 3 J.G.LIU JRNL TITL HYDROLYTIC ENDONUCLEOLYTIC RIBOZYME (HYER) IS PROGRAMMABLE JRNL TITL 2 FOR SEQUENCE-SPECIFIC DNA CLEAVAGE. JRNL REF SCIENCE V. 383 H4859 2024 JRNL REFN ESSN 1095-9203 JRNL PMID 38301022 JRNL DOI 10.1126/SCIENCE.ADH4859 REMARK 2 REMARK 2 RESOLUTION. 2.99 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : NULL 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) : 2.990 REMARK 3 NUMBER OF PARTICLES : 127680 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 8K0P COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-JUL-23. REMARK 100 THE DEPOSITION ID IS D_1300039274. 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 : THE ANOXYBACILLUS REMARK 245 PUSHCHINOENSIS ORF-LESS GROUP REMARK 245 IIC INTRON HYER1 AT SYMMETRIC REMARK 245 APO STATE 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 : 7.40 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 : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1500.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2000.00 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) : 5000.00 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C 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 C A 404 REMARK 465 C A 405 REMARK 465 U A 406 REMARK 465 U A 407 REMARK 465 G A 408 REMARK 465 G A 409 REMARK 465 C A 410 REMARK 465 A A 411 REMARK 465 U A 412 REMARK 465 U A 413 REMARK 465 C A 414 REMARK 465 A A 415 REMARK 465 G A 416 REMARK 465 U A 417 REMARK 465 A A 418 REMARK 465 C A 419 REMARK 465 G A 420 REMARK 465 U A 421 REMARK 465 C A 422 REMARK 465 A A 423 REMARK 465 U A 424 REMARK 465 G A 425 REMARK 465 A A 426 REMARK 465 U A 427 REMARK 465 G A 428 REMARK 465 A A 429 REMARK 465 A A 430 REMARK 465 C A 431 REMARK 465 A A 432 REMARK 465 C A 433 REMARK 465 A A 434 REMARK 465 G A 435 REMARK 465 A A 436 REMARK 465 A A 437 REMARK 465 A A 438 REMARK 465 A A 439 REMARK 465 C A 440 REMARK 465 A A 441 REMARK 465 U A 442 REMARK 465 G A 443 REMARK 465 G A 444 REMARK 465 U A 445 REMARK 465 A A 446 REMARK 465 C A 447 REMARK 465 C A 448 REMARK 465 U A 449 REMARK 465 C A 450 REMARK 465 C A 451 REMARK 465 C A 452 REMARK 465 A A 453 REMARK 465 A A 454 REMARK 465 G A 455 REMARK 465 A A 456 REMARK 465 U A 486 REMARK 465 U A 487 REMARK 465 U A 488 REMARK 465 U A 489 REMARK 465 G A 490 REMARK 465 G A 491 REMARK 465 A A 492 REMARK 465 G A 493 REMARK 465 G A 494 REMARK 465 G A 495 REMARK 465 U A 496 REMARK 465 G A 497 REMARK 465 G A 498 REMARK 465 A A 499 REMARK 465 G A 500 REMARK 465 U A 501 REMARK 465 G A 502 REMARK 465 A A 503 REMARK 465 C A 504 REMARK 465 G A 505 REMARK 465 A A 506 REMARK 465 C A 507 REMARK 465 U A 508 REMARK 465 G A 509 REMARK 465 G A 510 REMARK 465 C A 511 REMARK 465 A A 512 REMARK 465 U A 513 REMARK 465 A A 514 REMARK 465 A A 515 REMARK 465 G A 516 REMARK 465 A A 517 REMARK 465 A A 518 REMARK 465 G A 519 REMARK 465 A A 520 REMARK 465 U A 521 REMARK 465 C A 522 REMARK 465 A A 523 REMARK 465 C C 404 REMARK 465 C C 405 REMARK 465 U C 406 REMARK 465 U C 407 REMARK 465 G C 408 REMARK 465 G C 409 REMARK 465 C C 410 REMARK 465 A C 411 REMARK 465 U C 412 REMARK 465 U C 413 REMARK 465 C C 414 REMARK 465 A C 415 REMARK 465 G C 416 REMARK 465 U C 417 REMARK 465 A C 418 REMARK 465 C C 419 REMARK 465 G C 420 REMARK 465 U C 421 REMARK 465 C C 422 REMARK 465 A C 423 REMARK 465 U C 424 REMARK 465 G C 425 REMARK 465 A C 426 REMARK 465 U C 427 REMARK 465 G C 428 REMARK 465 A C 429 REMARK 465 A C 430 REMARK 465 C C 431 REMARK 465 A C 432 REMARK 465 C C 433 REMARK 465 A C 434 REMARK 465 G C 435 REMARK 465 A C 436 REMARK 465 A C 437 REMARK 465 A C 438 REMARK 465 A C 439 REMARK 465 C C 440 REMARK 465 A C 441 REMARK 465 U C 442 REMARK 465 G C 443 REMARK 465 G C 444 REMARK 465 U C 445 REMARK 465 A C 446 REMARK 465 C C 447 REMARK 465 C C 448 REMARK 465 U C 449 REMARK 465 C C 450 REMARK 465 C C 451 REMARK 465 C C 452 REMARK 465 A C 453 REMARK 465 A C 454 REMARK 465 G C 455 REMARK 465 A C 456 REMARK 465 U C 486 REMARK 465 U C 487 REMARK 465 U C 488 REMARK 465 U C 489 REMARK 465 G C 490 REMARK 465 G C 491 REMARK 465 A C 492 REMARK 465 G C 493 REMARK 465 G C 494 REMARK 465 G C 495 REMARK 465 U C 496 REMARK 465 G C 497 REMARK 465 G C 498 REMARK 465 A C 499 REMARK 465 G C 500 REMARK 465 U C 501 REMARK 465 G C 502 REMARK 465 A C 503 REMARK 465 C C 504 REMARK 465 G C 505 REMARK 465 A C 506 REMARK 465 C C 507 REMARK 465 U C 508 REMARK 465 G C 509 REMARK 465 G C 510 REMARK 465 C C 511 REMARK 465 A C 512 REMARK 465 U C 513 REMARK 465 A C 514 REMARK 465 A C 515 REMARK 465 G C 516 REMARK 465 A C 517 REMARK 465 A C 518 REMARK 465 G C 519 REMARK 465 A C 520 REMARK 465 U C 521 REMARK 465 C C 522 REMARK 465 A C 523 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 702 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 C A 566 OP1 REMARK 620 2 G A 567 OP2 74.8 REMARK 620 3 C A 585 OP1 82.7 82.6 REMARK 620 4 U A 633 O3' 71.9 75.8 150.1 REMARK 620 5 U A 633 O2' 111.4 160.7 115.8 88.7 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 701 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U A 583 OP1 REMARK 620 2 C A 585 OP2 87.5 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG C 702 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 C C 566 OP1 REMARK 620 2 G C 567 OP2 74.8 REMARK 620 3 C C 585 OP1 82.7 82.7 REMARK 620 4 U C 633 O3' 71.9 75.8 150.1 REMARK 620 5 U C 633 O2' 111.4 160.7 115.8 88.6 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG C 701 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U C 583 OP1 REMARK 620 2 C C 585 OP2 87.5 REMARK 620 N 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-36776 RELATED DB: EMDB REMARK 900 THE ANOXYBACILLUS PUSHCHINOENSIS ORF-LESS GROUP IIC INTRON HYER1 AT REMARK 900 SYMMETRIC APO STATE DBREF 8K0P A 1 633 PDB 8K0P 8K0P 1 633 DBREF 8K0P C 1 633 PDB 8K0P 8K0P 1 633 SEQRES 1 A 633 G U G C G C U C G G C A U SEQRES 2 A 633 G G G U G C A A U C U C U SEQRES 3 A 633 A G G G U G A A A G U C C SEQRES 4 A 633 C G A A C U G C G A A G G SEQRES 5 A 633 C A G A A G U A G C A G U SEQRES 6 A 633 U A G C U U A A C G C A A SEQRES 7 A 633 G G G U G U C C G U G G U SEQRES 8 A 633 G A C G C G G A A U C U G SEQRES 9 A 633 A A G G A A G C G G G C G SEQRES 10 A 633 G C A A A C U U C C G G U SEQRES 11 A 633 C U G A G G A A C A C G A SEQRES 12 A 633 A C U U C A U A U A A G G SEQRES 13 A 633 C U A G G U A U C A U U G SEQRES 14 A 633 G A U G A G U U U G C A A SEQRES 15 A 633 G A C A A A A C A A A G U SEQRES 16 A 633 C C U U U C U G C C G A A SEQRES 17 A 633 G G U G A U A C A G A G U SEQRES 18 A 633 A A A U G A A G C A G A U SEQRES 19 A 633 A G A U G G A A G G A A A SEQRES 20 A 633 G A U U G U A C U C U U A SEQRES 21 A 633 C C C G A G G A G G U C U SEQRES 22 A 633 G A U G G A U A C G U G A SEQRES 23 A 633 A G U G C G C U U C A U A SEQRES 24 A 633 A C C U A C U U A G U G A SEQRES 25 A 633 U A A G U A A C U G A A C SEQRES 26 A 633 C A U C A G A A G U C A G SEQRES 27 A 633 C A G A G G U C A U A G U SEQRES 28 A 633 A C G A A U C G G U C U A SEQRES 29 A 633 G A A C G A U U C G G A A SEQRES 30 A 633 G G A C U G A A C A A U C SEQRES 31 A 633 A A G A G A A A A U A G C SEQRES 32 A 633 C C U U G G C A U U C A G SEQRES 33 A 633 U A C G U C A U G A U G A SEQRES 34 A 633 A C A C A G A A A A C A U SEQRES 35 A 633 G G U A C C U C C C A A G SEQRES 36 A 633 A G A A A G G A A A C G G SEQRES 37 A 633 U G A A U C C C G U G G G SEQRES 38 A 633 A A U C U U U U G G A G G SEQRES 39 A 633 G U G G A G U G A C G A C SEQRES 40 A 633 U G G C A U A A G A A G A SEQRES 41 A 633 U C A G C U A U U U A C G SEQRES 42 A 633 G A A G G A A G C U U G C SEQRES 43 A 633 G U C A U U A U C U U G A SEQRES 44 A 633 U U G A A C C G C C G U A SEQRES 45 A 633 U A C G G A A C C G U A C SEQRES 46 A 633 G U A C G G U G G U G U G SEQRES 47 A 633 A G A G G A C G G A G G U SEQRES 48 A 633 U A A U C A C C U C C U C SEQRES 49 A 633 C U A C U C G A U SEQRES 1 C 633 G U G C G C U C G G C A U SEQRES 2 C 633 G G G U G C A A U C U C U SEQRES 3 C 633 A G G G U G A A A G U C C SEQRES 4 C 633 C G A A C U G C G A A G G SEQRES 5 C 633 C A G A A G U A G C A G U SEQRES 6 C 633 U A G C U U A A C G C A A SEQRES 7 C 633 G G G U G U C C G U G G U SEQRES 8 C 633 G A C G C G G A A U C U G SEQRES 9 C 633 A A G G A A G C G G G C G SEQRES 10 C 633 G C A A A C U U C C G G U SEQRES 11 C 633 C U G A G G A A C A C G A SEQRES 12 C 633 A C U U C A U A U A A G G SEQRES 13 C 633 C U A G G U A U C A U U G SEQRES 14 C 633 G A U G A G U U U G C A A SEQRES 15 C 633 G A C A A A A C A A A G U SEQRES 16 C 633 C C U U U C U G C C G A A SEQRES 17 C 633 G G U G A U A C A G A G U SEQRES 18 C 633 A A A U G A A G C A G A U SEQRES 19 C 633 A G A U G G A A G G A A A SEQRES 20 C 633 G A U U G U A C U C U U A SEQRES 21 C 633 C C C G A G G A G G U C U SEQRES 22 C 633 G A U G G A U A C G U G A SEQRES 23 C 633 A G U G C G C U U C A U A SEQRES 24 C 633 A C C U A C U U A G U G A SEQRES 25 C 633 U A A G U A A C U G A A C SEQRES 26 C 633 C A U C A G A A G U C A G SEQRES 27 C 633 C A G A G G U C A U A G U SEQRES 28 C 633 A C G A A U C G G U C U A SEQRES 29 C 633 G A A C G A U U C G G A A SEQRES 30 C 633 G G A C U G A A C A A U C SEQRES 31 C 633 A A G A G A A A A U A G C SEQRES 32 C 633 C C U U G G C A U U C A G SEQRES 33 C 633 U A C G U C A U G A U G A SEQRES 34 C 633 A C A C A G A A A A C A U SEQRES 35 C 633 G G U A C C U C C C A A G SEQRES 36 C 633 A G A A A G G A A A C G G SEQRES 37 C 633 U G A A U C C C G U G G G SEQRES 38 C 633 A A U C U U U U G G A G G SEQRES 39 C 633 G U G G A G U G A C G A C SEQRES 40 C 633 U G G C A U A A G A A G A SEQRES 41 C 633 U C A G C U A U U U A C G SEQRES 42 C 633 G A A G G A A G C U U G C SEQRES 43 C 633 G U C A U U A U C U U G A SEQRES 44 C 633 U U G A A C C G C C G U A SEQRES 45 C 633 U A C G G A A C C G U A C SEQRES 46 C 633 G U A C G G U G G U G U G SEQRES 47 C 633 A G A G G A C G G A G G U SEQRES 48 C 633 U A A U C A C C U C C U C SEQRES 49 C 633 C U A C U C G A U HET MG A 701 1 HET MG A 702 1 HET MG C 701 1 HET MG C 702 1 HETNAM MG MAGNESIUM ION FORMUL 3 MG 4(MG 2+) LINK OP1 C A 566 MG MG A 702 1555 1555 2.48 LINK OP2 G A 567 MG MG A 702 1555 1555 2.82 LINK OP1 U A 583 MG MG A 701 1555 1555 1.80 LINK OP2 C A 585 MG MG A 701 1555 1555 2.13 LINK OP1 C A 585 MG MG A 702 1555 1555 2.09 LINK O3' U A 633 MG MG A 702 1555 1555 1.79 LINK O2' U A 633 MG MG A 702 1555 1555 1.98 LINK OP1 C C 566 MG MG C 702 1555 1555 2.48 LINK OP2 G C 567 MG MG C 702 1555 1555 2.82 LINK OP1 U C 583 MG MG C 701 1555 1555 1.80 LINK OP2 C C 585 MG MG C 701 1555 1555 2.13 LINK OP1 C C 585 MG MG C 702 1555 1555 2.09 LINK O3' U C 633 MG MG C 702 1555 1555 1.79 LINK O2' U C 633 MG MG C 702 1555 1555 1.98 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