HEADER DE NOVO PROTEIN 15-JAN-25 9MVR TITLE AI-DESIGNED CAS13 ANTI-CRISPR AICRVIA1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: AICRVIA1; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 3 ORGANISM_TAXID: 32630; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ANTI-CRISPR, ACR, CRISPR, CAS13, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.TAVENEAU,H.X.CHAI,G.J.KNOTT REVDAT 1 25-FEB-26 9MVR 0 JRNL AUTH C.TAVENEAU,X.H.CHAI,J.D'SIVLA,R.S.BAMERT,J.PURCELL, JRNL AUTH 2 H.VENUGOPAL,D.CURWEN,F.MUNDER,R.CALVERT,B.K.HAYES,L.MARTIN, JRNL AUTH 3 J.BARR,J.ROSENBLUH,R.GRINTER,G.J.KNOTT JRNL TITL DE NOVO DESIGN OF POTENT CRISPR-CAS13 INHIBITORS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.94 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.94 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.46 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 25525 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.204 REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.246 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.070 REMARK 3 FREE R VALUE TEST SET COUNT : 2571 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 42.4600 - 5.0800 1.00 1292 140 0.1929 0.2723 REMARK 3 2 5.0600 - 4.0300 1.00 1273 145 0.1714 0.2319 REMARK 3 3 4.0300 - 3.5200 1.00 1294 141 0.1773 0.2251 REMARK 3 4 3.5200 - 3.2000 1.00 1287 146 0.1927 0.2398 REMARK 3 5 3.2000 - 2.9700 1.00 1268 146 0.2071 0.2336 REMARK 3 6 2.9700 - 2.7900 1.00 1269 147 0.1991 0.2241 REMARK 3 7 2.7900 - 2.6500 1.00 1292 143 0.2156 0.2741 REMARK 3 8 2.6500 - 2.5400 1.00 1296 139 0.2157 0.2353 REMARK 3 9 2.5400 - 2.4400 1.00 1277 150 0.1944 0.1831 REMARK 3 10 2.4400 - 2.3600 1.00 1259 139 0.1920 0.2507 REMARK 3 11 2.3600 - 2.2800 1.00 1332 147 0.2084 0.2605 REMARK 3 12 2.2800 - 2.2200 1.00 1250 137 0.2101 0.2609 REMARK 3 13 2.2200 - 2.1600 1.00 1277 140 0.2203 0.2721 REMARK 3 14 2.1600 - 2.1100 1.00 1290 149 0.2509 0.2947 REMARK 3 15 2.1100 - 2.0600 1.00 1299 148 0.2505 0.2574 REMARK 3 16 2.0600 - 2.0200 1.00 1266 143 0.2662 0.3037 REMARK 3 17 2.0100 - 1.9700 1.00 1255 137 0.2632 0.3227 REMARK 3 18 1.9700 - 1.9400 0.90 1178 134 0.3221 0.3534 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.241 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.748 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 36.74 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 43.25 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.003 1280 REMARK 3 ANGLE : 0.570 1721 REMARK 3 CHIRALITY : 0.046 187 REMARK 3 PLANARITY : 0.003 220 REMARK 3 DIHEDRAL : 3.771 160 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 9MVR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-JAN-25. REMARK 100 THE DEPOSITION ID IS D_1000290320. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-JUL-24 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.95365 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25959 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.940 REMARK 200 RESOLUTION RANGE LOW (A) : 42.460 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : 0.08700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.94 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.4 REMARK 200 DATA REDUNDANCY IN SHELL : 6.50 REMARK 200 R MERGE FOR SHELL (I) : 1.05000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.080 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX 1.20.1_4487 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.39 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M BIS-TRIS PROPANE, 2.6M AMMONIUM REMARK 280 SULFATE, PH 7.2, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 16.70150 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 42.46350 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.45000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 42.46350 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.70150 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.45000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: A 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 HIS A 80 REMARK 465 HIS A 81 REMARK 465 HIS A 82 REMARK 465 HIS A 83 REMARK 465 GLY B 76 REMARK 465 SER B 77 REMARK 465 HIS B 78 REMARK 465 HIS B 79 REMARK 465 HIS B 80 REMARK 465 HIS B 81 REMARK 465 HIS B 82 REMARK 465 HIS B 83 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 ASP A 13 58.89 -100.26 REMARK 500 ASP B 14 67.45 -159.96 REMARK 500 REMARK 500 REMARK: NULL DBREF 9MVR A 1 83 PDB 9MVR 9MVR 1 83 DBREF 9MVR B 1 83 PDB 9MVR 9MVR 1 83 SEQRES 1 A 83 MET LYS THR ILE LYS VAL ASP VAL ILE VAL VAL GLY ASP SEQRES 2 A 83 ASP GLU GLU LEU VAL GLU GLU TYR LYS LYS GLU ALA GLU SEQRES 3 A 83 LEU ILE GLY LYS GLU TYR GLY VAL LYS ILE GLU VAL GLU SEQRES 4 A 83 PRO TYR PHE LEU GLU GLU GLY LYS PHE PRO TRP LEU ASP SEQRES 5 A 83 VAL ASP PHE ALA TYR ASN THR THR GLN GLU GLU LEU ASP SEQRES 6 A 83 LYS ALA GLU LYS GLU ALA LYS LYS ILE ALA GLY SER HIS SEQRES 7 A 83 HIS HIS HIS HIS HIS SEQRES 1 B 83 MET LYS THR ILE LYS VAL ASP VAL ILE VAL VAL GLY ASP SEQRES 2 B 83 ASP GLU GLU LEU VAL GLU GLU TYR LYS LYS GLU ALA GLU SEQRES 3 B 83 LEU ILE GLY LYS GLU TYR GLY VAL LYS ILE GLU VAL GLU SEQRES 4 B 83 PRO TYR PHE LEU GLU GLU GLY LYS PHE PRO TRP LEU ASP SEQRES 5 B 83 VAL ASP PHE ALA TYR ASN THR THR GLN GLU GLU LEU ASP SEQRES 6 B 83 LYS ALA GLU LYS GLU ALA LYS LYS ILE ALA GLY SER HIS SEQRES 7 B 83 HIS HIS HIS HIS HIS HET CL A 101 1 HETNAM CL CHLORIDE ION FORMUL 3 CL CL 1- FORMUL 4 HOH *82(H2 O) HELIX 1 AA1 ASP A 14 GLY A 33 1 20 HELIX 2 AA2 ASP A 52 SER A 77 1 26 HELIX 3 AA3 ASP B 14 GLY B 33 1 20 HELIX 4 AA4 ASP B 52 ALA B 75 1 24 SHEET 1 AA1 2 THR A 3 VAL A 11 0 SHEET 2 AA1 2 LYS A 35 LEU A 43 1 O TYR A 41 N VAL A 8 SHEET 1 AA2 2 THR B 3 VAL B 11 0 SHEET 2 AA2 2 LYS B 35 LEU B 43 1 O GLU B 37 N ILE B 4 CRYST1 33.403 62.900 84.927 90.00 90.00 90.00 P 21 21 21 8 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 0.029937 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015898 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011775 0.00000 MASTER 249 0 1 4 4 0 0 6 1341 2 0 14 END