HEADER VIRAL PROTEIN 04-AUG-23 8KBL TITLE STRUCTURE OF ACRIIA7 COMPLEXED WITH 1',3'-CADPR AND CGG COMPND MOL_ID: 1; COMPND 2 MOLECULE: INHIBITOR OF TYPE II CRISPR-CAS SYSTEM; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METAGENOME; SOURCE 3 ORGANISM_TAXID: 256318; SOURCE 4 GENE: ACRIIA7; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Y.XIAO,Y.FENG REVDAT 4 04-DEC-24 8KBL 1 JRNL REMARK REVDAT 3 13-NOV-24 8KBL 1 JRNL REVDAT 2 06-NOV-24 8KBL 1 JRNL REVDAT 1 07-AUG-24 8KBL 0 JRNL AUTH D.LI,Y.XIAO,I.FEDOROVA,W.XIONG,Y.WANG,X.LIU,E.HUITING,J.REN, JRNL AUTH 2 Z.GAO,X.ZHAO,X.CAO,Y.ZHANG,J.BONDY-DENOMY,Y.FENG JRNL TITL SINGLE PHAGE PROTEINS SEQUESTER SIGNALS FROM TIR AND JRNL TITL 2 CGAS-LIKE ENZYMES. JRNL REF NATURE V. 635 719 2024 JRNL REFN ESSN 1476-4687 JRNL PMID 39478223 JRNL DOI 10.1038/S41586-024-08122-4 REMARK 2 REMARK 2 RESOLUTION. 1.98 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) : 1.98 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.68 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 9568 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.220 REMARK 3 R VALUE (WORKING SET) : 0.219 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.490 REMARK 3 FREE R VALUE TEST SET COUNT : 430 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 36.6800 - 4.2700 1.00 1011 46 0.2002 0.2258 REMARK 3 2 4.2600 - 3.3800 1.00 957 29 0.1854 0.1888 REMARK 3 3 3.3800 - 2.9600 1.00 920 42 0.2174 0.1957 REMARK 3 4 2.9600 - 2.6900 1.00 905 37 0.2427 0.2332 REMARK 3 5 2.6900 - 2.4900 1.00 888 62 0.2440 0.2342 REMARK 3 6 2.4900 - 2.3500 1.00 895 43 0.2453 0.2651 REMARK 3 7 2.3500 - 2.2300 1.00 899 44 0.2480 0.3019 REMARK 3 8 2.2300 - 2.1300 1.00 872 52 0.2349 0.2463 REMARK 3 9 2.1300 - 2.0500 1.00 887 41 0.2422 0.2989 REMARK 3 10 2.0500 - 1.9800 1.00 904 34 0.2588 0.3314 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) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.510 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 : 0.016 931 REMARK 3 ANGLE : 1.596 1277 REMARK 3 CHIRALITY : 0.127 140 REMARK 3 PLANARITY : 0.010 148 REMARK 3 DIHEDRAL : 17.601 369 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 8KBL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-AUG-23. REMARK 100 THE DEPOSITION ID IS D_1300039777. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-MAY-23 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 : SSRF REMARK 200 BEAMLINE : BL02U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9583 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.980 REMARK 200 RESOLUTION RANGE LOW (A) : 36.710 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 24.30 REMARK 200 R MERGE (I) : 0.21100 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 18.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.98 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.03 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 26.00 REMARK 200 R MERGE FOR SHELL (I) : 2.16100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.67 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM SULFATE, 25% W/V REMARK 280 POLYETHYLENE GLYCOL 4000, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 42 2 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 -Y,X,Z+1/2 REMARK 290 4555 Y,-X,Z+1/2 REMARK 290 5555 -X,Y,-Z REMARK 290 6555 X,-Y,-Z REMARK 290 7555 Y,X,-Z+1/2 REMARK 290 8555 -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 31.57650 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 31.57650 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 31.57650 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 31.57650 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 O4 OJC A 201 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 346 LIES ON A SPECIAL POSITION. 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 369 O HOH A 376 1.30 REMARK 500 O HOH A 321 O HOH A 374 2.04 REMARK 500 O HOH A 336 O HOH A 379 2.05 REMARK 500 OE1 GLU A 64 O HOH A 302 2.08 REMARK 500 O HOH A 326 O HOH A 362 2.09 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 377 O HOH A 377 6555 1.84 REMARK 500 OG SER A 63 CG2 THR A 65 5656 2.04 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 GLN A 44 -43.13 -137.53 REMARK 500 SER A 47 39.23 -89.56 REMARK 500 REMARK 500 REMARK: NULL DBREF1 8KBL A 1 103 UNP A0A447EB45_9ZZZZ DBREF2 8KBL A A0A447EB45 1 103 SEQADV 8KBL SER A 0 UNP A0A447EB4 EXPRESSION TAG SEQRES 1 A 104 SER MET THR PHE GLY GLN ALA LEU GLU SER LEU LYS ARG SEQRES 2 A 104 GLY HIS LEU VAL ALA ARG LYS GLY TRP ASN GLY LYS GLY SEQRES 3 A 104 MET PHE ILE PHE MET ARG PRO GLU ASP SER LEU PRO THR SEQRES 4 A 104 ASN MET ILE VAL ASN GLN VAL LYS SER LEU PRO GLU SER SEQRES 5 A 104 PHE LYS ARG TRP VAL ALA ASN ASN HIS GLY ASP SER GLU SEQRES 6 A 104 THR ASP ARG ILE LYS PHE THR ALA TYR LEU CYS MET LYS SEQRES 7 A 104 ALA ALA ASP GLY THR ILE VAL ASN GLY TRP LEU ALA SER SEQRES 8 A 104 GLN THR ASP MET LEU ALA ASN ASP TRP VAL ILE VAL GLU HET OJC A 201 35 HET C2E A 202 46 HETNAM OJC (2R,3R,3AS,5S,6R,7S,8R,11R,13S,15AR)-2-(6-AMINO-9H- HETNAM 2 OJC PURIN-9-YL)-3,6,7,11,13-PENTAHYDROXYOCTAHYDRO-2H,5H, HETNAM 3 OJC 11H,13H-5,8-EPOXY-11LAMBDA~5~,13LAMBDA~5~-FURO[2,3- HETNAM 4 OJC G][1,3,5,9,2,4]TETRAOXADIPHOSPHACYCLOTETRADECINE-11, HETNAM 5 OJC 13-DIONE HETNAM C2E 9,9'-[(2R,3R,3AS,5S,7AR,9R,10R,10AS,12S,14AR)-3,5,10, HETNAM 2 C2E 12-TETRAHYDROXY-5,12-DIOXIDOOCTAHYDRO-2H,7H-DIFURO[3, HETNAM 3 C2E 2-D:3',2'-J][1,3,7,9,2, HETNAM 4 C2E 8]TETRAOXADIPHOSPHACYCLODODECINE-2,9-DIYL]BIS(2-AMINO- HETNAM 5 C2E 1,9-DIHYDRO-6H-PURIN-6-ONE) HETSYN C2E C-DI-GMP; CYCLIC DIGUANOSINE MONOPHOSPHATE FORMUL 2 OJC C15 H21 N5 O13 P2 FORMUL 3 C2E C20 H24 N10 O14 P2 FORMUL 4 HOH *89(H2 O) HELIX 1 AA1 THR A 2 ARG A 12 1 11 HELIX 2 AA2 THR A 38 GLN A 44 1 7 HELIX 3 AA3 PRO A 49 GLY A 61 1 13 HELIX 4 AA4 SER A 90 ALA A 96 1 7 SHEET 1 AA1 2 LEU A 15 ARG A 18 0 SHEET 2 AA1 2 TRP A 99 GLU A 103 -1 O VAL A 102 N LEU A 15 SHEET 1 AA2 3 PHE A 27 ARG A 31 0 SHEET 2 AA2 3 TYR A 73 LYS A 77 -1 O TYR A 73 N ARG A 31 SHEET 3 AA2 3 ILE A 83 ASN A 85 -1 O VAL A 84 N MET A 76 SHEET 1 AA3 2 ASP A 34 PRO A 37 0 SHEET 2 AA3 2 ARG A 67 PHE A 70 -1 O PHE A 70 N ASP A 34 CRYST1 63.729 63.729 63.153 90.00 90.00 90.00 P 42 2 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 0.015691 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015691 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015835 0.00000