HEADER IMMUNE SYSTEM 17-JUN-21 7F45 TITLE STRUCTURE OF AN ANTI-CRISPR PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: ACRIF5; COMPND 3 CHAIN: A, P; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS AERUGINOSA; SOURCE 3 ORGANISM_TAXID: 287; SOURCE 4 GENE: IPC1164_31450; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS MONOMER, MIXED ALPHA-BETA STRUCTURE, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR Y.FENG REVDAT 4 29-NOV-23 7F45 1 REMARK REVDAT 3 08-JUN-22 7F45 1 JRNL REVDAT 2 06-APR-22 7F45 1 JRNL REVDAT 1 09-MAR-22 7F45 0 JRNL AUTH Y.XIE,L.ZHANG,Z.GAO,P.YIN,H.WANG,H.LI,Z.CHEN,Y.ZHANG,M.YANG, JRNL AUTH 2 Y.FENG JRNL TITL ACRIF5 SPECIFICALLY TARGETS DNA-BOUND CRISPR-CAS JRNL TITL 2 SURVEILLANCE COMPLEX FOR INHIBITION. JRNL REF NAT.CHEM.BIOL. V. 18 670 2022 JRNL REFN ESSN 1552-4469 JRNL PMID 35301482 JRNL DOI 10.1038/S41589-022-00995-8 REMARK 2 REMARK 2 RESOLUTION. 3.52 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 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) : 3.52 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.97 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.910 REMARK 3 COMPLETENESS FOR RANGE (%) : 82.7 REMARK 3 NUMBER OF REFLECTIONS : 3075 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.257 REMARK 3 R VALUE (WORKING SET) : 0.255 REMARK 3 FREE R VALUE : 0.311 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.680 REMARK 3 FREE R VALUE TEST SET COUNT : 144 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 3.6500 - 3.5200 0.83 2931 144 0.2551 0.3110 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) : 0.660 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.860 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 71.11 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -6.0604 -26.6438 -8.5743 REMARK 3 T TENSOR REMARK 3 T11: 0.4116 T22: 0.3167 REMARK 3 T33: 0.3841 T12: -0.1340 REMARK 3 T13: 0.0435 T23: 0.0280 REMARK 3 L TENSOR REMARK 3 L11: 4.7412 L22: 0.8668 REMARK 3 L33: 4.5297 L12: -1.6709 REMARK 3 L13: -1.7600 L23: 1.4278 REMARK 3 S TENSOR REMARK 3 S11: -0.1611 S12: 0.6197 S13: 0.1644 REMARK 3 S21: 0.2946 S22: 0.1815 S23: 0.1135 REMARK 3 S31: 0.3167 S32: -0.6267 S33: -0.1251 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : 1 REMARK 3 NCS GROUP : 1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: (CHAIN A AND (RESID 3 THROUGH 45 OR REMARK 3 (RESID 46 THROUGH 47 AND (NAME N OR NAME REMARK 3 CA OR NAME C OR NAME O OR NAME CB )) OR REMARK 3 RESID 48 THROUGH 77)) REMARK 3 SELECTION : (CHAIN P AND (RESID 3 THROUGH 32 OR REMARK 3 (RESID 33 THROUGH 36 AND (NAME N OR NAME REMARK 3 CA OR NAME C OR NAME O OR NAME CB )) OR REMARK 3 RESID 37 THROUGH 77)) REMARK 3 ATOM PAIRS NUMBER : 446 REMARK 3 RMSD : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7F45 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 18-JUN-21. REMARK 100 THE DEPOSITION ID IS D_1300022822. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-OCT-20 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 : BL19U1 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 PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 3096 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.520 REMARK 200 RESOLUTION RANGE LOW (A) : 43.970 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 22.90 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.2500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.52 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.65 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 7EQG REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 68.84 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.95 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, VAPOR DIFFUSION, REMARK 280 TEMPERATURE 293K 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 60.49000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 33.37050 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 33.37050 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 30.24500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 33.37050 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 33.37050 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 90.73500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 33.37050 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 33.37050 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 30.24500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 33.37050 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 33.37050 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 90.73500 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 60.49000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: P 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 MET A 1 REMARK 465 SER A 2 REMARK 465 MET P 1 REMARK 465 SER P 2 REMARK 465 LYS P 78 REMARK 465 MET P 79 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 25 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 33 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 35 CG CD NE CZ NH1 NH2 REMARK 470 ARG P 25 CG CD NE CZ NH1 NH2 REMARK 470 ARG P 35 CG CD NE CZ NH1 NH2 REMARK 470 LYS P 46 CG CD CE NZ 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 56 -132.64 52.22 REMARK 500 SER P 56 -125.45 62.22 REMARK 500 REMARK 500 REMARK: NULL DBREF1 7F45 A 1 79 UNP A0A7M3A7R4_PSEAI DBREF2 7F45 A A0A7M3A7R4 1 79 DBREF1 7F45 P 1 79 UNP A0A7M3A7R4_PSEAI DBREF2 7F45 P A0A7M3A7R4 1 79 SEQRES 1 A 79 MET SER ARG PRO THR VAL VAL THR VAL THR GLU THR PRO SEQRES 2 A 79 ARG ASN PRO GLY SER TYR GLU VAL ASN VAL GLU ARG ASP SEQRES 3 A 79 GLY LYS MET VAL VAL GLY ARG ALA ARG ALA GLY SER ASP SEQRES 4 A 79 PRO GLY ALA ALA ALA ALA LYS ALA MET GLN MET ALA MET SEQRES 5 A 79 GLU TRP GLY SER PRO ASN TYR VAL ILE LEU GLY SER ASN SEQRES 6 A 79 LYS VAL LEU ALA PHE ILE PRO GLU GLN LEU ARG VAL LYS SEQRES 7 A 79 MET SEQRES 1 P 79 MET SER ARG PRO THR VAL VAL THR VAL THR GLU THR PRO SEQRES 2 P 79 ARG ASN PRO GLY SER TYR GLU VAL ASN VAL GLU ARG ASP SEQRES 3 P 79 GLY LYS MET VAL VAL GLY ARG ALA ARG ALA GLY SER ASP SEQRES 4 P 79 PRO GLY ALA ALA ALA ALA LYS ALA MET GLN MET ALA MET SEQRES 5 P 79 GLU TRP GLY SER PRO ASN TYR VAL ILE LEU GLY SER ASN SEQRES 6 P 79 LYS VAL LEU ALA PHE ILE PRO GLU GLN LEU ARG VAL LYS SEQRES 7 P 79 MET HELIX 1 AA1 ASP A 39 TRP A 54 1 16 HELIX 2 AA2 SER A 64 ALA A 69 1 6 HELIX 3 AA3 PRO A 72 ARG A 76 1 5 HELIX 4 AA4 ASP P 39 TRP P 54 1 16 HELIX 5 AA5 SER P 64 ALA P 69 1 6 HELIX 6 AA6 PRO P 72 VAL P 77 1 6 SHEET 1 AA1 5 LYS A 28 ALA A 36 0 SHEET 2 AA1 5 TYR A 19 ARG A 25 -1 N VAL A 21 O ALA A 34 SHEET 3 AA1 5 THR A 5 GLU A 11 -1 N THR A 8 O ASN A 22 SHEET 4 AA1 5 TYR A 59 GLY A 63 1 O LEU A 62 N VAL A 9 SHEET 5 AA1 5 VAL A 77 LYS A 78 -1 O LYS A 78 N TYR A 59 SHEET 1 AA2 4 LYS P 28 ALA P 36 0 SHEET 2 AA2 4 TYR P 19 ARG P 25 -1 N VAL P 21 O ALA P 34 SHEET 3 AA2 4 VAL P 6 GLU P 11 -1 N THR P 8 O ASN P 22 SHEET 4 AA2 4 VAL P 60 GLY P 63 1 O LEU P 62 N VAL P 7 CRYST1 66.741 66.741 120.980 90.00 90.00 90.00 P 41 21 2 16 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 0.014983 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014983 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008266 0.00000