HEADER VIRAL PROTEIN 19-AUG-25 9WDL TITLE CRYSTAL STRUCTURE OF ANTI-CRISPR PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: ANTI-CRISPR PROTEIN, ACRIE9; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONADACEAE; SOURCE 3 ORGANISM_TAXID: 135621; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS ANTI-CRISPR PROTEIN, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.KANG,E.BAE,J.KOO,H.OH REVDAT 1 29-JUL-26 9WDL 0 JRNL AUTH J.KANG,J.KOO,H.OH,E.BAE JRNL TITL STRUCTURAL INVESTIGATION OF THE ANTI-CRISPR PROTEIN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.73 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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) : 1.73 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 21.53 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.970 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.3 REMARK 3 NUMBER OF REFLECTIONS : 13075 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.215 REMARK 3 R VALUE (WORKING SET) : 0.213 REMARK 3 FREE R VALUE : 0.243 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 1286 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 21.5300 - 3.5900 0.94 2685 144 0.1712 0.1959 REMARK 3 2 3.5900 - 2.8500 0.94 2721 142 0.1922 0.2310 REMARK 3 3 2.8500 - 2.4900 0.95 2703 146 0.2248 0.2525 REMARK 3 4 2.4900 - 2.2700 0.94 2722 144 0.2144 0.2696 REMARK 3 5 2.2700 - 2.1000 0.95 2692 141 0.2167 0.2586 REMARK 3 6 2.1000 - 1.9800 0.95 2750 143 0.2368 0.2357 REMARK 3 7 1.9800 - 1.8800 0.94 2698 140 0.2761 0.2911 REMARK 3 8 1.8800 - 1.8000 0.95 2671 142 0.3326 0.3342 REMARK 3 9 1.8000 - 1.7300 0.94 2750 144 0.3566 0.3917 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) : 0.250 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.390 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 : 0.007 1074 REMARK 3 ANGLE : 0.993 1440 REMARK 3 CHIRALITY : 0.058 149 REMARK 3 PLANARITY : 0.011 190 REMARK 3 DIHEDRAL : 14.800 382 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 9WDL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-AUG-25. REMARK 100 THE DEPOSITION ID IS D_1300062765. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-APR-24 REMARK 200 TEMPERATURE (KELVIN) : 100 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 : 7A (6B, 6C1) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9793 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 S 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13091 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.730 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.8 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.08200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.6700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.73 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.79 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.68000 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 1.9_1692 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.54 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.94 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES-NAOH, PH 7.0, 0.2 M SODIUM REMARK 280 CHLORIDE, 25 % (W/V) PEG3350, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3810 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7660 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -36.0 KCAL/MOL 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 GLY A -5 REMARK 465 SER A -4 REMARK 465 GLY A -3 REMARK 465 SER A -2 REMARK 465 GLY A -1 REMARK 465 SER A 0 REMARK 465 ARG A 73 REMARK 465 GLY A 74 REMARK 465 GLU A 75 REMARK 465 GLY B -5 REMARK 465 SER B -4 REMARK 465 GLY B -3 REMARK 465 SER B -2 REMARK 465 GLY B -1 REMARK 465 SER B 0 REMARK 465 ARG B 8 REMARK 465 LYS B 9 REMARK 465 LEU B 10 REMARK 465 ARG B 73 REMARK 465 GLY B 74 REMARK 465 GLU B 75 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 8 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 9 CG CD CE NZ REMARK 470 LEU A 10 CG CD1 CD2 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 147 O HOH A 152 2.00 REMARK 500 O HOH B 140 O HOH B 150 2.04 REMARK 500 O HOH A 131 O HOH B 148 2.09 REMARK 500 NE2 GLN A 59 O HOH A 101 2.09 REMARK 500 N MET B 1 O HOH B 101 2.16 REMARK 500 OD1 ASP A 55 O HOH A 102 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 133 O HOH B 139 1455 2.14 REMARK 500 O HOH B 149 O HOH B 151 1565 2.14 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 SER A 22 -15.54 -155.05 REMARK 500 ASP A 27 47.67 -82.61 REMARK 500 SER B 22 -19.78 -151.26 REMARK 500 ASP B 27 42.08 -78.23 REMARK 500 REMARK 500 REMARK: NULL DBREF 9WDL A -5 75 PDB 9WDL 9WDL -5 75 DBREF 9WDL B -5 75 PDB 9WDL 9WDL -5 75 SEQRES 1 A 81 GLY SER GLY SER GLY SER MET GLU MET GLN ILE ASN SER SEQRES 2 A 81 ARG LYS LEU GLY ARG THR ILE THR PHE SER ARG PRO GLY SEQRES 3 A 81 ALA SER TYR ILE PHE ALA ASP LEU ASN GLY LYS SER GLY SEQRES 4 A 81 THR LEU GLY CYS GLN ILE CYS SER GLY GLY GLY THR MET SEQRES 5 A 81 GLY SER THR LEU SER TYR ASP GLY ASP ASP GLN ALA GLN SEQRES 6 A 81 PHE GLU ALA ILE CYS ARG ARG TRP TYR ARG ALA HIS VAL SEQRES 7 A 81 ARG GLY GLU SEQRES 1 B 81 GLY SER GLY SER GLY SER MET GLU MET GLN ILE ASN SER SEQRES 2 B 81 ARG LYS LEU GLY ARG THR ILE THR PHE SER ARG PRO GLY SEQRES 3 B 81 ALA SER TYR ILE PHE ALA ASP LEU ASN GLY LYS SER GLY SEQRES 4 B 81 THR LEU GLY CYS GLN ILE CYS SER GLY GLY GLY THR MET SEQRES 5 B 81 GLY SER THR LEU SER TYR ASP GLY ASP ASP GLN ALA GLN SEQRES 6 B 81 PHE GLU ALA ILE CYS ARG ARG TRP TYR ARG ALA HIS VAL SEQRES 7 B 81 ARG GLY GLU FORMUL 3 HOH *120(H2 O) HELIX 1 AA1 SER A 32 GLY A 36 5 5 HELIX 2 AA2 THR A 45 THR A 49 5 5 HELIX 3 AA3 ASP A 56 VAL A 72 1 17 HELIX 4 AA4 SER B 32 GLY B 36 5 5 HELIX 5 AA5 ASP B 56 VAL B 72 1 17 SHEET 1 AA1 4 GLU A 2 SER A 7 0 SHEET 2 AA1 4 ARG A 12 SER A 17 -1 O PHE A 16 N MET A 3 SHEET 3 AA1 4 PHE A 25 ALA A 26 -1 O PHE A 25 N SER A 17 SHEET 4 AA1 4 CYS A 37 GLN A 38 -1 O CYS A 37 N ALA A 26 SHEET 1 AA2 5 GLU B 2 ASN B 6 0 SHEET 2 AA2 5 THR B 13 SER B 17 -1 O ILE B 14 N ILE B 5 SHEET 3 AA2 5 PHE B 25 ALA B 26 -1 O PHE B 25 N SER B 17 SHEET 4 AA2 5 CYS B 37 ILE B 39 -1 O CYS B 37 N ALA B 26 SHEET 5 AA2 5 THR B 45 MET B 46 -1 O MET B 46 N GLN B 38 CRYST1 25.340 37.170 40.700 114.10 90.10 104.70 P 1 2 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 0.039463 0.010353 0.004904 0.00000 SCALE2 0.000000 0.027814 0.012969 0.00000 SCALE3 0.000000 0.000000 0.027110 0.00000 MASTER 282 0 0 5 9 0 0 6 1177 2 0 14 END