HEADER TRANSCRIPTION 28-SEP-21 7VJN TITLE CRYSTAL STRUCTURE OF ANTI-CRISPR-ASSOCIATED PROTEIN ACA1 IN TITLE 2 PSEUDOMONAS PHAGE JBD30 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ANTI-CRISPR-ASSOCIATED PROTEIN ACA1; COMPND 3 CHAIN: B, A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: 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 DNA BINDING, AUTOREGULATION, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR Y.H.LIU,L.S.ZHANG,B.X.WU,H.D.HUANG REVDAT 3 29-NOV-23 7VJN 1 REMARK REVDAT 2 02-FEB-22 7VJN 1 JRNL REVDAT 1 13-OCT-21 7VJN 0 SPRSDE 13-OCT-21 7VJN 7FA2 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. 1.80 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.83 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 14401 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.192 REMARK 3 R VALUE (WORKING SET) : 0.190 REMARK 3 FREE R VALUE : 0.215 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.060 REMARK 3 FREE R VALUE TEST SET COUNT : 729 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 39.8290 - 3.0761 1.00 2845 171 0.1783 0.1999 REMARK 3 2 3.0761 - 2.4417 1.00 2765 139 0.1986 0.2148 REMARK 3 3 2.4417 - 2.1331 0.99 2698 143 0.1938 0.2195 REMARK 3 4 2.1331 - 1.9381 1.00 2686 152 0.2001 0.2566 REMARK 3 5 1.9381 - 1.7992 0.99 2678 124 0.2400 0.2788 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) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.920 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 27.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.23 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 : 0.013 1129 REMARK 3 ANGLE : 1.211 1532 REMARK 3 CHIRALITY : 0.070 162 REMARK 3 PLANARITY : 0.008 206 REMARK 3 DIHEDRAL : 2.106 704 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 7VJN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-OCT-21. REMARK 100 THE DEPOSITION ID IS D_1300024766. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-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 V705C REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14457 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.799 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 10.20 REMARK 200 R MERGE (I) : 0.06900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 29.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 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: 7FA3 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.82 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M DI-POTASSIUM HYDROGEN PHOSPHATE, REMARK 280 20% (W/V) PEG 3350, VAPOR DIFFUSION, 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 22.84900 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 32.46200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.21750 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 32.46200 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.84900 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 25.21750 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: 1350 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7590 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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 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 MET B 1 REMARK 465 ARG B 2 REMARK 465 PHE B 3 REMARK 465 PRO B 4 REMARK 465 GLY B 5 REMARK 465 VAL B 6 REMARK 465 SER B 78 REMARK 465 ALA B 79 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 MET A 1 REMARK 465 ARG A 2 REMARK 465 PHE A 3 REMARK 465 PRO A 4 REMARK 465 GLY A 5 REMARK 465 LYS A 55 REMARK 465 GLU A 56 REMARK 465 GLY A 57 REMARK 465 SER A 78 REMARK 465 ALA A 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 LYS B 55 CG CD CE NZ REMARK 470 VAL A 6 CG1 CG2 REMARK 470 LYS A 7 CG CD CE NZ REMARK 470 ILE A 54 CG1 CG2 CD1 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 ASN B 74 NH2 ARG A 59 2575 2.09 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 ASP A 15 89.95 -152.21 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 B 173 DISTANCE = 6.38 ANGSTROMS DBREF 7VJN B 1 79 UNP L7P845 L7P845_9CAUD 1 79 DBREF 7VJN A 1 79 UNP L7P845 L7P845_9CAUD 1 79 SEQADV 7VJN GLY B -4 UNP L7P845 EXPRESSION TAG SEQADV 7VJN PRO B -3 UNP L7P845 EXPRESSION TAG SEQADV 7VJN LEU B -2 UNP L7P845 EXPRESSION TAG SEQADV 7VJN GLY B -1 UNP L7P845 EXPRESSION TAG SEQADV 7VJN SER B 0 UNP L7P845 EXPRESSION TAG SEQADV 7VJN SER B 71 UNP L7P845 CYS 71 ENGINEERED MUTATION SEQADV 7VJN GLY A -4 UNP L7P845 EXPRESSION TAG SEQADV 7VJN PRO A -3 UNP L7P845 EXPRESSION TAG SEQADV 7VJN LEU A -2 UNP L7P845 EXPRESSION TAG SEQADV 7VJN GLY A -1 UNP L7P845 EXPRESSION TAG SEQADV 7VJN SER A 0 UNP L7P845 EXPRESSION TAG SEQADV 7VJN SER A 71 UNP L7P845 CYS 71 ENGINEERED MUTATION SEQRES 1 B 84 GLY PRO LEU GLY SER MET 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 MET 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 SER LEU ALA SEQRES 7 B 84 ASN ASP PRO PRO SER ALA SEQRES 1 A 84 GLY PRO LEU GLY SER MET 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 MET 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 SER LEU ALA SEQRES 7 A 84 ASN ASP PRO PRO SER ALA FORMUL 3 HOH *131(H2 O) HELIX 1 AA1 ASP B 10 HIS B 14 5 5 HELIX 2 AA2 ASP B 17 GLY B 29 1 13 HELIX 3 AA3 SER B 31 GLY B 40 1 10 HELIX 4 AA4 SER B 42 SER B 51 1 10 HELIX 5 AA5 PRO B 62 ASP B 75 1 14 HELIX 6 AA6 ASP A 10 HIS A 14 5 5 HELIX 7 AA7 ASP A 17 GLY A 29 1 13 HELIX 8 AA8 SER A 31 GLY A 40 1 10 HELIX 9 AA9 SER A 42 SER A 51 1 10 HELIX 10 AB1 PRO A 62 ASP A 75 1 14 CRYST1 45.698 50.435 64.924 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 0.021883 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019828 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015403 0.00000