HEADER PROTEIN BINDING 10-NOV-22 8F3K TITLE ANTI-CRISPR PROTEIN ACRIIC5 INHIBITS CRISPR-CAS9 BY ACTING AS A DNA TITLE 2 MIMIC COMPND MOL_ID: 1; COMPND 2 MOLECULE: ACRIIC5NCH; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: THE DATASET USED IS SELENIUM LABELLED HENCE MET 87 IS COMPND 6 LABELLED AS MSE SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NEISSERIA CHENWENGUII; SOURCE 3 ORGANISM_TAXID: 1853278; SOURCE 4 GENE: BG910_04735; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PHAT4 KEYWDS ANTI-CRISPR, CRISPR-CAS, CAS9, INHIBITION, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR M.SHAH,H.SUNGWON,A.R.DAVIDSON,K.L.MAXWELL,T.F.MORAES REVDAT 2 12-APR-23 8F3K 1 JRNL REVDAT 1 08-MAR-23 8F3K 0 JRNL AUTH S.HWANG,M.SHAH,B.GARCIA,N.HASHEM,A.R.DAVIDSON,T.F.MORAES, JRNL AUTH 2 K.L.MAXWELL JRNL TITL ANTI-CRISPR PROTEIN ACRIIC5 INHIBITS CRISPR-CAS9 BY JRNL TITL 2 OCCUPYING THE TARGET DNA BINDING POCKET. JRNL REF J.MOL.BIOL. V. 435 67991 2023 JRNL REFN ESSN 1089-8638 JRNL PMID 36736884 JRNL DOI 10.1016/J.JMB.2023.167991 REMARK 2 REMARK 2 RESOLUTION. 2.10 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.50 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.7 REMARK 3 NUMBER OF REFLECTIONS : 14852 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.210 REMARK 3 R VALUE (WORKING SET) : 0.205 REMARK 3 FREE R VALUE : 0.254 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.050 REMARK 3 FREE R VALUE TEST SET COUNT : 1492 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 38.5000 - 4.6700 0.98 1244 142 0.1756 0.2211 REMARK 3 2 4.6700 - 3.7100 0.99 1267 144 0.1455 0.1725 REMARK 3 3 3.7000 - 3.2400 0.98 1240 137 0.1762 0.2301 REMARK 3 4 3.2400 - 2.9400 1.00 1269 143 0.2117 0.2763 REMARK 3 5 2.9400 - 2.7300 0.96 1236 125 0.2165 0.2875 REMARK 3 6 2.7300 - 2.5700 0.98 1264 137 0.2266 0.2899 REMARK 3 7 2.5700 - 2.4400 0.99 1253 153 0.2381 0.3160 REMARK 3 8 2.4400 - 2.3400 0.99 1235 138 0.2440 0.2694 REMARK 3 9 2.3400 - 2.2500 0.85 1066 134 0.3113 0.3796 REMARK 3 10 2.2500 - 2.1700 0.80 1045 96 0.3355 0.3222 REMARK 3 11 2.1700 - 2.1000 0.99 1241 143 0.2798 0.3301 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) : 0.290 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.860 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.008 933 REMARK 3 ANGLE : 0.791 1336 REMARK 3 CHIRALITY : 0.047 131 REMARK 3 PLANARITY : 0.008 171 REMARK 3 DIHEDRAL : 8.747 133 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN A AND RESID 11:124) REMARK 3 ORIGIN FOR THE GROUP (A): -6.5386 13.1397 -9.1798 REMARK 3 T TENSOR REMARK 3 T11: 0.1658 T22: 0.1471 REMARK 3 T33: 0.1208 T12: 0.0290 REMARK 3 T13: 0.0033 T23: -0.0110 REMARK 3 L TENSOR REMARK 3 L11: 3.5973 L22: 3.9778 REMARK 3 L33: 1.9564 L12: 1.9881 REMARK 3 L13: -0.8482 L23: -0.8327 REMARK 3 S TENSOR REMARK 3 S11: 0.0037 S12: -0.0831 S13: 0.0073 REMARK 3 S21: 0.2319 S22: -0.0182 S23: 0.1182 REMARK 3 S31: -0.0287 S32: -0.1510 S33: 0.0254 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 8F3K COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-NOV-22. REMARK 100 THE DEPOSITION ID IS D_1000269899. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-AUG-18 REMARK 200 TEMPERATURE (KELVIN) : 105 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14852 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 38.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.8 REMARK 200 DATA REDUNDANCY : 7.200 REMARK 200 R MERGE (I) : 0.06900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 38.50 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.8 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.08170 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD 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 (%): 48.43 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.38 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS PH 8.5 AND 2.0M AMMONIUM REMARK 280 SULFATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K 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 21.31100 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 34.98700 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.05250 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 34.98700 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.31100 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 23.05250 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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: 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 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 MSE A 1 REMARK 465 THR A 2 REMARK 465 ILE A 3 REMARK 465 LYS A 4 REMARK 465 GLU A 5 REMARK 465 ASP A 6 REMARK 465 GLY A 7 REMARK 465 MSE A 8 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 HIS A 22 -66.89 -109.12 REMARK 500 SER A 102 -113.29 -146.11 REMARK 500 REMARK 500 REMARK: NULL DBREF1 8F3K A 1 124 UNP A0A220S190_9NEIS DBREF2 8F3K A A0A220S190 1 124 SEQRES 1 A 124 MSE THR ILE LYS GLU ASP GLY MSE SER GLU THR GLN TYR SEQRES 2 A 124 PHE VAL SER HIS ASP GLY ASN ARG HIS ASP LEU PHE ASP SEQRES 3 A 124 THR LEU GLU GLN ALA GLU HIS TYR ILE LEU LYS LYS ASN SEQRES 4 A 124 GLY TRP THR ASP GLY GLU ILE ALA GLU LYS TRP ALA PHE SEQRES 5 A 124 VAL LYS LYS GLU ALA ARG LYS TYR GLY GLY ASP PRO PHE SEQRES 6 A 124 SER SER ASN GLY ARG HIS SER LEU TRP PHE ILE THR GLU SEQRES 7 A 124 LEU LYS LEU SER ASP GLY VAL ILE MSE GLU VAL ASP GLY SEQRES 8 A 124 GLN LEU PHE ASP ASP TYR VAL GLU SER ILE SER ALA GLU SEQRES 9 A 124 ARG GLY THR GLU GLU PHE ALA GLU THR LYS ARG ARG LEU SEQRES 10 A 124 VAL GLY TYR TYR LEU GLY TRP MODRES 8F3K MSE A 87 MET MODIFIED RESIDUE HET MSE A 87 8 HET TRS A 201 8 HET NH4 A 202 1 HET NH4 A 203 1 HET NH4 A 204 1 HET GOL A 205 6 HET NH4 A 206 1 HET NH4 A 207 1 HET NH4 A 208 1 HET NH4 A 209 1 HET NH4 A 210 1 HET NH4 A 211 1 HET NH4 A 212 1 HET NH4 A 213 1 HET NH4 A 214 1 HET NH4 A 215 1 HETNAM MSE SELENOMETHIONINE HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETNAM NH4 AMMONIUM ION HETNAM GOL GLYCEROL HETSYN TRS TRIS BUFFER HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 MSE C5 H11 N O2 SE FORMUL 2 TRS C4 H12 N O3 1+ FORMUL 3 NH4 13(H4 N 1+) FORMUL 6 GOL C3 H8 O3 FORMUL 17 HOH *59(H2 O) HELIX 1 AA1 THR A 27 ASN A 39 1 13 HELIX 2 AA2 THR A 42 TYR A 60 1 19 HELIX 3 AA3 PHE A 94 SER A 102 1 9 HELIX 4 AA4 THR A 107 GLY A 123 1 17 SHEET 1 AA1 5 ASN A 20 PHE A 25 0 SHEET 2 AA1 5 GLU A 10 HIS A 17 -1 N TYR A 13 O PHE A 25 SHEET 3 AA1 5 TRP A 74 SER A 82 -1 O THR A 77 N PHE A 14 SHEET 4 AA1 5 VAL A 85 VAL A 89 -1 O MSE A 87 N LYS A 80 SHEET 5 AA1 5 GLN A 92 LEU A 93 -1 O GLN A 92 N VAL A 89 LINK C ILE A 86 N MSE A 87 1555 1555 1.33 LINK C MSE A 87 N GLU A 88 1555 1555 1.34 CRYST1 42.622 46.105 69.974 90.00 90.00 90.00 P 21 21 21 4 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 0.023462 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021690 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014291 0.00000