HEADER RNA BINDING PROTEIN/DNA/RNA 30-MAY-22 8D2Q TITLE STRUCTURE OF ACIDOTHERMUS CELLULOLYTICUS CAS9 TERNARY COMPLEX (POST- TITLE 2 CLEAVAGE 1) COMPND MOL_ID: 1; COMPND 2 MOLECULE: CRISPR-ASSOCIATED ENDONUCLEASE, CSN1 FAMILY; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: SINGLE GUIDE RNA (86-MER); COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: DNA TARGET STRAND (5'-D(P*CP*CP*AP*GP*GP*AP*TP*CP*TP*TP*G)- COMPND 11 3'); COMPND 12 CHAIN: T; COMPND 13 ENGINEERED: YES; COMPND 14 MOL_ID: 4; COMPND 15 MOLECULE: DNA TARGET STRAND (5'- COMPND 16 D(*AP*GP*CP*TP*TP*GP*GP*TP*GP*TP*AP*TP*A)-3'); COMPND 17 CHAIN: X; COMPND 18 ENGINEERED: YES; COMPND 19 MOL_ID: 5; COMPND 20 MOLECULE: DNA NON-TARGET STRAND (5'- COMPND 21 D(P*AP*TP*AP*CP*AP*CP*CP*AP*AP*GP*CP*T)-3'); COMPND 22 CHAIN: D; COMPND 23 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ACIDOTHERMUS CELLULOLYTICUS 11B; SOURCE 3 ORGANISM_TAXID: 351607; SOURCE 4 STRAIN: ATCC 43068 / DSM 8971 / 11B; SOURCE 5 GENE: ACEL_1951; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: ACIDOTHERMUS CELLULOLYTICUS 11B; SOURCE 10 ORGANISM_TAXID: 351607; SOURCE 11 STRAIN: ATCC 43068 / DSM 8971 / 11B; SOURCE 12 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 14 MOL_ID: 3; SOURCE 15 SYNTHETIC: YES; SOURCE 16 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 17 ORGANISM_TAXID: 32630; SOURCE 18 MOL_ID: 4; SOURCE 19 SYNTHETIC: YES; SOURCE 20 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 21 ORGANISM_TAXID: 32630; SOURCE 22 MOL_ID: 5; SOURCE 23 SYNTHETIC: YES; SOURCE 24 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 25 ORGANISM_TAXID: 32630 KEYWDS CAS9, ACECAS9, CRISPR, POST-CLEAVAGE 1, RNA BINDING PROTEIN, RNA KEYWDS 2 BINDING PROTEIN-DNA-RNA COMPLEX EXPDTA ELECTRON MICROSCOPY AUTHOR J.RAI,A.DAS,H.LI REVDAT 2 01-MAY-24 8D2Q 1 JRNL REVDAT 1 20-DEC-23 8D2Q 0 JRNL AUTH A.DAS,J.RAI,M.O.ROTH,Y.SHU,M.L.MEDINA,M.R.BARAKAT,H.LI JRNL TITL COUPLED CATALYTIC STATES AND THE ROLE OF METAL COORDINATION JRNL TITL 2 IN CAS9. JRNL REF NAT CATAL V. 6 969 2023 JRNL REFN ESSN 2520-1158 JRNL PMID 38348449 JRNL DOI 10.1038/S41929-023-01031-1 REMARK 2 REMARK 2 RESOLUTION. 2.58 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : RELION 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 : 459996 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 8D2Q COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-MAY-22. REMARK 100 THE DEPOSITION ID IS D_1000265913. 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 : CRYOEM STRUCTURE OF ACECAS9 REMARK 245 (POST-CLEAVAGE 1); CRISPR- REMARK 245 ASSOCIATED ENDONUCLEASE, CSN1 REMARK 245 FAMILY/RNA; DNA 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 : 7.50 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 : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 BIOQUANTUM (6K X REMARK 245 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1000.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2200.00 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) : 6000.00 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: PENTAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, T, X, D 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 MET A 1 REMARK 465 GLY A 2 REMARK 465 GLY A 3 REMARK 465 SER A 4 REMARK 465 GLU A 5 REMARK 465 VAL A 6 REMARK 465 ALA A 204 REMARK 465 GLY A 205 REMARK 465 ARG A 206 REMARK 465 ARG A 207 REMARK 465 ALA A 208 REMARK 465 GLU A 209 REMARK 465 GLY A 264 REMARK 465 ARG A 265 REMARK 465 ASP A 266 REMARK 465 PRO A 267 REMARK 465 LEU A 268 REMARK 465 ASP A 269 REMARK 465 PRO A 270 REMARK 465 SER A 271 REMARK 465 GLN A 272 REMARK 465 LEU A 273 REMARK 465 ARG A 274 REMARK 465 ALA A 275 REMARK 465 SER A 276 REMARK 465 ARG A 277 REMARK 465 ALA A 278 REMARK 465 CYS A 279 REMARK 465 LEU A 280 REMARK 465 GLU A 281 REMARK 465 PHE A 282 REMARK 465 GLN A 283 REMARK 465 GLU A 284 REMARK 465 TYR A 285 REMARK 465 ARG A 286 REMARK 465 ILE A 287 REMARK 465 VAL A 288 REMARK 465 ALA A 289 REMARK 465 ALA A 290 REMARK 465 VAL A 291 REMARK 465 ALA A 292 REMARK 465 ASN A 293 REMARK 465 LEU A 294 REMARK 465 ARG A 295 REMARK 465 ILE A 296 REMARK 465 ARG A 297 REMARK 465 ASP A 298 REMARK 465 GLY A 299 REMARK 465 SER A 300 REMARK 465 GLY A 301 REMARK 465 SER A 302 REMARK 465 ARG A 303 REMARK 465 PRO A 304 REMARK 465 LEU A 305 REMARK 465 SER A 306 REMARK 465 LEU A 307 REMARK 465 GLU A 308 REMARK 465 GLU A 309 REMARK 465 ARG A 310 REMARK 465 ASN A 311 REMARK 465 ALA A 312 REMARK 465 VAL A 313 REMARK 465 ILE A 314 REMARK 465 GLU A 315 REMARK 465 ALA A 316 REMARK 465 LEU A 317 REMARK 465 LEU A 318 REMARK 465 ALA A 319 REMARK 465 GLN A 320 REMARK 465 THR A 321 REMARK 465 GLU A 322 REMARK 465 ARG A 323 REMARK 465 SER A 324 REMARK 465 LEU A 325 REMARK 465 THR A 326 REMARK 465 TRP A 327 REMARK 465 SER A 328 REMARK 465 ASP A 329 REMARK 465 ILE A 330 REMARK 465 ALA A 331 REMARK 465 LEU A 332 REMARK 465 GLU A 333 REMARK 465 ILE A 334 REMARK 465 LEU A 335 REMARK 465 LYS A 336 REMARK 465 LEU A 337 REMARK 465 PRO A 338 REMARK 465 ASN A 339 REMARK 465 GLU A 340 REMARK 465 SER A 341 REMARK 465 ASP A 342 REMARK 465 LEU A 343 REMARK 465 THR A 344 REMARK 465 SER A 345 REMARK 465 VAL A 346 REMARK 465 PRO A 347 REMARK 465 GLU A 348 REMARK 465 GLU A 349 REMARK 465 ASP A 350 REMARK 465 GLY A 351 REMARK 465 PRO A 352 REMARK 465 SER A 353 REMARK 465 SER A 354 REMARK 465 LEU A 355 REMARK 465 ALA A 356 REMARK 465 TYR A 357 REMARK 465 SER A 358 REMARK 465 GLN A 359 REMARK 465 PHE A 360 REMARK 465 ALA A 361 REMARK 465 PRO A 362 REMARK 465 PHE A 363 REMARK 465 ASP A 364 REMARK 465 GLU A 365 REMARK 465 THR A 366 REMARK 465 SER A 367 REMARK 465 ALA A 368 REMARK 465 ARG A 369 REMARK 465 ILE A 370 REMARK 465 ALA A 371 REMARK 465 GLU A 372 REMARK 465 PHE A 373 REMARK 465 ILE A 374 REMARK 465 ALA A 375 REMARK 465 LYS A 376 REMARK 465 ASN A 377 REMARK 465 ARG A 378 REMARK 465 ARG A 379 REMARK 465 LYS A 380 REMARK 465 ILE A 381 REMARK 465 PRO A 382 REMARK 465 THR A 383 REMARK 465 PHE A 384 REMARK 465 ALA A 385 REMARK 465 GLN A 386 REMARK 465 TRP A 387 REMARK 465 TRP A 388 REMARK 465 GLN A 389 REMARK 465 GLU A 390 REMARK 465 GLN A 391 REMARK 465 ASP A 392 REMARK 465 ARG A 393 REMARK 465 THR A 394 REMARK 465 SER A 395 REMARK 465 ARG A 396 REMARK 465 SER A 397 REMARK 465 ASP A 398 REMARK 465 LEU A 399 REMARK 465 VAL A 400 REMARK 465 ALA A 401 REMARK 465 ALA A 402 REMARK 465 LEU A 403 REMARK 465 ALA A 404 REMARK 465 ASP A 405 REMARK 465 ASN A 406 REMARK 465 SER A 407 REMARK 465 ILE A 408 REMARK 465 ALA A 409 REMARK 465 GLY A 410 REMARK 465 GLU A 411 REMARK 465 GLU A 412 REMARK 465 GLU A 413 REMARK 465 GLN A 414 REMARK 465 GLU A 415 REMARK 465 LEU A 416 REMARK 465 LEU A 417 REMARK 465 VAL A 418 REMARK 465 HIS A 419 REMARK 465 LEU A 420 REMARK 465 PRO A 421 REMARK 465 ASP A 422 REMARK 465 ALA A 423 REMARK 465 GLU A 424 REMARK 465 LEU A 425 REMARK 465 GLU A 426 REMARK 465 ALA A 427 REMARK 465 LEU A 428 REMARK 465 GLU A 429 REMARK 465 GLY A 430 REMARK 465 LEU A 431 REMARK 465 ALA A 432 REMARK 465 LEU A 433 REMARK 465 PRO A 434 REMARK 465 SER A 435 REMARK 465 GLY A 436 REMARK 465 ARG A 437 REMARK 465 VAL A 438 REMARK 465 ALA A 439 REMARK 465 TYR A 440 REMARK 465 SER A 441 REMARK 465 ARG A 442 REMARK 465 LEU A 443 REMARK 465 THR A 444 REMARK 465 LEU A 445 REMARK 465 SER A 446 REMARK 465 GLY A 447 REMARK 465 LEU A 448 REMARK 465 THR A 449 REMARK 465 ARG A 450 REMARK 465 VAL A 451 REMARK 465 MET A 452 REMARK 465 ARG A 453 REMARK 465 ASP A 454 REMARK 465 ASP A 455 REMARK 465 GLY A 456 REMARK 465 VAL A 457 REMARK 465 ASP A 458 REMARK 465 VAL A 459 REMARK 465 HIS A 460 REMARK 465 ASN A 461 REMARK 465 ALA A 462 REMARK 465 ARG A 463 REMARK 465 LYS A 464 REMARK 465 THR A 465 REMARK 465 CYS A 466 REMARK 465 PHE A 467 REMARK 465 GLY A 468 REMARK 465 VAL A 469 REMARK 465 ASP A 470 REMARK 465 ASP A 471 REMARK 465 ASN A 472 REMARK 465 TRP A 473 REMARK 465 SER A 785 REMARK 465 ASP A 786 REMARK 465 VAL A 787 REMARK 465 ASN A 788 REMARK 465 ARG A 789 REMARK 465 HIS A 790 REMARK 465 GLY A 1135 REMARK 465 GLY A 1136 REMARK 465 THR A 1137 REMARK 465 PRO A 1138 REMARK 465 GTP B 1 REMARK 465 G B 2 REMARK 465 U B 3 REMARK 465 A B 4 REMARK 465 G B 5 REMARK 465 G B 6 REMARK 465 A B 7 REMARK 465 U B 8 REMARK 465 G B 9 REMARK 465 G B 10 REMARK 465 U B 61 REMARK 465 U B 62 REMARK 465 C B 63 REMARK 465 G B 64 REMARK 465 C B 90 REMARK 465 A B 91 REMARK 465 G B 92 REMARK 465 C B 93 REMARK 465 A B 94 REMARK 465 C B 106 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 ARG A 262 CG CD NE CZ NH1 NH2 REMARK 470 ILE A 263 CG1 CG2 CD1 REMARK 470 GLU A 779 CG CD OE1 OE2 REMARK 470 PHE A 780 CG CD1 CD2 CE1 CE2 CZ REMARK 470 TRP A 781 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP A 781 CZ3 CH2 REMARK 470 ARG A 782 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 783 CG CD NE CZ NH1 NH2 REMARK 470 PRO A 784 CG CD 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 DC T 14 P DC T 14 OP3 -0.127 REMARK 500 DC T 21 O3' DC T 21 C3' -0.048 REMARK 500 DT T 22 O3' DT T 22 C3' 0.083 REMARK 500 DT T 23 C1' DT T 23 N1 0.119 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 PRO A 476 N - CD - CG ANGL. DEV. = -10.1 DEGREES REMARK 500 PRO A 487 CA - N - CD ANGL. DEV. = -14.1 DEGREES REMARK 500 PRO A 487 N - CD - CG ANGL. DEV. = -14.0 DEGREES REMARK 500 A B 12 O4' - C1' - N9 ANGL. DEV. = 5.9 DEGREES REMARK 500 A B 12 C5 - C6 - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 A B 12 C3' - O3' - P ANGL. DEV. = 13.6 DEGREES REMARK 500 G B 14 N3 - C4 - C5 ANGL. DEV. = -4.3 DEGREES REMARK 500 G B 14 N3 - C4 - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 U B 24 N3 - C2 - O2 ANGL. DEV. = -4.5 DEGREES REMARK 500 C B 58 C6 - N1 - C2 ANGL. DEV. = -2.9 DEGREES REMARK 500 C B 58 N1 - C2 - O2 ANGL. DEV. = 3.6 DEGREES REMARK 500 C B 58 C2 - N1 - C1' ANGL. DEV. = 6.8 DEGREES REMARK 500 U B 65 C3' - O3' - P ANGL. DEV. = 7.4 DEGREES REMARK 500 G B 66 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 DG T 17 O4' - C1' - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 DT T 20 O4' - C1' - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 DT T 22 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ALA A 580 77.45 52.88 REMARK 500 SER A 587 -65.56 -93.59 REMARK 500 ASP A 597 35.66 -99.65 REMARK 500 ASN A 601 32.28 -94.16 REMARK 500 ARG A 619 -5.01 72.01 REMARK 500 THR A 628 50.04 -94.10 REMARK 500 ARG A 631 -8.01 71.64 REMARK 500 ARG A 635 -4.02 73.09 REMARK 500 GLU A 676 -159.73 -149.36 REMARK 500 VAL A 677 43.69 -104.49 REMARK 500 SER A 739 -178.28 61.62 REMARK 500 CYS A 807 33.34 -97.20 REMARK 500 LEU A 966 51.57 -90.93 REMARK 500 CYS A1089 -127.91 56.84 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 HIS A 574 CYS A 575 146.48 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 A1201 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 18 OD2 REMARK 620 2 HOH A1301 O 78.0 REMARK 620 N 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 8D2P RELATED DB: PDB REMARK 900 RELATED ID: EMD-27145 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-27146 RELATED DB: EMDB REMARK 900 STRUCTURE OF ACIDOTHERMUS CELLULOLYTICUS CAS9 TERNARY COMPLEX (POST- REMARK 900 CLEAVAGE 1) DBREF 8D2Q A 1 1138 UNP A0LWB3 A0LWB3_ACIC1 1 1138 DBREF 8D2Q B 1 106 PDB 8D2Q 8D2Q 1 106 DBREF 8D2Q T 14 24 PDB 8D2Q 8D2Q 14 24 DBREF 8D2Q X 1 13 PDB 8D2Q 8D2Q 1 13 DBREF 8D2Q D 29 40 PDB 8D2Q 8D2Q 29 40 SEQRES 1 A 1138 MET GLY GLY SER GLU VAL GLY THR VAL PRO VAL THR TRP SEQRES 2 A 1138 ARG LEU GLY VAL ASP VAL GLY GLU ARG SER ILE GLY LEU SEQRES 3 A 1138 ALA ALA VAL SER TYR GLU GLU ASP LYS PRO LYS GLU ILE SEQRES 4 A 1138 LEU ALA ALA VAL SER TRP ILE HIS ASP GLY GLY VAL GLY SEQRES 5 A 1138 ASP GLU ARG SER GLY ALA SER ARG LEU ALA LEU ARG GLY SEQRES 6 A 1138 MET ALA ARG ARG ALA ARG ARG LEU ARG ARG PHE ARG ARG SEQRES 7 A 1138 ALA ARG LEU ARG ASP LEU ASP MET LEU LEU SER GLU LEU SEQRES 8 A 1138 GLY TRP THR PRO LEU PRO ASP LYS ASN VAL SER PRO VAL SEQRES 9 A 1138 ASP ALA TRP LEU ALA ARG LYS ARG LEU ALA GLU GLU TYR SEQRES 10 A 1138 VAL VAL ASP GLU THR GLU ARG ARG ARG LEU LEU GLY TYR SEQRES 11 A 1138 ALA VAL SER HIS MET ALA ARG HIS ARG GLY TRP ARG ASN SEQRES 12 A 1138 PRO TRP THR THR ILE LYS ASP LEU LYS ASN LEU PRO GLN SEQRES 13 A 1138 PRO SER ASP SER TRP GLU ARG THR ARG GLU SER LEU GLU SEQRES 14 A 1138 ALA ARG TYR SER VAL SER LEU GLU PRO GLY THR VAL GLY SEQRES 15 A 1138 GLN TRP ALA GLY TYR LEU LEU GLN ARG ALA PRO GLY ILE SEQRES 16 A 1138 ARG LEU ASN PRO THR GLN GLN SER ALA GLY ARG ARG ALA SEQRES 17 A 1138 GLU LEU SER ASN ALA THR ALA PHE GLU THR ARG LEU ARG SEQRES 18 A 1138 GLN GLU ASP VAL LEU TRP GLU LEU ARG CYS ILE ALA ASP SEQRES 19 A 1138 VAL GLN GLY LEU PRO GLU ASP VAL VAL SER ASN VAL ILE SEQRES 20 A 1138 ASP ALA VAL PHE CYS GLN LYS ARG PRO SER VAL PRO ALA SEQRES 21 A 1138 GLU ARG ILE GLY ARG ASP PRO LEU ASP PRO SER GLN LEU SEQRES 22 A 1138 ARG ALA SER ARG ALA CYS LEU GLU PHE GLN GLU TYR ARG SEQRES 23 A 1138 ILE VAL ALA ALA VAL ALA ASN LEU ARG ILE ARG ASP GLY SEQRES 24 A 1138 SER GLY SER ARG PRO LEU SER LEU GLU GLU ARG ASN ALA SEQRES 25 A 1138 VAL ILE GLU ALA LEU LEU ALA GLN THR GLU ARG SER LEU SEQRES 26 A 1138 THR TRP SER ASP ILE ALA LEU GLU ILE LEU LYS LEU PRO SEQRES 27 A 1138 ASN GLU SER ASP LEU THR SER VAL PRO GLU GLU ASP GLY SEQRES 28 A 1138 PRO SER SER LEU ALA TYR SER GLN PHE ALA PRO PHE ASP SEQRES 29 A 1138 GLU THR SER ALA ARG ILE ALA GLU PHE ILE ALA LYS ASN SEQRES 30 A 1138 ARG ARG LYS ILE PRO THR PHE ALA GLN TRP TRP GLN GLU SEQRES 31 A 1138 GLN ASP ARG THR SER ARG SER ASP LEU VAL ALA ALA LEU SEQRES 32 A 1138 ALA ASP ASN SER ILE ALA GLY GLU GLU GLU GLN GLU LEU SEQRES 33 A 1138 LEU VAL HIS LEU PRO ASP ALA GLU LEU GLU ALA LEU GLU SEQRES 34 A 1138 GLY LEU ALA LEU PRO SER GLY ARG VAL ALA TYR SER ARG SEQRES 35 A 1138 LEU THR LEU SER GLY LEU THR ARG VAL MET ARG ASP ASP SEQRES 36 A 1138 GLY VAL ASP VAL HIS ASN ALA ARG LYS THR CYS PHE GLY SEQRES 37 A 1138 VAL ASP ASP ASN TRP ARG PRO PRO LEU PRO ALA LEU HIS SEQRES 38 A 1138 GLU ALA THR GLY HIS PRO VAL VAL ASP ARG ASN LEU ALA SEQRES 39 A 1138 ILE LEU ARG LYS PHE LEU SER SER ALA THR MET ARG TRP SEQRES 40 A 1138 GLY PRO PRO GLN SER ILE VAL VAL GLU LEU ALA ARG GLY SEQRES 41 A 1138 ALA SER GLU SER ARG GLU ARG GLN ALA GLU GLU GLU ALA SEQRES 42 A 1138 ALA ARG ARG ALA HIS ARG LYS ALA ASN ASP ARG ILE ARG SEQRES 43 A 1138 ALA GLU LEU ARG ALA SER GLY LEU SER ASP PRO SER PRO SEQRES 44 A 1138 ALA ASP LEU VAL ARG ALA ARG LEU LEU GLU LEU TYR ASP SEQRES 45 A 1138 CYS HIS CYS MET TYR CYS GLY ALA PRO ILE SER TRP GLU SEQRES 46 A 1138 ASN SER GLU LEU ASP HIS ILE VAL PRO ARG THR ASP GLY SEQRES 47 A 1138 GLY SER ASN ARG HIS GLU ASN LEU ALA ILE THR CYS GLY SEQRES 48 A 1138 ALA CYS ASN LYS GLU LYS GLY ARG ARG PRO PHE ALA SER SEQRES 49 A 1138 TRP ALA GLU THR SER ASN ARG VAL GLN LEU ARG ASP VAL SEQRES 50 A 1138 ILE ASP ARG VAL GLN LYS LEU LYS TYR SER GLY ASN MET SEQRES 51 A 1138 TYR TRP THR ARG ASP GLU PHE SER ARG TYR LYS LYS SER SEQRES 52 A 1138 VAL VAL ALA ARG LEU LYS ARG ARG THR SER ASP PRO GLU SEQRES 53 A 1138 VAL ILE GLN SER ILE GLU SER THR GLY TYR ALA ALA VAL SEQRES 54 A 1138 ALA LEU ARG ASP ARG LEU LEU SER TYR GLY GLU LYS ASN SEQRES 55 A 1138 GLY VAL ALA GLN VAL ALA VAL PHE ARG GLY GLY VAL THR SEQRES 56 A 1138 ALA GLU ALA ARG ARG TRP LEU ASP ILE SER ILE GLU ARG SEQRES 57 A 1138 LEU PHE SER ARG VAL ALA ILE PHE ALA GLN SER THR SER SEQRES 58 A 1138 THR LYS ARG LEU ASP ARG ARG HIS HIS ALA VAL ASP ALA SEQRES 59 A 1138 VAL VAL LEU THR THR LEU THR PRO GLY VAL ALA LYS THR SEQRES 60 A 1138 LEU ALA ASP ALA ARG SER ARG ARG VAL SER ALA GLU PHE SEQRES 61 A 1138 TRP ARG ARG PRO SER ASP VAL ASN ARG HIS SER THR GLU SEQRES 62 A 1138 GLU PRO GLN SER PRO ALA TYR ARG GLN TRP LYS GLU SER SEQRES 63 A 1138 CYS SER GLY LEU GLY ASP LEU LEU ILE SER THR ALA ALA SEQRES 64 A 1138 ARG ASP SER ILE ALA VAL ALA ALA PRO LEU ARG LEU ARG SEQRES 65 A 1138 PRO THR GLY ALA LEU HIS GLU GLU THR LEU ARG ALA PHE SEQRES 66 A 1138 SER GLU HIS THR VAL GLY ALA ALA TRP LYS GLY ALA GLU SEQRES 67 A 1138 LEU ARG ARG ILE VAL GLU PRO GLU VAL TYR ALA ALA PHE SEQRES 68 A 1138 LEU ALA LEU THR ASP PRO GLY GLY ARG PHE LEU LYS VAL SEQRES 69 A 1138 SER PRO SER GLU ASP VAL LEU PRO ALA ASP GLU ASN ARG SEQRES 70 A 1138 HIS ILE VAL LEU SER ASP ARG VAL LEU GLY PRO ARG ASP SEQRES 71 A 1138 ARG VAL LYS LEU PHE PRO ASP ASP ARG GLY SER ILE ARG SEQRES 72 A 1138 VAL ARG GLY GLY ALA ALA TYR ILE ALA SER PHE HIS HIS SEQRES 73 A 1138 ALA ARG VAL PHE ARG TRP GLY SER SER HIS SER PRO SER SEQRES 74 A 1138 PHE ALA LEU LEU ARG VAL SER LEU ALA ASP LEU ALA VAL SEQRES 75 A 1138 ALA GLY LEU LEU ARG ASP GLY VAL ASP VAL PHE THR ALA SEQRES 76 A 1138 GLU LEU PRO PRO TRP THR PRO ALA TRP ARG TYR ALA SER SEQRES 77 A 1138 ILE ALA LEU VAL LYS ALA VAL GLU SER GLY ASP ALA LYS SEQRES 78 A 1138 GLN VAL GLY TRP LEU VAL PRO GLY ASP GLU LEU ASP PHE SEQRES 79 A 1138 GLY PRO GLU GLY VAL THR THR ALA ALA GLY ASP LEU SER SEQRES 80 A 1138 MET PHE LEU LYS TYR PHE PRO GLU ARG HIS TRP VAL VAL SEQRES 81 A 1138 THR GLY PHE GLU ASP ASP LYS ARG ILE ASN LEU LYS PRO SEQRES 82 A 1138 ALA PHE LEU SER ALA GLU GLN ALA GLU VAL LEU ARG THR SEQRES 83 A 1138 GLU ARG SER ASP ARG PRO ASP THR LEU THR GLU ALA GLY SEQRES 84 A 1138 GLU ILE LEU ALA GLN PHE PHE PRO ARG CYS TRP ARG ALA SEQRES 85 A 1138 THR VAL ALA LYS VAL LEU CYS HIS PRO GLY LEU THR VAL SEQRES 86 A 1138 ILE ARG ARG THR ALA LEU GLY GLN PRO ARG TRP ARG ARG SEQRES 87 A 1138 GLY HIS LEU PRO TYR SER TRP ARG PRO TRP SER ALA ASP SEQRES 88 A 1138 PRO TRP SER GLY GLY THR PRO SEQRES 1 B 106 GTP G U A G G A U G G C A A SEQRES 2 B 106 G A U C C U G G U A U G C SEQRES 3 B 106 U G G G G A G C C U G A A SEQRES 4 B 106 A A G G C U A C C U A G C SEQRES 5 B 106 A A G A C C C C U U C G U SEQRES 6 B 106 G G G G U C G C A U U C U SEQRES 7 B 106 U C A C C C C C U C G C A SEQRES 8 B 106 G C A G C G A G G G G G U SEQRES 9 B 106 U C SEQRES 1 T 11 DC DC DA DG DG DA DT DC DT DT DG SEQRES 1 X 13 DA DG DC DT DT DG DG DT DG DT DA DT DA SEQRES 1 D 12 DA DT DA DC DA DC DC DA DA DG DC DT HET MG A1201 1 HET MG B 201 1 HET MG B 202 1 HET MG B 203 1 HET MG B 204 1 HETNAM MG MAGNESIUM ION FORMUL 6 MG 5(MG 2+) FORMUL 11 HOH *2(H2 O) HELIX 1 AA1 SER A 59 GLY A 92 1 34 HELIX 2 AA2 VAL A 104 GLU A 116 1 13 HELIX 3 AA3 ASP A 120 HIS A 138 1 19 HELIX 4 AA4 THR A 147 ASN A 153 1 7 HELIX 5 AA5 SER A 158 SER A 173 1 16 HELIX 6 AA6 THR A 180 ALA A 192 1 13 HELIX 7 AA7 ARG A 221 GLY A 237 1 17 HELIX 8 AA8 PRO A 239 PHE A 251 1 13 HELIX 9 AA9 HIS A 486 GLY A 508 1 23 HELIX 10 AB1 SER A 524 SER A 552 1 29 HELIX 11 AB2 SER A 558 ASP A 572 1 15 HELIX 12 AB3 ASP A 636 LYS A 643 1 8 HELIX 13 AB4 THR A 653 LYS A 669 1 17 HELIX 14 AB5 GLY A 685 GLY A 703 1 19 HELIX 15 AB6 VAL A 714 TRP A 721 1 8 HELIX 16 AB7 SER A 725 PHE A 730 1 6 HELIX 17 AB8 ARG A 748 THR A 758 1 11 HELIX 18 AB9 THR A 761 ARG A 782 1 22 HELIX 19 AC1 SER A 797 CYS A 807 1 11 HELIX 20 AC2 GLY A 809 ARG A 820 1 12 HELIX 21 AC3 GLY A 856 ARG A 861 1 6 HELIX 22 AC4 GLU A 864 ASP A 876 1 13 HELIX 23 AC5 LEU A 957 ALA A 963 1 7 HELIX 24 AC6 THR A 981 TYR A 986 1 6 HELIX 25 AC7 SER A 988 SER A 997 1 10 HELIX 26 AC8 GLY A 1024 PHE A 1033 1 10 HELIX 27 AC9 ALA A 1058 ARG A 1071 1 14 HELIX 28 AD1 THR A 1076 PHE A 1086 1 11 HELIX 29 AD2 VAL A 1094 LEU A 1098 1 5 SHEET 1 AA1 6 GLN A 706 ARG A 711 0 SHEET 2 AA1 6 SER A 512 LEU A 517 1 N VAL A 515 O PHE A 710 SHEET 3 AA1 6 TRP A 13 VAL A 19 1 N LEU A 15 O VAL A 514 SHEET 4 AA1 6 SER A 23 TYR A 31 -1 O GLY A 25 N ASP A 18 SHEET 5 AA1 6 PRO A 36 ILE A 46 -1 O GLU A 38 N SER A 30 SHEET 6 AA1 6 ALA A 824 ALA A 826 1 O ALA A 826 N ILE A 46 SHEET 1 AA2 2 ASP A 590 HIS A 591 0 SHEET 2 AA2 2 LEU A 606 ALA A 607 -1 O ALA A 607 N ASP A 590 SHEET 1 AA3 2 SER A 846 THR A 849 0 SHEET 2 AA3 2 ARG A 911 LEU A 914 -1 O VAL A 912 N HIS A 848 SHEET 1 AA4 2 TRP A 854 LYS A 855 0 SHEET 2 AA4 2 ASP A 889 LEU A 891 -1 O LEU A 891 N TRP A 854 SHEET 1 AA5 2 ILE A 899 VAL A 900 0 SHEET 2 AA5 2 VAL A 905 LEU A 906 -1 O LEU A 906 N ILE A 899 SHEET 1 AA6 2 SER A 921 VAL A 924 0 SHEET 2 AA6 2 GLY A 927 TYR A 930 -1 O ALA A 929 N ILE A 922 SHEET 1 AA7 3 PRO A 948 SER A 956 0 SHEET 2 AA7 3 PHE A 934 GLY A 943 -1 N HIS A 936 O VAL A 955 SHEET 3 AA7 3 LYS A1001 LEU A1006 -1 O LEU A1006 N ALA A 937 SHEET 1 AA8 5 TRP A1090 THR A1093 0 SHEET 2 AA8 5 ARG A1048 PRO A1053 -1 N ILE A1049 O ALA A1092 SHEET 3 AA8 5 HIS A1037 ASP A1045 -1 N VAL A1039 O LYS A1052 SHEET 4 AA8 5 GLU A1011 ASP A1013 -1 N LEU A1012 O TRP A1038 SHEET 5 AA8 5 THR A1104 ILE A1106 -1 O THR A1104 N ASP A1013 SSBOND 1 CYS A 575 CYS A 578 1555 1555 2.03 SSBOND 2 CYS A 575 CYS A 610 1555 1555 2.04 SSBOND 3 CYS A 575 CYS A 613 1555 1555 2.03 SSBOND 4 CYS A 578 CYS A 610 1555 1555 2.03 SSBOND 5 CYS A 610 CYS A 613 1555 1555 2.03 LINK OD2 ASP A 18 MG MG A1201 1555 1555 2.11 LINK MG MG A1201 O HOH A1301 1555 1555 2.67 LINK OP1 U B 22 MG MG B 203 1555 1555 2.56 LINK OP2 U B 49 MG MG B 201 1555 1555 2.72 LINK OP2 U B 49 MG MG B 202 1555 1555 2.70 LINK OP1 C B 52 MG MG B 204 1555 1555 2.24 CISPEP 1 GLN A 156 PRO A 157 0 0.70 CISPEP 2 GLU A 177 PRO A 178 0 -6.08 CISPEP 3 PRO A 675 GLU A 676 0 -4.86 CISPEP 4 GLY A 712 GLY A 713 0 -1.92 CISPEP 5 SER A 791 THR A 792 0 0.35 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