HEADER PROTEIN BINDING 02-MAR-22 7X4B TITLE CRYSTAL STRUCTURE OF AN ANTI-CRISPR PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: ANTI-CRISPR PROTEIN (ACRIIC1); 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 BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS ANTI-CRISPR, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR J.HU,S.ZHANG,J.Y.GAO,X.LIU,J.LIU REVDAT 3 29-NOV-23 7X4B 1 REMARK REVDAT 2 22-FEB-23 7X4B 1 JRNL REVDAT 1 26-OCT-22 7X4B 0 JRNL AUTH Y.ZHAO,J.HU,S.S.YANG,J.ZHONG,J.LIU,S.WANG,Y.JIAO,F.JIANG, JRNL AUTH 2 R.ZHAI,B.REN,H.CONG,Y.ZHU,F.HAN,J.ZHANG,Y.XU,Z.HUANG, JRNL AUTH 3 S.ZHANG,F.YANG JRNL TITL A REDOX SWITCH REGULATES THE ASSEMBLY AND ANTI-CRISPR JRNL TITL 2 ACTIVITY OF ACRIIC1. JRNL REF NAT COMMUN V. 13 7071 2022 JRNL REFN ESSN 2041-1723 JRNL PMID 36400778 JRNL DOI 10.1038/S41467-022-34551-8 REMARK 2 REMARK 2 RESOLUTION. 1.61 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2_4158 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) : 1.61 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.24 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 30566 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.198 REMARK 3 R VALUE (WORKING SET) : 0.198 REMARK 3 FREE R VALUE : 0.210 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.790 REMARK 3 FREE R VALUE TEST SET COUNT : 1465 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 29.2400 - 3.4700 1.00 2993 162 0.1645 0.1714 REMARK 3 2 3.4700 - 2.7500 1.00 2948 158 0.2088 0.2141 REMARK 3 3 2.7500 - 2.4100 1.00 2931 124 0.2149 0.2405 REMARK 3 4 2.4000 - 2.1900 1.00 2914 134 0.2238 0.2241 REMARK 3 5 2.1900 - 2.0300 1.00 2875 146 0.2038 0.2498 REMARK 3 6 2.0300 - 1.9100 1.00 2909 142 0.2216 0.2497 REMARK 3 7 1.9100 - 1.8100 1.00 2872 152 0.2159 0.2716 REMARK 3 8 1.8100 - 1.7300 1.00 2897 144 0.2389 0.2425 REMARK 3 9 1.7300 - 1.6700 1.00 2904 151 0.2195 0.2463 REMARK 3 10 1.6700 - 1.6100 1.00 2858 152 0.2380 0.2578 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.124 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.467 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 26.31 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.80 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 1294 REMARK 3 ANGLE : 0.922 1760 REMARK 3 CHIRALITY : 0.055 188 REMARK 3 PLANARITY : 0.006 223 REMARK 3 DIHEDRAL : 5.690 189 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 7X4B COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 03-MAR-22. REMARK 100 THE DEPOSITION ID IS D_1300027942. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-NOV-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL18U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979150 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 : XDS 20210323 REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30571 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.610 REMARK 200 RESOLUTION RANGE LOW (A) : 29.240 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 8.100 REMARK 200 R MERGE (I) : 0.07345 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.3900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.61 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.67 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 8.20 REMARK 200 R MERGE FOR SHELL (I) : 0.94890 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.380 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.8.3 REMARK 200 STARTING MODEL: 5VGB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.05 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.8 M (NH4)2SO4, 0.1 M BIS-TRIS PH6.5, REMARK 280 2% (V/V) POLYETHYLENE GLYCOL MONOMETHYL ETHER 550, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 42 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 -Y,X,Z+1/2 REMARK 290 4555 Y,-X,Z+1/2 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 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 17.21100 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 17.21100 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: 580 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9200 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -30.0 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 286 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 188 LIES ON A SPECIAL POSITION. 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 0 REMARK 465 ALA A 1 REMARK 465 ASN A 2 REMARK 465 MET B 0 REMARK 465 ALA B 1 REMARK 465 ASN B 2 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 LYS A 6 CG CD CE NZ REMARK 470 LYS A 9 CG CD CE NZ REMARK 470 GLU A 25 OE1 OE2 REMARK 470 GLU A 27 CD OE1 OE2 REMARK 470 ASP A 42 CG OD1 OD2 REMARK 470 ASP A 44 CG OD1 OD2 REMARK 470 LYS A 46 CD CE NZ REMARK 470 ARG A 52 NH1 NH2 REMARK 470 GLU A 81 OE1 OE2 REMARK 470 LYS B 6 CG CD CE NZ REMARK 470 LYS B 9 CG CD CE NZ REMARK 470 GLU B 25 CG CD OE1 OE2 REMARK 470 GLU B 27 CD OE1 OE2 REMARK 470 LYS B 32 CE NZ REMARK 470 ASP B 42 CG OD1 OD2 REMARK 470 ASP B 44 OD1 OD2 REMARK 470 LYS B 46 CE NZ REMARK 470 LEU B 64 CD1 CD2 REMARK 470 GLU B 81 CD OE1 OE2 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 MET A 66 CG - SD - CE ANGL. DEV. = -9.8 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 ASP A 14 43.45 -142.79 REMARK 500 ASP B 14 45.41 -150.11 REMARK 500 REMARK 500 REMARK: NULL DBREF1 7X4B A 0 85 UNP A0A2D0TCG3_NEIME DBREF2 7X4B A A0A2D0TCG3 1 86 DBREF1 7X4B B 0 85 UNP A0A2D0TCG3_NEIME DBREF2 7X4B B A0A2D0TCG3 1 86 SEQRES 1 A 86 MET ALA ASN LYS THR TYR LYS ILE GLY LYS ASN ALA GLY SEQRES 2 A 86 TYR ASP GLY CYS GLY LEU CYS LEU ALA ALA ILE SER GLU SEQRES 3 A 86 ASN GLU ALA ILE LYS VAL LYS TYR LEU ARG ASP ILE CYS SEQRES 4 A 86 PRO ASP TYR ASP GLY ASP ASP LYS ALA GLU ASP TRP LEU SEQRES 5 A 86 ARG TRP GLY THR ASP SER ARG VAL LYS ALA ALA ALA LEU SEQRES 6 A 86 GLU MET GLU GLN TYR ALA TYR THR SER VAL GLY MET ALA SEQRES 7 A 86 SER CYS TRP GLU PHE VAL GLU LEU SEQRES 1 B 86 MET ALA ASN LYS THR TYR LYS ILE GLY LYS ASN ALA GLY SEQRES 2 B 86 TYR ASP GLY CYS GLY LEU CYS LEU ALA ALA ILE SER GLU SEQRES 3 B 86 ASN GLU ALA ILE LYS VAL LYS TYR LEU ARG ASP ILE CYS SEQRES 4 B 86 PRO ASP TYR ASP GLY ASP ASP LYS ALA GLU ASP TRP LEU SEQRES 5 B 86 ARG TRP GLY THR ASP SER ARG VAL LYS ALA ALA ALA LEU SEQRES 6 B 86 GLU MET GLU GLN TYR ALA TYR THR SER VAL GLY MET ALA SEQRES 7 B 86 SER CYS TRP GLU PHE VAL GLU LEU HET SO4 A 101 5 HETNAM SO4 SULFATE ION FORMUL 3 SO4 O4 S 2- FORMUL 4 HOH *178(H2 O) HELIX 1 AA1 LEU A 34 CYS A 38 1 5 HELIX 2 AA2 GLU A 48 GLY A 54 1 7 HELIX 3 AA3 ASP A 56 GLN A 68 1 13 HELIX 4 AA4 LEU B 34 CYS B 38 1 5 HELIX 5 AA5 GLU B 48 GLY B 54 1 7 HELIX 6 AA6 ASP B 56 GLN B 68 1 13 SHEET 1 AA1 6 THR A 4 ILE A 7 0 SHEET 2 AA1 6 GLU A 27 TYR A 33 1 O ALA A 28 N LYS A 6 SHEET 3 AA1 6 GLY A 17 SER A 24 -1 N SER A 24 O GLU A 27 SHEET 4 AA1 6 TYR A 71 SER A 78 -1 O TYR A 71 N ILE A 23 SHEET 5 AA1 6 GLU A 81 GLU A 84 -1 O VAL A 83 N MET A 76 SHEET 6 AA1 6 THR A 4 ILE A 7 -1 N TYR A 5 O PHE A 82 SHEET 1 AA2 6 THR B 4 ILE B 7 0 SHEET 2 AA2 6 GLU B 27 TYR B 33 1 O ALA B 28 N LYS B 6 SHEET 3 AA2 6 GLY B 17 SER B 24 -1 N LEU B 20 O LYS B 32 SHEET 4 AA2 6 TYR B 71 SER B 78 -1 O TYR B 71 N ILE B 23 SHEET 5 AA2 6 GLU B 81 GLU B 84 -1 O VAL B 83 N MET B 76 SHEET 6 AA2 6 THR B 4 ILE B 7 -1 N TYR B 5 O PHE B 82 SSBOND 1 CYS A 16 CYS B 79 1555 1555 2.03 SSBOND 2 CYS A 79 CYS B 16 1555 1555 2.04 CRYST1 82.710 82.710 34.422 90.00 90.00 90.00 P 42 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 0.012090 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012090 0.000000 0.00000 SCALE3 0.000000 0.000000 0.029051 0.00000