HEADER RNA 10-JUL-23 8K15 TITLE THE STREPTOCOCCUS AZIZII ORF-LESS GROUP IIC INTRON HYER2 AT APO STATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (470-MER); COMPND 3 CHAIN: C; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOCOCCUS AZIZII; SOURCE 3 ORGANISM_TAXID: 1579424; 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 8K15 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. 2.58 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) : 2.580 REMARK 3 NUMBER OF PARTICLES : 335884 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 8K15 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 13-JUL-23. REMARK 100 THE DEPOSITION ID IS D_1300039280. 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 STREPTOCOCCUS AZIZII ORF REMARK 245 -LESS GROUP IIC INTRON HYER2 AT 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 A C 286 REMARK 465 U C 384 REMARK 465 G C 385 REMARK 465 A C 386 REMARK 465 U C 387 REMARK 465 A C 388 REMARK 465 C C 389 REMARK 465 C C 390 REMARK 465 C C 391 REMARK 465 U C 392 REMARK 465 A C 393 REMARK 465 U C 394 REMARK 465 C C 395 REMARK 465 U C 396 REMARK 465 A C 397 REMARK 465 A C 398 REMARK 465 C C 399 REMARK 465 U C 400 REMARK 465 G C 401 REMARK 465 A C 402 REMARK 465 U C 403 REMARK 465 U C 404 REMARK 465 U C 405 REMARK 465 U C 406 REMARK 465 G C 407 REMARK 465 U C 408 REMARK 465 C C 409 REMARK 465 U C 410 REMARK 465 G C 411 REMARK 465 C C 412 REMARK 465 C C 413 REMARK 465 C C 414 REMARK 465 U C 415 REMARK 465 A C 416 REMARK 465 A C 417 REMARK 465 C C 418 REMARK 465 A C 419 REMARK 465 C C 420 REMARK 465 C C 421 REMARK 465 U C 422 REMARK 465 G C 423 REMARK 465 G C 424 REMARK 465 U C 425 REMARK 465 C C 426 REMARK 465 U C 427 REMARK 465 G C 428 REMARK 465 A C 429 REMARK 465 A C 430 REMARK 465 A C 431 REMARK 465 U C 432 REMARK 465 G C 433 REMARK 465 A C 434 REMARK 465 C C 435 REMARK 465 G C 436 REMARK 465 G C 437 REMARK 465 U C 438 REMARK 465 A C 439 REMARK 465 C C 440 REMARK 465 U C 441 REMARK 465 C C 442 REMARK 465 G C 443 REMARK 465 A C 458 REMARK 465 A C 459 REMARK 465 A C 460 REMARK 465 G C 461 REMARK 465 A C 462 REMARK 465 G C 463 REMARK 465 G C 464 REMARK 465 C C 465 REMARK 465 U C 466 REMARK 465 G C 467 REMARK 465 C C 468 REMARK 465 U C 469 REMARK 465 C C 470 REMARK 465 A C 471 REMARK 465 C C 472 REMARK 465 A C 473 REMARK 465 A C 474 REMARK 465 A C 475 REMARK 465 U C 476 REMARK 465 A C 477 REMARK 465 U C 478 REMARK 465 A C 479 REMARK 465 G C 480 REMARK 465 G C 481 REMARK 465 A C 482 REMARK 465 C C 483 REMARK 465 G C 484 REMARK 465 G C 485 REMARK 465 C C 486 REMARK 465 A C 487 REMARK 465 C C 488 REMARK 465 A C 489 REMARK 465 A C 490 REMARK 465 G C 491 REMARK 465 C C 492 REMARK 465 G C 493 REMARK 465 G C 494 REMARK 465 A C 495 REMARK 465 A C 496 REMARK 465 C C 497 REMARK 465 G C 498 REMARK 465 A C 499 REMARK 465 A C 500 REMARK 465 A C 501 REMARK 465 U C 502 REMARK 465 C C 503 REMARK 465 A C 504 REMARK 465 U C 505 REMARK 465 A C 506 REMARK 465 U C 507 REMARK 465 A C 508 REMARK 465 U C 509 REMARK 465 A C 510 REMARK 465 G C 511 REMARK 465 G C 512 REMARK 465 U C 513 REMARK 465 A C 514 REMARK 465 G C 515 REMARK 465 G C 516 REMARK 465 U C 517 REMARK 465 G C 518 REMARK 465 U C 519 REMARK 465 G C 520 REMARK 465 G C 521 REMARK 465 G C 522 REMARK 465 A C 523 REMARK 465 A C 524 REMARK 465 C C 525 REMARK 465 A C 526 REMARK 465 A C 527 REMARK 465 A C 528 REMARK 465 A C 529 REMARK 465 A C 530 REMARK 465 A C 531 REMARK 465 A C 532 REMARK 465 G C 533 REMARK 465 U C 534 REMARK 465 G C 535 REMARK 465 U C 536 REMARK 465 U C 537 REMARK 465 C C 538 REMARK 465 U C 539 REMARK 465 C C 540 REMARK 465 G C 541 REMARK 465 C C 542 REMARK 465 C C 543 REMARK 465 A C 544 REMARK 465 A C 545 REMARK 465 A C 546 REMARK 465 G C 547 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 C 93 C2' - C3' - O3' ANGL. DEV. = 9.8 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 C 702 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 C C 559 OP1 REMARK 620 2 G C 560 OP2 110.2 REMARK 620 3 C C 578 OP1 63.9 101.8 REMARK 620 4 C C 578 OP2 117.3 88.2 53.6 REMARK 620 5 U C 621 O3' 87.0 103.8 146.4 147.8 REMARK 620 6 U C 621 O2' 74.6 170.1 88.1 97.4 67.3 REMARK 620 N 1 2 3 4 5 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 C C 576 OP1 REMARK 620 2 C C 578 OP2 95.0 REMARK 620 N 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-36786 RELATED DB: EMDB REMARK 900 THE STREPTOCOCCUS AZIZII ORF-LESS GROUP IIC INTRON HYER2 AT APO REMARK 900 STATE DBREF 8K15 C 1 621 PDB 8K15 8K15 1 621 SEQRES 1 C 621 G U A C G A C G G G C A U SEQRES 2 C 621 G U C G U A C A U C U G A SEQRES 3 C 621 G G U G C A A G U C C U C SEQRES 4 C 621 U G U G G A C A C C U G C SEQRES 5 C 621 U A C C G G U G A A C C C SEQRES 6 C 621 A A U A G C G A C U C C C SEQRES 7 C 621 A A G C C U G A C U A U C SEQRES 8 C 621 G C G A G G U A A C G G G SEQRES 9 C 621 G A G A G G A A G G G A U SEQRES 10 C 621 A G C G A A A U C G U G G SEQRES 11 C 621 C U C U A C G A A C A G A SEQRES 12 C 621 A A C G U G A U A U U A A SEQRES 13 C 621 G G C G U A U A U A G U G SEQRES 14 C 621 G A U G A G G G G G C U A SEQRES 15 C 621 G G C A C U C U A A A G U SEQRES 16 C 621 C C A A A A A G G U A G U SEQRES 17 C 621 C G U A A U C U A U G U G SEQRES 18 C 621 C G U A A A U C A C G A G SEQRES 19 C 621 A G U A A A C G A G G A A SEQRES 20 C 621 A G A U G U A C G A C U U SEQRES 21 C 621 A U C C C G U G A G G U C SEQRES 22 C 621 U C A U G A G C G U C A A SEQRES 23 C 621 G U A G A C G U A G U A A SEQRES 24 C 621 U A A C G A A U C A U G A SEQRES 25 C 621 G A A G U C A G C C G A G SEQRES 26 C 621 G U C A U A G U A G U G A SEQRES 27 C 621 U G A A G U U U C U G U A SEQRES 28 C 621 A U G G A A A C G G A G C SEQRES 29 C 621 G A A G G A C C G A A C G SEQRES 30 C 621 A U U A A A U G A U A C C SEQRES 31 C 621 C U A U C U A A C U G A U SEQRES 32 C 621 U U U G U C U G C C C U A SEQRES 33 C 621 A C A C C U G G U C U G A SEQRES 34 C 621 A A U G A C G G U A C U C SEQRES 35 C 621 G C A G A A C G U A U G C SEQRES 36 C 621 U G A A A G A G G C U G C SEQRES 37 C 621 U C A C A A A U A U A G G SEQRES 38 C 621 A C G G C A C A A G C G G SEQRES 39 C 621 A A C G A A A U C A U A U SEQRES 40 C 621 A U A G G U A G G U G U G SEQRES 41 C 621 G G A A C A A A A A A A G SEQRES 42 C 621 U G U U C U C G C C A A A SEQRES 43 C 621 G U U U A G U U G A A C C SEQRES 44 C 621 G C C G U G U G C C G A A SEQRES 45 C 621 C G G C A C G C A C G G U SEQRES 46 C 621 G G U G U G A G A G G G A SEQRES 47 C 621 C U A U C A A U U A G U C SEQRES 48 C 621 C C U A C U C G A U HET MG C 701 1 HET MG C 702 1 HETNAM MG MAGNESIUM ION FORMUL 2 MG 2(MG 2+) LINK OP1 C C 559 MG MG C 702 1555 1555 2.38 LINK OP2 G C 560 MG MG C 702 1555 1555 1.85 LINK OP1 C C 576 MG MG C 701 1555 1555 2.22 LINK OP2 C C 578 MG MG C 701 1555 1555 2.47 LINK OP1 C C 578 MG MG C 702 1555 1555 2.93 LINK OP2 C C 578 MG MG C 702 1555 1555 2.75 LINK O3' U C 621 MG MG C 702 1555 1555 1.96 LINK O2' U C 621 MG MG C 702 1555 1555 2.67 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