HEADER PROTEIN BINDING 19-FEB-19 6JHV TITLE STRUCTURE OF ANTI-CRISPR ACRIIC3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ACRIIC3; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NEISSERIA MENINGITIDIS; SOURCE 3 ORGANISM_TAXID: 487; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS INHIBITOR, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR J.Y.SUH,B.J.LEE,S.J.LEE,Y.KIM REVDAT 3 18-DEC-19 6JHV 1 JRNL REVDAT 2 11-SEP-19 6JHV 1 SOURCE DBREF SEQADV REVDAT 1 28-AUG-19 6JHV 0 JRNL AUTH Y.KIM,S.J.LEE,H.J.YOON,N.K.KIM,B.J.LEE,J.Y.SUH JRNL TITL ANTI-CRISPR ACRIIC3 DISCRIMINATES BETWEEN CAS9 ORTHOLOGS VIA JRNL TITL 2 TARGETING THE VARIABLE SURFACE OF THE HNH NUCLEASE DOMAIN. JRNL REF FEBS J. V. 286 4661 2019 JRNL REFN ISSN 1742-464X JRNL PMID 31389128 JRNL DOI 10.1111/FEBS.15037 REMARK 2 REMARK 2 RESOLUTION. 2.32 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.12_2829: ???) 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.32 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.71 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 11533 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.196 REMARK 3 R VALUE (WORKING SET) : 0.190 REMARK 3 FREE R VALUE : 0.242 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.090 REMARK 3 FREE R VALUE TEST SET COUNT : 2140 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 35.7112 - 5.7164 0.98 1243 142 0.1767 0.1923 REMARK 3 2 5.7164 - 4.5402 1.00 1274 146 0.1683 0.2023 REMARK 3 3 4.5402 - 3.9672 1.00 1261 148 0.1551 0.2050 REMARK 3 4 3.9672 - 3.6048 1.00 1296 143 0.1588 0.2174 REMARK 3 5 3.6048 - 3.3466 1.00 1256 144 0.1929 0.2563 REMARK 3 6 3.3466 - 3.1494 1.00 1282 139 0.2003 0.2854 REMARK 3 7 3.1494 - 2.9918 1.00 1271 135 0.2038 0.2964 REMARK 3 8 2.9918 - 2.8616 1.00 1282 134 0.2108 0.2336 REMARK 3 9 2.8616 - 2.7515 1.00 1303 135 0.2293 0.2710 REMARK 3 10 2.7515 - 2.6566 1.00 1254 148 0.2227 0.2575 REMARK 3 11 2.6566 - 2.5735 1.00 1293 143 0.2097 0.2759 REMARK 3 12 2.5735 - 2.5000 1.00 1286 138 0.2199 0.2652 REMARK 3 13 2.5000 - 2.4342 1.00 1269 150 0.2116 0.2550 REMARK 3 14 2.4342 - 2.3748 1.00 1264 147 0.2301 0.3405 REMARK 3 15 2.3748 - 2.3209 0.98 1235 148 0.2326 0.2831 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 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) : 0.270 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.880 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 1908 REMARK 3 ANGLE : 0.864 2560 REMARK 3 CHIRALITY : 0.046 280 REMARK 3 PLANARITY : 0.004 330 REMARK 3 DIHEDRAL : 3.104 1164 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: THE ENTRY CONTAINS FRIEDEL PAIRS IN REMARK 3 F_PLUS/MINUS COLUMNS AND I_PLUS/MINUS COLUMNS REMARK 4 REMARK 4 6JHV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-FEB-19. REMARK 100 THE DEPOSITION ID IS D_1300011105. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-JUL-18 REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 11C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97940 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11533 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.320 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 17.50 REMARK 200 R MERGE (I) : 0.11000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 38.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.32 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.36 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.42900 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: AUTOSOL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS REMARK 200 AND I_PLUS/MINUS COLUMNS 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: 20 MM HEPES-NAOH, PH 7.4, 200 MM NACL, REMARK 280 5% (V/V) GLYCEROL, 2 MM BME, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 37.10400 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.95950 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 37.10400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 23.95950 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 MSE A 1 REMARK 465 MSE B 1 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 MSE A 2 CG SE CE REMARK 470 MSE B 2 CG SE CE REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 205 O HOH A 268 1.87 REMARK 500 O HOH A 245 O HOH A 258 1.88 REMARK 500 O HOH A 214 O HOH B 238 2.10 REMARK 500 NH1 ARG B 25 O HOH B 201 2.16 REMARK 500 OE2 GLU B 39 O HOH B 202 2.18 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 ASP A 38 55.47 -100.95 REMARK 500 ASP A 45 49.85 -88.69 REMARK 500 LYS B 116 79.65 -166.79 REMARK 500 REMARK 500 REMARK: NULL REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE SEQUENCE DATABASE MATCH UNP A0A3E2QDI5_NEIME WAS OBSOLETED WITH REMARK 999 NO SUPERSEDE. THERE IS NO MATCH IN UNIPROT. DBREF 6JHV A 1 117 PDB 6JHV 6JHV 1 117 DBREF 6JHV B 1 117 PDB 6JHV 6JHV 1 117 SEQRES 1 A 117 MSE MSE PHE LYS ARG ALA ILE ILE PHE THR SER PHE ASN SEQRES 2 A 117 GLY PHE GLU LYS VAL SER ARG THR GLU LYS ARG ARG LEU SEQRES 3 A 117 ALA LYS ILE ILE ASN ALA ARG VAL SER ILE ILE ASP GLU SEQRES 4 A 117 TYR LEU ARG ALA LYS ASP THR ASN ALA SER LEU ASP GLY SEQRES 5 A 117 GLN TYR ARG ALA PHE LEU PHE ASN ASP GLU SER PRO ALA SEQRES 6 A 117 MSE THR GLU PHE LEU ALA LYS LEU LYS ALA PHE ALA GLU SEQRES 7 A 117 SER CYS THR GLY ILE SER ILE ASP ALA TRP GLU ILE GLU SEQRES 8 A 117 GLU SER GLU TYR VAL ARG LEU PRO VAL GLU ARG ARG ASP SEQRES 9 A 117 PHE LEU ALA ALA ALA ASN GLY LYS GLU ILE PHE LYS ILE SEQRES 1 B 117 MSE MSE PHE LYS ARG ALA ILE ILE PHE THR SER PHE ASN SEQRES 2 B 117 GLY PHE GLU LYS VAL SER ARG THR GLU LYS ARG ARG LEU SEQRES 3 B 117 ALA LYS ILE ILE ASN ALA ARG VAL SER ILE ILE ASP GLU SEQRES 4 B 117 TYR LEU ARG ALA LYS ASP THR ASN ALA SER LEU ASP GLY SEQRES 5 B 117 GLN TYR ARG ALA PHE LEU PHE ASN ASP GLU SER PRO ALA SEQRES 6 B 117 MSE THR GLU PHE LEU ALA LYS LEU LYS ALA PHE ALA GLU SEQRES 7 B 117 SER CYS THR GLY ILE SER ILE ASP ALA TRP GLU ILE GLU SEQRES 8 B 117 GLU SER GLU TYR VAL ARG LEU PRO VAL GLU ARG ARG ASP SEQRES 9 B 117 PHE LEU ALA ALA ALA ASN GLY LYS GLU ILE PHE LYS ILE MODRES 6JHV MSE A 2 MET MODIFIED RESIDUE MODRES 6JHV MSE A 66 MET MODIFIED RESIDUE MODRES 6JHV MSE B 2 MET MODIFIED RESIDUE MODRES 6JHV MSE B 66 MET MODIFIED RESIDUE HET MSE A 2 5 HET MSE A 66 8 HET MSE B 2 5 HET MSE B 66 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 4(C5 H11 N O2 SE) FORMUL 3 HOH *114(H2 O) HELIX 1 AA1 SER A 19 ALA A 32 1 14 HELIX 2 AA2 ASP A 38 ARG A 42 5 5 HELIX 3 AA3 THR A 46 ASP A 51 1 6 HELIX 4 AA4 PRO A 64 CYS A 80 1 17 HELIX 5 AA5 GLU A 92 ARG A 97 1 6 HELIX 6 AA6 ARG A 102 ASN A 110 1 9 HELIX 7 AA7 SER B 19 VAL B 34 1 16 HELIX 8 AA8 SER B 35 ARG B 42 5 8 HELIX 9 AA9 THR B 46 ASP B 51 1 6 HELIX 10 AB1 PRO B 64 CYS B 80 1 17 HELIX 11 AB2 GLU B 92 VAL B 96 1 5 HELIX 12 AB3 ARG B 102 ASN B 110 1 9 SHEET 1 AA1 4 GLN A 53 ASN A 60 0 SHEET 2 AA1 4 PHE A 3 PHE A 12 -1 N LYS A 4 O PHE A 59 SHEET 3 AA1 4 ILE A 83 GLU A 91 -1 O SER A 84 N SER A 11 SHEET 4 AA1 4 LYS A 112 ILE A 117 -1 O ILE A 114 N ALA A 87 SHEET 1 AA2 4 GLN B 53 ASN B 60 0 SHEET 2 AA2 4 PHE B 3 PHE B 12 -1 N ALA B 6 O PHE B 57 SHEET 3 AA2 4 ILE B 83 GLU B 91 -1 O TRP B 88 N ILE B 7 SHEET 4 AA2 4 LYS B 112 LYS B 116 -1 O LYS B 112 N GLU B 89 LINK C MSE A 2 N PHE A 3 1555 1555 1.33 LINK C ALA A 65 N MSE A 66 1555 1555 1.33 LINK C MSE A 66 N THR A 67 1555 1555 1.34 LINK C MSE B 2 N PHE B 3 1555 1555 1.33 LINK C ALA B 65 N MSE B 66 1555 1555 1.34 LINK C MSE B 66 N THR B 67 1555 1555 1.34 CRYST1 74.208 47.919 71.414 90.00 90.00 90.00 P 21 21 2 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 0.013476 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020869 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014003 0.00000 HETATM 1 N MSE A 2 13.592 13.879 24.995 1.00 38.34 N HETATM 2 CA MSE A 2 13.097 12.993 26.044 1.00 31.02 C HETATM 3 C MSE A 2 14.233 12.240 26.730 1.00 31.19 C HETATM 4 O MSE A 2 14.177 12.023 27.947 1.00 34.71 O HETATM 5 CB MSE A 2 12.082 12.025 25.493 1.00 29.75 C