HEADER VIRAL PROTEIN 03-DEC-21 7T26 TITLE STRUCTURE OF PHAGE FBB1 ANTI-CBASS NUCLEASE ACB1 IN APO STATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ACB1; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ERWINIA PHAGE FBB1; SOURCE 3 ORGANISM_TAXID: 2776772; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ANTI-CBASS, NUCLEASE, IMMUNE EVASION, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.J.HOBBS,T.WEIN,A.LU,B.R.MOREHOUSE,J.SCHNABEL,R.SOREK,P.J.KRANZUSCH REVDAT 3 28-FEB-24 7T26 1 REMARK REVDAT 2 01-JUN-22 7T26 1 JRNL REVDAT 1 20-APR-22 7T26 0 JRNL AUTH S.J.HOBBS,T.WEIN,A.LU,B.R.MOREHOUSE,J.SCHNABEL,A.LEAVITT, JRNL AUTH 2 E.YIRMIYA,R.SOREK,P.J.KRANZUSCH JRNL TITL PHAGE ANTI-CBASS AND ANTI-PYCSAR NUCLEASES SUBVERT BACTERIAL JRNL TITL 2 IMMUNITY. JRNL REF NATURE V. 605 522 2022 JRNL REFN ESSN 1476-4687 JRNL PMID 35395152 JRNL DOI 10.1038/S41586-022-04716-Y REMARK 2 REMARK 2 RESOLUTION. 1.14 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) : 1.14 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.17 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.5 REMARK 3 NUMBER OF REFLECTIONS : 53246 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.161 REMARK 3 R VALUE (WORKING SET) : 0.160 REMARK 3 FREE R VALUE : 0.181 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.190 REMARK 3 FREE R VALUE TEST SET COUNT : 2231 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 42.1700 - 2.8800 1.00 3664 161 0.1778 0.1904 REMARK 3 2 2.8800 - 2.2800 1.00 3440 150 0.1615 0.1751 REMARK 3 3 2.2800 - 2.0000 1.00 3384 148 0.1347 0.1492 REMARK 3 4 2.0000 - 1.8100 1.00 3372 148 0.1411 0.1607 REMARK 3 5 1.8100 - 1.6800 1.00 3335 145 0.1426 0.1773 REMARK 3 6 1.6800 - 1.5800 1.00 3332 146 0.1376 0.1743 REMARK 3 7 1.5800 - 1.5000 1.00 3316 145 0.1459 0.1978 REMARK 3 8 1.5000 - 1.4400 1.00 3307 146 0.1618 0.2033 REMARK 3 9 1.4400 - 1.3800 1.00 3287 143 0.1650 0.1860 REMARK 3 10 1.3800 - 1.3400 1.00 3300 143 0.1616 0.1824 REMARK 3 11 1.3400 - 1.2900 1.00 3252 142 0.1565 0.1993 REMARK 3 12 1.2900 - 1.2600 1.00 3290 145 0.1638 0.1875 REMARK 3 13 1.2600 - 1.2200 0.99 3259 142 0.1678 0.2019 REMARK 3 14 1.2200 - 1.1900 0.98 3218 140 0.1922 0.2214 REMARK 3 15 1.1900 - 1.1700 0.98 3221 141 0.2187 0.2724 REMARK 3 16 1.1700 - 1.1400 0.32 1038 46 0.1829 0.2162 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) : 0.089 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.799 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.43 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.35 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 : 0.011 1133 REMARK 3 ANGLE : 1.281 1547 REMARK 3 CHIRALITY : 0.083 175 REMARK 3 PLANARITY : 0.012 199 REMARK 3 DIHEDRAL : 12.054 427 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 7T26 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-DEC-21. REMARK 100 THE DEPOSITION ID IS D_1000261537. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-SEP-21 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : NULL 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) : 0.97918 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 : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 53419 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.140 REMARK 200 RESOLUTION RANGE LOW (A) : 43.190 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 24.00 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 23.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.17 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.3 REMARK 200 DATA REDUNDANCY IN SHELL : 12.70 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.400 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: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.99 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2 M AMMONIUM SULFATE, 0.1 M SODIUM REMARK 280 CITRATE PH 4.6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z 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 77.07500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 21.92250 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 21.92250 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 38.53750 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 21.92250 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 21.92250 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 115.61250 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 21.92250 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 21.92250 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 38.53750 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 21.92250 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 21.92250 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 115.61250 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 0.00000 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 77.07500 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 LEU A 138 REMARK 465 GLU A 139 REMARK 465 TRP A 140 REMARK 465 SER A 141 REMARK 465 ASP A 142 REMARK 465 LYS A 143 REMARK 465 ASP A 144 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 253 O HOH A 280 1.88 REMARK 500 O HOH A 419 O HOH A 423 1.90 REMARK 500 N SER A 1 O HOH A 201 1.93 REMARK 500 OH TYR A 132 O HOH A 202 1.93 REMARK 500 O SER A 1 O HOH A 201 2.00 REMARK 500 O HOH A 388 O HOH A 391 2.04 REMARK 500 O HOH A 203 O HOH A 246 2.06 REMARK 500 O HOH A 328 O HOH A 370 2.12 REMARK 500 O ALA A 51 O HOH A 203 2.13 REMARK 500 O HOH A 253 O HOH A 360 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 414 O HOH A 436 7555 1.69 REMARK 500 O HOH A 342 O HOH A 404 3445 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 ASN A 112 108.93 -168.20 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 446 DISTANCE = 6.58 ANGSTROMS DBREF1 7T26 A 2 144 UNP A0A868BQY3_9CAUD DBREF2 7T26 A A0A868BQY3 10 152 SEQADV 7T26 SER A 1 UNP A0A868BQY CLONING ARTIFACT SEQRES 1 A 144 SER GLY LEU TYR VAL ALA ALA LYS PHE SER GLU SER THR SEQRES 2 A 144 LEU ASP ALA LEU GLU GLU LEU GLN ARG SER LEU LYS LEU SEQRES 3 A 144 PRO ASN PRO VAL PRO ARG ASP LYS LEU HIS THR THR ILE SEQRES 4 A 144 VAL TYR SER ARG VAL ASN VAL PRO TYR LYS VAL ALA SER SEQRES 5 A 144 GLY SER PHE GLU ILE ALA ASP LYS GLY LYS LEU THR VAL SEQRES 6 A 144 PHE GLU THR GLN SER GLY ASN ARG ALA LEU VAL LEU GLU SEQRES 7 A 144 MET ASP SER ASP TYR LEU SER ALA ARG HIS SER TYR ALA SEQRES 8 A 144 LYS ALA LEU GLY ALA SER TYR ASP TYR PRO ASP TYR ARG SEQRES 9 A 144 PRO HIS ILE THR LEU SER TYR ASN ILE GLY VAL LEU ASN SEQRES 10 A 144 PHE SER GLY GLU TYR LYS VAL PRO VAL VAL LEU ASP ARG SEQRES 11 A 144 GLU TYR SER GLU GLU LEU ASP LEU GLU TRP SER ASP LYS SEQRES 12 A 144 ASP FORMUL 2 HOH *246(H2 O) HELIX 1 AA1 SER A 10 LEU A 24 1 15 HELIX 2 AA2 PRO A 31 LEU A 35 5 5 HELIX 3 AA3 SER A 81 GLY A 95 1 15 SHEET 1 AA1 6 THR A 37 SER A 42 0 SHEET 2 AA1 6 GLY A 2 PHE A 9 -1 N VAL A 5 O ILE A 39 SHEET 3 AA1 6 GLU A 121 LEU A 136 -1 O ASP A 129 N LYS A 8 SHEET 4 AA1 6 PHE A 55 GLU A 67 -1 N ILE A 57 O VAL A 126 SHEET 5 AA1 6 ARG A 73 GLU A 78 -1 O GLU A 78 N LYS A 62 SHEET 6 AA1 6 HIS A 106 SER A 110 -1 O LEU A 109 N LEU A 75 CRYST1 43.845 43.845 154.150 90.00 90.00 90.00 P 41 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 0.022808 0.000000 0.000000 0.00000 SCALE2 0.000000 0.022808 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006487 0.00000