HEADER ANTIVIRAL PROTEIN/RNA 15-JUN-23 8T65 TITLE CA4 BOUND CAM1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CAM1; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: RNA (5'-R(P*AP*AP*AP*A)-3'); COMPND 7 CHAIN: C; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NITROSOCOCCUS HALOPHILUS NC 4; SOURCE 3 ORGANISM_TAXID: 472759; SOURCE 4 STRAIN: NC4; SOURCE 5 GENE: NHAL_2839; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: NITROSOCOCCUS HALOPHILUS NC 4; SOURCE 11 ORGANISM_TAXID: 472759 KEYWDS CARF, SAVED, CRISPR, MEMBRANE, CYCLIC ADENYLATE, IMMUNE SYSTEM, KEYWDS 2 ANTIVIRAL PROTEIN, ANTIVIRAL PROTEIN-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Y.YU,D.J.PATEL REVDAT 3 07-FEB-24 8T65 1 JRNL REVDAT 2 24-JAN-24 8T65 1 JRNL REVDAT 1 10-JAN-24 8T65 0 JRNL AUTH C.F.BACA,Y.YU,J.T.ROSTOL,P.MAJUMDER,D.J.PATEL,L.A.MARRAFFINI JRNL TITL THE CRISPR EFFECTOR CAM1 MEDIATES MEMBRANE DEPOLARIZATION JRNL TITL 2 FOR PHAGE DEFENCE. JRNL REF NATURE V. 625 797 2024 JRNL REFN ESSN 1476-4687 JRNL PMID 38200316 JRNL DOI 10.1038/S41586-023-06902-Y REMARK 2 REMARK 2 RESOLUTION. 2.09 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) : 2.09 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.05 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.430 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 3 NUMBER OF REFLECTIONS : 16010 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.174 REMARK 3 R VALUE (WORKING SET) : 0.172 REMARK 3 FREE R VALUE : 0.221 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.550 REMARK 3 FREE R VALUE TEST SET COUNT : 728 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 46.0500 - 3.5800 0.99 3143 152 0.1624 0.2026 REMARK 3 2 3.5800 - 2.8400 0.99 3077 183 0.1805 0.2358 REMARK 3 3 2.8400 - 2.4800 0.99 3093 111 0.1820 0.2220 REMARK 3 4 2.4800 - 2.2600 0.99 3112 142 0.1798 0.2383 REMARK 3 5 2.2600 - 2.0900 0.92 2857 140 0.1685 0.2449 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) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.280 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 30.61 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 2439 REMARK 3 ANGLE : 0.904 3335 REMARK 3 CHIRALITY : 0.057 390 REMARK 3 PLANARITY : 0.005 425 REMARK 3 DIHEDRAL : 24.268 379 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 8T65 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-JUN-23. REMARK 100 THE DEPOSITION ID IS D_1000275325. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-JUL-21 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 : APS REMARK 200 BEAMLINE : 24-ID-E REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16011 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.090 REMARK 200 RESOLUTION RANGE LOW (A) : 64.860 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 200 DATA REDUNDANCY : 4.400 REMARK 200 R MERGE (I) : 0.06900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.09 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.15 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.30100 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: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.89 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM SULFATE, 0.1 M REMARK 280 PHOSPHATE CITRATE, PH 4.2, 20% (W/V) PEG300, 10% GLYCEROL, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-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 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 32.43050 REMARK 290 SMTRY3 2 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4280 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13020 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -24.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 400 REMARK 400 COMPOUND REMARK 400 CYCLIC OLIGOADENYLATES SUCH AS C-TETRAAMP WERE FOUND TO BE NOVEL REMARK 400 BACTERIAL SECOND MESSENGERS. 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 SER A 41 REMARK 465 ARG A 42 REMARK 465 GLU A 43 REMARK 465 ASP A 44 REMARK 465 LEU A 45 REMARK 465 ARG A 46 REMARK 465 ALA A 47 REMARK 465 TRP A 48 REMARK 465 LEU A 49 REMARK 465 THR A 50 REMARK 465 ARG A 51 REMARK 465 SER B 41 REMARK 465 ARG B 42 REMARK 465 GLU B 43 REMARK 465 ASP B 44 REMARK 465 LEU B 45 REMARK 465 ARG B 46 REMARK 465 ALA B 47 REMARK 465 TRP B 48 REMARK 465 LEU B 49 REMARK 465 THR B 50 REMARK 465 ARG B 51 REMARK 465 ASN B 52 REMARK 465 ARG B 53 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 A C 4 O3' A C 1 P -0.087 REMARK 500 A C 1 O3' A C 2 P -0.078 REMARK 500 A C 3 P A C 3 OP2 -0.108 REMARK 500 REMARK 500 REMARK: NULL DBREF 8T65 A 42 206 UNP D5BXZ3 D5BXZ3_NITHN 42 206 DBREF 8T65 B 42 206 UNP D5BXZ3 D5BXZ3_NITHN 42 206 DBREF 8T65 C 4 3 PDB 8T65 8T65 4 3 SEQADV 8T65 SER A 41 UNP D5BXZ3 EXPRESSION TAG SEQADV 8T65 SER B 41 UNP D5BXZ3 EXPRESSION TAG SEQRES 1 A 166 SER ARG GLU ASP LEU ARG ALA TRP LEU THR ARG ASN ARG SEQRES 2 A 166 PHE PRO ARG VAL GLY GLY VAL SER GLU SER THR VAL GLN SEQRES 3 A 166 TRP GLU GLY VAL VAL PHE THR VAL SER ASN GLU SER VAL SEQRES 4 A 166 PRO ARG TRP VAL MET ALA GLN ILE GLN PRO ALA TYR MET SEQRES 5 A 166 GLY LEU VAL ALA THR GLN ALA SER LEU ALA ALA ALA GLU SEQRES 6 A 166 ALA VAL ALA ALA VAL ALA ARG ARG ARG GLY ILE GLU VAL SEQRES 7 A 166 HIS GLY PRO LEU GLN VAL ALA ASP PRO ASN ASP PRO ALA SEQRES 8 A 166 ALA SER ARG SER GLN VAL ALA LEU LEU LEU SER GLU LEU SEQRES 9 A 166 ARG ARG ALA GLY CYS ARG GLU ILE ALA VAL ASP LEU THR SEQRES 10 A 166 GLY GLY LYS LEU PRO MET SER LEU GLY ALA PHE MET ALA SEQRES 11 A 166 ALA GLU GLU ALA GLY VAL ALA SER LEU TYR VAL ALA THR SEQRES 12 A 166 ASP PHE ASP LYS HIS LEU LYS VAL PRO ASP MET ARG THR SEQRES 13 A 166 ALA THR LEU ARG GLN ILE SER GLN PRO GLU SEQRES 1 B 166 SER ARG GLU ASP LEU ARG ALA TRP LEU THR ARG ASN ARG SEQRES 2 B 166 PHE PRO ARG VAL GLY GLY VAL SER GLU SER THR VAL GLN SEQRES 3 B 166 TRP GLU GLY VAL VAL PHE THR VAL SER ASN GLU SER VAL SEQRES 4 B 166 PRO ARG TRP VAL MET ALA GLN ILE GLN PRO ALA TYR MET SEQRES 5 B 166 GLY LEU VAL ALA THR GLN ALA SER LEU ALA ALA ALA GLU SEQRES 6 B 166 ALA VAL ALA ALA VAL ALA ARG ARG ARG GLY ILE GLU VAL SEQRES 7 B 166 HIS GLY PRO LEU GLN VAL ALA ASP PRO ASN ASP PRO ALA SEQRES 8 B 166 ALA SER ARG SER GLN VAL ALA LEU LEU LEU SER GLU LEU SEQRES 9 B 166 ARG ARG ALA GLY CYS ARG GLU ILE ALA VAL ASP LEU THR SEQRES 10 B 166 GLY GLY LYS LEU PRO MET SER LEU GLY ALA PHE MET ALA SEQRES 11 B 166 ALA GLU GLU ALA GLY VAL ALA SER LEU TYR VAL ALA THR SEQRES 12 B 166 ASP PHE ASP LYS HIS LEU LYS VAL PRO ASP MET ARG THR SEQRES 13 B 166 ALA THR LEU ARG GLN ILE SER GLN PRO GLU SEQRES 1 C 4 A A A A FORMUL 4 HOH *128(H2 O) HELIX 1 AA1 GLU A 62 GLN A 66 5 5 HELIX 2 AA2 GLU A 77 GLN A 88 1 12 HELIX 3 AA3 SER A 100 ARG A 114 1 15 HELIX 4 AA4 ASP A 129 ALA A 147 1 19 HELIX 5 AA5 LYS A 160 GLY A 175 1 16 HELIX 6 AA6 ASP A 193 ALA A 197 5 5 HELIX 7 AA7 GLU B 77 GLN B 88 1 12 HELIX 8 AA8 SER B 100 ARG B 114 1 15 HELIX 9 AA9 ASP B 129 ALA B 147 1 19 HELIX 10 AB1 LYS B 160 GLY B 175 1 16 HELIX 11 AB2 ASP B 193 ALA B 197 5 5 SHEET 1 AA1 6 GLU A 117 VAL A 124 0 SHEET 2 AA1 6 TYR A 91 THR A 97 1 N ALA A 96 O LEU A 122 SHEET 3 AA1 6 GLY A 69 THR A 73 1 N PHE A 72 O GLY A 93 SHEET 4 AA1 6 ILE A 152 ASP A 155 1 O ASP A 155 N VAL A 71 SHEET 5 AA1 6 ALA A 177 ALA A 182 1 O LEU A 179 N VAL A 154 SHEET 6 AA1 6 THR A 198 SER A 203 -1 O THR A 198 N ALA A 182 SHEET 1 AA2 2 ARG B 56 VAL B 57 0 SHEET 2 AA2 2 SER B 203 GLN B 204 -1 O GLN B 204 N ARG B 56 SHEET 1 AA3 6 GLU B 117 GLN B 123 0 SHEET 2 AA3 6 TYR B 91 ALA B 96 1 N ALA B 96 O LEU B 122 SHEET 3 AA3 6 GLY B 69 THR B 73 1 N PHE B 72 O GLY B 93 SHEET 4 AA3 6 ILE B 152 ASP B 155 1 O ASP B 155 N VAL B 71 SHEET 5 AA3 6 ALA B 177 ALA B 182 1 O LEU B 179 N VAL B 154 SHEET 6 AA3 6 THR B 198 GLN B 201 -1 O ARG B 200 N TYR B 180 LINK O3' A C 3 P A C 4 1555 1555 1.51 CISPEP 1 GLY A 120 PRO A 121 0 7.33 CISPEP 2 GLY B 120 PRO B 121 0 5.09 CRYST1 46.987 64.861 50.129 90.00 113.28 90.00 P 1 21 1 4 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 0.021282 0.000000 0.009156 0.00000 SCALE2 0.000000 0.015418 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021716 0.00000