HEADER TRANSCRIPTION/DNA 09-AUG-20 7CQA OBSLTE 20-OCT-21 7CQA 7VJQ TITLE PECTOBACTERIUM PHAGE ZF40 APO-ACA2 COMPLEXED WITH 26BP DNA SUBSTRATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: UNCHARACTERIZED PROTEIN ACA2; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (27-MER); COMPND 7 CHAIN: C; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: DNA (27-MER); COMPND 11 CHAIN: D; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PECTOBACTERIUM PHAGE ZF40; SOURCE 3 ORGANISM_TAXID: 1127516; SOURCE 4 GENE: ZF40_0030; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 SYNTHETIC: YES; SOURCE 9 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 10 ORGANISM_TAXID: 32630; SOURCE 11 MOL_ID: 3; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 14 ORGANISM_TAXID: 32630 KEYWDS ANTI-CRISPR, ACA2, ANTI-CRISPR-ASSOCIATED PROTEIN, CRISPR, KEYWDS 2 REPRESSION, COMPLEX, TRANSCRIPTION, TRANSCRIPTION-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Y.H.LIU,L.S.ZHANG,B.X.WU,H.D.HUANG REVDAT 2 20-OCT-21 7CQA 1 OBSLTE REVDAT 1 11-AUG-21 7CQA 0 JRNL AUTH Y.H.LIU,L.S.ZHANG,B.X.WU,H.D.HUANG JRNL TITL PECTOBACTERIUM PHAGE ZF40 APO-ACA2 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.50 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 30516 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.209 REMARK 3 R VALUE (WORKING SET) : 0.208 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL 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 2.5807 - 2.5000 0.99 0 0 0.3991 0.4334 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 79.49 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 : 0.009 3215 REMARK 3 ANGLE : 1.036 4582 REMARK 3 CHIRALITY : 0.050 501 REMARK 3 PLANARITY : 0.007 400 REMARK 3 DIHEDRAL : 25.332 1733 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 7CQA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 19-AUG-20. REMARK 100 THE DEPOSITION ID IS D_1300018054. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JUL-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) : 0.97915 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 : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33841 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.420 REMARK 200 RESOLUTION RANGE LOW (A) : 42.080 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : 0.12300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.42 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.60 REMARK 200 R MERGE FOR SHELL (I) : 1.49100 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: 7CQ8 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 76.05 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 5.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS PH8.0, 1.6M LI2SO4, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 64.76000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 84.15500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 64.76000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 84.15500 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7760 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19690 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -94.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 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 DG D 7 O3' DG D 7 C3' -0.036 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES 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,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) 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 ATM2 ATM3 REMARK 500 DC C 4 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 DT C 6 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 DG C 7 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES REMARK 500 DA C 20 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 DA C 25 C3' - C2' - C1' ANGL. DEV. = -4.9 DEGREES REMARK 500 DT C 26 C3' - C2' - C1' ANGL. DEV. = -6.1 DEGREES REMARK 500 DT C 26 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 DA D 1 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 DG D 7 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 DA D 20 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 REMARK 500 REMARK: NULL DBREF 7CQA A 1 116 UNP H9C180 H9C180_9CAUD 1 116 DBREF 7CQA B 1 116 UNP H9C180 H9C180_9CAUD 1 116 DBREF 7CQA C 1 27 PDB 7CQA 7CQA 1 27 DBREF 7CQA D 1 27 PDB 7CQA 7CQA 1 27 SEQADV 7CQA PRO A -3 UNP H9C180 EXPRESSION TAG SEQADV 7CQA LEU A -2 UNP H9C180 EXPRESSION TAG SEQADV 7CQA GLY A -1 UNP H9C180 EXPRESSION TAG SEQADV 7CQA SER A 0 UNP H9C180 EXPRESSION TAG SEQADV 7CQA PRO B -3 UNP H9C180 EXPRESSION TAG SEQADV 7CQA LEU B -2 UNP H9C180 EXPRESSION TAG SEQADV 7CQA GLY B -1 UNP H9C180 EXPRESSION TAG SEQADV 7CQA SER B 0 UNP H9C180 EXPRESSION TAG SEQRES 1 A 120 PRO LEU GLY SER MET THR ASN LYS GLU LEU GLN ALA ILE SEQRES 2 A 120 ARG LYS LEU LEU MET LEU ASP VAL SER GLU ALA ALA GLU SEQRES 3 A 120 HIS ILE GLY ARG VAL SER ALA ARG SER TRP GLN TYR TRP SEQRES 4 A 120 GLU SER GLY ARG SER ALA VAL PRO ASP ASP VAL GLU GLN SEQRES 5 A 120 GLU MET LEU ASP LEU ALA SER VAL ARG ILE GLU MET MET SEQRES 6 A 120 SER ALA ILE ASP LYS ARG LEU ALA ASP GLY GLU ARG PRO SEQRES 7 A 120 LYS LEU ARG PHE TYR ASN LYS LEU ASP GLU TYR LEU ALA SEQRES 8 A 120 ASP ASN PRO ASP HIS ASN VAL ILE GLY TRP ARG LEU SER SEQRES 9 A 120 GLN SER VAL ALA ALA LEU TYR TYR THR GLU GLY HIS ALA SEQRES 10 A 120 ASP LEU ILE SEQRES 1 B 120 PRO LEU GLY SER MET THR ASN LYS GLU LEU GLN ALA ILE SEQRES 2 B 120 ARG LYS LEU LEU MET LEU ASP VAL SER GLU ALA ALA GLU SEQRES 3 B 120 HIS ILE GLY ARG VAL SER ALA ARG SER TRP GLN TYR TRP SEQRES 4 B 120 GLU SER GLY ARG SER ALA VAL PRO ASP ASP VAL GLU GLN SEQRES 5 B 120 GLU MET LEU ASP LEU ALA SER VAL ARG ILE GLU MET MET SEQRES 6 B 120 SER ALA ILE ASP LYS ARG LEU ALA ASP GLY GLU ARG PRO SEQRES 7 B 120 LYS LEU ARG PHE TYR ASN LYS LEU ASP GLU TYR LEU ALA SEQRES 8 B 120 ASP ASN PRO ASP HIS ASN VAL ILE GLY TRP ARG LEU SER SEQRES 9 B 120 GLN SER VAL ALA ALA LEU TYR TYR THR GLU GLY HIS ALA SEQRES 10 B 120 ASP LEU ILE SEQRES 1 C 27 DT DT DG DC DT DT DG DT DT DC DG DC DG SEQRES 2 C 27 DA DT DT DG DC DG DA DA DC DA DT DA DT SEQRES 3 C 27 DA SEQRES 1 D 27 DA DT DA DT DA DT DG DT DT DC DG DC DA SEQRES 2 D 27 DA DT DC DG DC DG DA DA DC DA DA DG DC SEQRES 3 D 27 DA HET SO4 A 201 5 HET SO4 A 202 5 HET SO4 B 201 5 HET SO4 B 202 5 HETNAM SO4 SULFATE ION FORMUL 5 SO4 4(O4 S 2-) FORMUL 9 HOH *5(H2 O) HELIX 1 AA1 THR A 2 LEU A 13 1 12 HELIX 2 AA2 ASP A 16 ILE A 24 1 9 HELIX 3 AA3 SER A 28 GLY A 38 1 11 HELIX 4 AA4 PRO A 43 ASP A 70 1 28 HELIX 5 AA5 LYS A 81 ASP A 88 1 8 HELIX 6 AA6 ASN A 93 GLU A 110 1 18 HELIX 7 AA7 THR B 2 LEU B 13 1 12 HELIX 8 AA8 ASP B 16 ILE B 24 1 9 HELIX 9 AA9 SER B 28 GLY B 38 1 11 HELIX 10 AB1 PRO B 43 ASP B 70 1 28 HELIX 11 AB2 LYS B 81 ASP B 88 1 8 HELIX 12 AB3 ASN B 93 GLU B 110 1 18 SHEET 1 AA1 2 LYS A 75 ARG A 77 0 SHEET 2 AA1 2 ASP A 114 ILE A 116 1 O ILE A 116 N LEU A 76 SHEET 1 AA2 2 LYS B 75 ARG B 77 0 SHEET 2 AA2 2 ASP B 114 ILE B 116 1 O ASP B 114 N LEU B 76 CRYST1 129.520 168.310 41.440 90.00 89.98 90.00 C 1 2 1 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 0.007721 0.000000 -0.000003 0.00000 SCALE2 0.000000 0.005941 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024131 0.00000