HEADER ANTIFUNGAL PROTEIN 29-JUN-24 9ILD TITLE COMPLEX STRUCTURE OF CAP3 AND CD-NTASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CAP3; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: CYCLIC GMP-AMP SYNTHASE; COMPND 8 CHAIN: B; COMPND 9 SYNONYM: CD-NTASE; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: GOP25_26465; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 9 ORGANISM_TAXID: 562; SOURCE 10 GENE: ETECE562_01214; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CD-NTASE, CGAS, CD-NTASE CONJUGATION, CAP2, CAP3, CBASS, ANTIFUNGAL KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR F.Q.LI,W.F.MA REVDAT 1 31-JUL-24 9ILD 0 JRNL AUTH F.Q.LI,W.F.MA JRNL TITL STRUCTURAL AND FUNCTIONAL CHARACTERIZATION OF THE BACTERIAL JRNL TITL 2 CAP3 ENZYME IN DECONJUGATION AND REGULATION OF THE CYCLIC JRNL TITL 3 DINUCLEOTIDE TRANSFERASE CD-NTASE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.18 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.16_3549: ???) 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) : 2.18 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.21 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 9220 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.233 REMARK 3 R VALUE (WORKING SET) : 0.228 REMARK 3 FREE R VALUE : 0.283 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.920 REMARK 3 FREE R VALUE TEST SET COUNT : 915 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 39.2060 - 4.1665 1.00 1284 139 0.2003 0.2449 REMARK 3 2 4.1665 - 3.3076 1.00 1219 133 0.2036 0.2806 REMARK 3 3 3.3076 - 2.8897 1.00 1191 136 0.2421 0.2757 REMARK 3 4 2.8897 - 2.6255 1.00 1189 130 0.2617 0.3141 REMARK 3 5 2.6255 - 2.4374 1.00 1192 131 0.2809 0.3203 REMARK 3 6 2.4374 - 2.2937 1.00 1161 138 0.2653 0.3265 REMARK 3 7 2.2937 - 2.1790 0.90 1069 108 0.2837 0.3385 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) : 0.290 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.790 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 : 0.003 1474 REMARK 3 ANGLE : 0.477 1988 REMARK 3 CHIRALITY : 0.047 216 REMARK 3 PLANARITY : 0.003 256 REMARK 3 DIHEDRAL : 2.739 892 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 9ILD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 02-JUL-24. REMARK 100 THE DEPOSITION ID IS D_1300049070. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-JUN-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 : BL18U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.987 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 : XIA2 REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9260 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.179 REMARK 200 RESOLUTION RANGE LOW (A) : 39.206 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 13.10 REMARK 200 R MERGE (I) : 0.11700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.18 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.30 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.83900 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.22 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.02 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M NH4AC, 0.1 M NAAC (PH 4.6) AND REMARK 280 30% PEG 4000, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 26.02550 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 29.80300 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.42150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 29.80300 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.02550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 27.42150 REMARK 290 SMTRY3 4 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2960 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9000 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -51.0 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 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 ASN A 2 REMARK 465 VAL A 155 REMARK 465 SER A 156 REMARK 465 GLY B 35 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 MET A 154 CG SD CE REMARK 470 ILE B 9 CG1 CG2 CD1 REMARK 470 THR B 31 OG1 CG2 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 LYS A 144 -108.18 55.52 REMARK 500 THR B 31 83.92 60.11 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 102 NE2 REMARK 620 2 HOH B 103 O 117.1 REMARK 620 N 1 DBREF1 9ILD A 1 156 UNP A0A3J1GR98_ECOLX DBREF2 9ILD A A0A3J1GR98 1 156 DBREF1 9ILD B 9 35 UNP A0A7I8YYL1_ECOLX DBREF2 9ILD B A0A7I8YYL1 264 290 SEQRES 1 A 156 MET ASN MET ASN GLU LEU VAL PHE ILE ASP ASP PHE ASP SEQRES 2 A 156 ASN HIS VAL VAL ILE MET SER GLU VAL VAL MET ARG LEU SEQRES 3 A 156 ASN SER TYR ARG GLN THR HIS TYR THR SER THR GLU SER SEQRES 4 A 156 GLY GLY THR LEU ILE GLY GLU ARG ARG GLY GLN HIS LEU SEQRES 5 A 156 VAL ILE THR HIS ILE SER GLU PRO GLY GLN ASP ASP VAL SEQRES 6 A 156 ARG ASN ARG THR GLY LEU GLU ARG LYS GLY ILE HIS HIS SEQRES 7 A 156 GLN GLN LYS VAL ASN ASP LEU PHE GLN GLN SER ASN GLY SEQRES 8 A 156 PHE ILE VAL TYR LEU GLY GLU TRP HIS THR HIS PRO GLU SEQRES 9 A 156 ASP PHE PRO HIS PRO SER PHE ILE ASP ILE LYS SER TRP SEQRES 10 A 156 VAL MET GLY ILE VAL ALA THR GLU PRO MET ILE MET LEU SEQRES 11 A 156 ILE VAL GLY ARG LYS ASP ILE TRP ILE GLY LYS LYS ILE SEQRES 12 A 156 LYS ASN ASP ILE LYS LYS LEU LYS LYS LYS MET VAL SER SEQRES 1 B 27 ILE ALA ALA ALA PRO ALA PHE HIS VAL SER PRO SER ARG SEQRES 2 B 27 GLU PRO GLU PRO ARG LYS ILE ASN LYS THR MET VAL SER SEQRES 3 B 27 GLY HET ZN A 201 1 HETNAM ZN ZINC ION FORMUL 3 ZN ZN 2+ FORMUL 4 HOH *48(H2 O) HELIX 1 AA1 MET A 19 SER A 28 1 10 HELIX 2 AA2 GLY A 75 SER A 89 1 15 HELIX 3 AA3 SER A 110 ILE A 121 1 12 HELIX 4 AA4 ALA B 11 HIS B 16 1 6 SHEET 1 AA1 9 ASP A 146 LYS A 149 0 SHEET 2 AA1 9 ILE A 137 ILE A 143 -1 N LYS A 141 O LYS A 148 SHEET 3 AA1 9 MET A 127 VAL A 132 -1 N ILE A 131 O TRP A 138 SHEET 4 AA1 9 VAL A 94 THR A 101 1 N HIS A 100 O VAL A 132 SHEET 5 AA1 9 GLY A 40 ARG A 48 -1 N LEU A 43 O LEU A 96 SHEET 6 AA1 9 HIS A 51 ILE A 57 -1 O VAL A 53 N GLU A 46 SHEET 7 AA1 9 HIS A 15 ILE A 18 1 N VAL A 17 O ILE A 54 SHEET 8 AA1 9 LEU A 6 ILE A 9 -1 N PHE A 8 O VAL A 16 SHEET 9 AA1 9 LYS A 151 LYS A 152 -1 O LYS A 151 N ILE A 9 SHEET 1 AA2 3 VAL A 65 ARG A 66 0 SHEET 2 AA2 3 LEU A 71 ARG A 73 -1 O GLU A 72 N VAL A 65 SHEET 3 AA2 3 MET B 32 VAL B 33 -1 O MET B 32 N ARG A 73 LINK NE2 HIS A 102 ZN ZN A 201 1555 1555 2.52 LINK ZN ZN A 201 O HOH B 103 1555 1555 2.08 CRYST1 52.051 54.843 59.606 90.00 90.00 90.00 P 21 21 21 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 0.019212 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018234 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016777 0.00000