HEADER TRANSCRIPTION 05-JUL-21 7FA3 TITLE SELENOMETHIONINE-DERIVED STRUCTURE OF ACA1 IN PSEUDOMONAS PHAGE JBD30 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ACA1; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS PHAGE JBD30; SOURCE 3 ORGANISM_TAXID: 1223260; SOURCE 4 GENE: JBD30_036; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CRISPR, ANTI-CRISPR, ANTI-CRISPR-ASSOCIATED, DNA BINDING, KEYWDS 2 AUTOREGULATION, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR Y.LIU,L.ZHANG,B.WU,H.HUANG REVDAT 3 16-OCT-24 7FA3 1 REMARK REVDAT 2 02-FEB-22 7FA3 1 AUTHOR JRNL REVDAT 1 21-JUL-21 7FA3 0 SPRSDE 21-JUL-21 7FA3 7C0B JRNL AUTH Y.LIU,L.ZHANG,M.GUO,L.CHEN,B.WU,H.HUANG JRNL TITL STRUCTURAL BASIS FOR ANTI-CRISPR REPRESSION MEDIATED BY JRNL TITL 2 BACTERIAL OPERON PROTEINS ACA1 AND ACA2. JRNL REF J.BIOL.CHEM. V. 297 01357 2021 JRNL REFN ESSN 1083-351X JRNL PMID 34756887 JRNL DOI 10.1016/J.JBC.2021.101357 REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.10_2155 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) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 22.05 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.362 REMARK 3 COMPLETENESS FOR RANGE (%) : 87.4 REMARK 3 NUMBER OF REFLECTIONS : 11611 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.200 REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.220 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.728 REMARK 3 FREE R VALUE TEST SET COUNT : 549 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 22.0510 - 2.9297 1.00 3271 172 0.1917 0.2132 REMARK 3 2 2.9297 - 2.3262 1.00 3159 141 0.2162 0.2179 REMARK 3 3 2.3262 - 2.0324 0.85 2641 129 0.1931 0.2280 REMARK 3 4 2.0324 - 1.8470 0.64 1991 107 0.1979 0.2561 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) : 0.096 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.863 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.93 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.74 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 : 0.008 1159 REMARK 3 ANGLE : 0.969 1571 REMARK 3 CHIRALITY : 0.049 166 REMARK 3 PLANARITY : 0.008 210 REMARK 3 DIHEDRAL : 21.976 725 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN 'A' AND RESID 7 THROUGH 77) REMARK 3 ORIGIN FOR THE GROUP (A): 19.4544 -4.7027 -0.8447 REMARK 3 T TENSOR REMARK 3 T11: 0.0715 T22: 0.1157 REMARK 3 T33: 0.1741 T12: -0.0090 REMARK 3 T13: -0.0115 T23: -0.0565 REMARK 3 L TENSOR REMARK 3 L11: 3.2369 L22: 3.5196 REMARK 3 L33: 1.7353 L12: -0.2138 REMARK 3 L13: 0.0970 L23: -0.2082 REMARK 3 S TENSOR REMARK 3 S11: 0.1815 S12: -0.1505 S13: 0.1461 REMARK 3 S21: -0.0421 S22: 0.0432 S23: -0.6642 REMARK 3 S31: -0.0256 S32: 0.2553 S33: -0.1204 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN 'B' AND RESID 6 THROUGH 77) REMARK 3 ORIGIN FOR THE GROUP (A): 2.2582 4.5808 -1.5462 REMARK 3 T TENSOR REMARK 3 T11: 0.1562 T22: 0.1553 REMARK 3 T33: 0.1205 T12: 0.0740 REMARK 3 T13: 0.0345 T23: -0.0252 REMARK 3 L TENSOR REMARK 3 L11: 2.8759 L22: 4.6941 REMARK 3 L33: 1.6136 L12: 0.2007 REMARK 3 L13: -0.6597 L23: 0.7486 REMARK 3 S TENSOR REMARK 3 S11: 0.1200 S12: 0.0807 S13: 0.2465 REMARK 3 S21: -0.3956 S22: -0.0508 S23: 0.3581 REMARK 3 S31: -0.4008 S32: -0.4751 S33: 0.0042 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 (RESSEQ 8:32 OR RESSEQ 34:43 REMARK 3 OR (RESID 44 AND (NAME N OR NAME CA OR REMARK 3 NAME C OR NAME O OR NAME CB )) OR RESSEQ REMARK 3 45:46 OR RESSEQ 48:53 OR RESSEQ 56:77)) REMARK 3 SELECTION : (CHAIN B AND (RESSEQ 8:32 OR RESSEQ 34:46 REMARK 3 OR RESSEQ 48:53 OR RESSEQ 56:77)) REMARK 3 ATOM PAIRS NUMBER : NULL REMARK 3 RMSD : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7FA3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-JUL-21. REMARK 100 THE DEPOSITION ID IS D_1300023134. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-DEC-19 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 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11611 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.846 REMARK 200 RESOLUTION RANGE LOW (A) : 22.051 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 11.90 REMARK 200 R MERGE (I) : 0.08400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 4.5400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.92 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.6 REMARK 200 DATA REDUNDANCY IN SHELL : 9.30 REMARK 200 R MERGE FOR SHELL (I) : 0.64200 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: SAD 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 (%): 37.57 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.97 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM FORMATE; 20% (W/V) PEG REMARK 280 3,350., VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K 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 22.71450 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 32.37100 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.22150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 32.37100 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.71450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 25.22150 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: 1370 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7950 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -16.0 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 GLY A -4 REMARK 465 PRO A -3 REMARK 465 LEU A -2 REMARK 465 GLY A -1 REMARK 465 SER A 0 REMARK 465 MSE A 1 REMARK 465 ARG A 2 REMARK 465 PHE A 3 REMARK 465 PRO A 4 REMARK 465 GLY A 5 REMARK 465 VAL A 6 REMARK 465 SER A 78 REMARK 465 ALA A 79 REMARK 465 GLY B -4 REMARK 465 PRO B -3 REMARK 465 LEU B -2 REMARK 465 GLY B -1 REMARK 465 SER B 0 REMARK 465 MSE B 1 REMARK 465 ARG B 2 REMARK 465 PHE B 3 REMARK 465 PRO B 4 REMARK 465 GLY B 5 REMARK 465 SER B 78 REMARK 465 ALA B 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 B 44 CG CD NE CZ NH1 NH2 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 NZ LYS B 26 O HOH B 101 1.96 REMARK 500 O HOH A 137 O HOH A 147 2.19 REMARK 500 REMARK 500 REMARK: NULL DBREF 7FA3 A 1 79 UNP L7P845 L7P845_9CAUD 1 79 DBREF 7FA3 B 1 79 UNP L7P845 L7P845_9CAUD 1 79 SEQADV 7FA3 GLY A -4 UNP L7P845 EXPRESSION TAG SEQADV 7FA3 PRO A -3 UNP L7P845 EXPRESSION TAG SEQADV 7FA3 LEU A -2 UNP L7P845 EXPRESSION TAG SEQADV 7FA3 GLY A -1 UNP L7P845 EXPRESSION TAG SEQADV 7FA3 SER A 0 UNP L7P845 EXPRESSION TAG SEQADV 7FA3 GLY B -4 UNP L7P845 EXPRESSION TAG SEQADV 7FA3 PRO B -3 UNP L7P845 EXPRESSION TAG SEQADV 7FA3 LEU B -2 UNP L7P845 EXPRESSION TAG SEQADV 7FA3 GLY B -1 UNP L7P845 EXPRESSION TAG SEQADV 7FA3 SER B 0 UNP L7P845 EXPRESSION TAG SEQRES 1 A 84 GLY PRO LEU GLY SER MSE ARG PHE PRO GLY VAL LYS THR SEQRES 2 A 84 PRO ASP ALA SER ASN HIS ASP PRO ASP PRO ARG TYR LEU SEQRES 3 A 84 ARG GLY LEU LEU LYS LYS ALA GLY ILE SER GLN ARG ARG SEQRES 4 A 84 ALA ALA GLU LEU LEU GLY LEU SER ASP ARG VAL MSE ARG SEQRES 5 A 84 TYR TYR LEU SER GLU ASP ILE LYS GLU GLY TYR ARG PRO SEQRES 6 A 84 ALA PRO TYR THR VAL GLN PHE ALA LEU GLU CYS LEU ALA SEQRES 7 A 84 ASN ASP PRO PRO SER ALA SEQRES 1 B 84 GLY PRO LEU GLY SER MSE ARG PHE PRO GLY VAL LYS THR SEQRES 2 B 84 PRO ASP ALA SER ASN HIS ASP PRO ASP PRO ARG TYR LEU SEQRES 3 B 84 ARG GLY LEU LEU LYS LYS ALA GLY ILE SER GLN ARG ARG SEQRES 4 B 84 ALA ALA GLU LEU LEU GLY LEU SER ASP ARG VAL MSE ARG SEQRES 5 B 84 TYR TYR LEU SER GLU ASP ILE LYS GLU GLY TYR ARG PRO SEQRES 6 B 84 ALA PRO TYR THR VAL GLN PHE ALA LEU GLU CYS LEU ALA SEQRES 7 B 84 ASN ASP PRO PRO SER ALA MODRES 7FA3 MSE A 46 MET MODIFIED RESIDUE MODRES 7FA3 MSE B 46 MET MODIFIED RESIDUE HET MSE A 46 8 HET MSE B 46 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 2(C5 H11 N O2 SE) FORMUL 3 HOH *87(H2 O) HELIX 1 AA1 ASP A 10 HIS A 14 5 5 HELIX 2 AA2 ASP A 17 GLY A 29 1 13 HELIX 3 AA3 SER A 31 GLY A 40 1 10 HELIX 4 AA4 SER A 42 SER A 51 1 10 HELIX 5 AA5 PRO A 62 ASP A 75 1 14 HELIX 6 AA6 ASP B 10 HIS B 14 5 5 HELIX 7 AA7 ASP B 17 GLY B 29 1 13 HELIX 8 AA8 SER B 31 GLY B 40 1 10 HELIX 9 AA9 SER B 42 SER B 51 1 10 HELIX 10 AB1 PRO B 62 ASP B 75 1 14 LINK C VAL A 45 N MSE A 46 1555 1555 1.33 LINK C MSE A 46 N ARG A 47 1555 1555 1.34 LINK C VAL B 45 N MSE B 46 1555 1555 1.33 LINK C MSE B 46 N ARG B 47 1555 1555 1.33 CRYST1 45.429 50.443 64.742 90.00 90.00 90.00 P 21 21 21 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 0.022012 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019824 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015446 0.00000