HEADER VIRAL PROTEIN 18-DEC-19 6TRI TITLE CI-MOR REPRESSOR-ANTIREPRESSOR COMPLEX OF THE TEMPERATE BACTERIOPHAGE TITLE 2 TP901-1 FROM LACTOCOCCUS LACTIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: CI; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: MOR; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LACTOCOCCUS PHAGE TP901-1; SOURCE 3 ORGANISM_TAXID: 35345; SOURCE 4 GENE: CI; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: LACTOCOCCUS PHAGE TP901-1; SOURCE 9 ORGANISM_TAXID: 35345; SOURCE 10 GENE: MOR; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS COMPLEX, REGULATION, DNA-BINDING, TEMPERATE VIRUS, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR K.K.RASMUSSEN,M.BLACKLEDGE,T.HERRMANN,M.R.JENSEN,L.LO LEGGIO REVDAT 4 24-JAN-24 6TRI 1 REMARK REVDAT 3 02-SEP-20 6TRI 1 JRNL REVDAT 2 26-AUG-20 6TRI 1 JRNL REVDAT 1 19-AUG-20 6TRI 0 JRNL AUTH K.K.RASMUSSEN,A.PALENCIA,A.K.VARMING,H.EL-WALI,E.BOERI ERBA, JRNL AUTH 2 M.BLACKLEDGE,K.HAMMER,T.HERRMANN,M.KILSTRUP,L.LO LEGGIO, JRNL AUTH 3 M.R.JENSEN JRNL TITL REVEALING THE MECHANISM OF REPRESSOR INACTIVATION DURING JRNL TITL 2 SWITCHING OF A TEMPERATE BACTERIOPHAGE. JRNL REF PROC.NATL.ACAD.SCI.USA V. 117 20576 2020 JRNL REFN ESSN 1091-6490 JRNL PMID 32788352 JRNL DOI 10.1073/PNAS.2005218117 REMARK 2 REMARK 2 RESOLUTION. 2.28 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.28 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.88 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 7282 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.190 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.217 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 365 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 40.8700 - 3.2800 0.00 0 126 0.0000 0.1655 REMARK 3 2 3.2800 - 2.6000 0.00 0 122 0.0000 0.3171 REMARK 3 3 2.6000 - 2.2770 0.00 0 117 0.0000 0.3260 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 28.300 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 58.29 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 : 0.002 1222 REMARK 3 ANGLE : 0.642 1648 REMARK 3 CHIRALITY : 0.021 188 REMARK 3 PLANARITY : 0.004 204 REMARK 3 DIHEDRAL : 10.799 460 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A REMARK 3 ORIGIN FOR THE GROUP (A): 10.3585 41.7255 6.0448 REMARK 3 T TENSOR REMARK 3 T11: 0.2272 T22: 0.3120 REMARK 3 T33: 0.3875 T12: 0.0023 REMARK 3 T13: 0.0184 T23: 0.0032 REMARK 3 L TENSOR REMARK 3 L11: 7.0564 L22: 6.1440 REMARK 3 L33: 9.5254 L12: 0.9752 REMARK 3 L13: 1.1269 L23: -0.2618 REMARK 3 S TENSOR REMARK 3 S11: -0.0176 S12: 0.0739 S13: 0.1541 REMARK 3 S21: -0.0534 S22: -0.0032 S23: -0.0442 REMARK 3 S31: -0.3113 S32: 0.3060 S33: 0.0547 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN B REMARK 3 ORIGIN FOR THE GROUP (A): -5.7927 31.2344 14.8720 REMARK 3 T TENSOR REMARK 3 T11: 0.2815 T22: 0.2527 REMARK 3 T33: 0.3611 T12: -0.0689 REMARK 3 T13: 0.0055 T23: 0.0046 REMARK 3 L TENSOR REMARK 3 L11: 8.1192 L22: 5.0523 REMARK 3 L33: 6.0800 L12: -1.4693 REMARK 3 L13: -0.8413 L23: -1.1533 REMARK 3 S TENSOR REMARK 3 S11: -0.0197 S12: -0.0727 S13: -0.2458 REMARK 3 S21: 0.0144 S22: 0.0866 S23: -0.0616 REMARK 3 S31: -0.0038 S32: 0.1871 S33: -0.1000 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 6TRI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 19-DEC-19. REMARK 100 THE DEPOSITION ID IS D_1292105697. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-FEB-18 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 : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.972 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 : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7285 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.277 REMARK 200 RESOLUTION RANGE LOW (A) : 42.700 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 16.10 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.9500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.28 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.41 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: PHENIX REMARK 200 STARTING MODEL: 5A7L + MOR NMR STRUCTURE (JUST DEPOSITED 6TO6) REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.39 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M LITHIUM SULFATE, 0.1 M BIS-TRIS REMARK 280 PH 5.5, 25% PEG 3350 IN RESERVOIR, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 3 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 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: 1630 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7950 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -33.0 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 S SO4 B 101 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 210 LIES ON A SPECIAL POSITION. 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 GLU A 81 REMARK 465 SER A 82 REMARK 465 SER A 83 REMARK 465 LYS A 84 REMARK 465 ILE A 85 REMARK 465 GLU A 86 REMARK 465 ASN A 87 REMARK 465 ASP A 88 REMARK 465 SER A 89 REMARK 465 HIS A 90 REMARK 465 HIS A 91 REMARK 465 HIS A 92 REMARK 465 HIS A 93 REMARK 465 HIS A 94 REMARK 465 HIS A 95 REMARK 465 GLY B -1 REMARK 465 SER B 0 REMARK 465 MET B 1 REMARK 465 VAL B 71 REMARK 465 HIS B 72 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 THR A 3 -149.50 -131.69 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 101 DBREF 6TRI A 1 89 UNP O48503 O48503_9CAUD 1 89 DBREF 6TRI B 1 72 UNP O48504 O48504_9CAUD 1 72 SEQADV 6TRI GLN A 2 UNP O48503 LYS 2 CONFLICT SEQADV 6TRI HIS A 90 UNP O48503 EXPRESSION TAG SEQADV 6TRI HIS A 91 UNP O48503 EXPRESSION TAG SEQADV 6TRI HIS A 92 UNP O48503 EXPRESSION TAG SEQADV 6TRI HIS A 93 UNP O48503 EXPRESSION TAG SEQADV 6TRI HIS A 94 UNP O48503 EXPRESSION TAG SEQADV 6TRI HIS A 95 UNP O48503 EXPRESSION TAG SEQADV 6TRI GLY B -1 UNP O48504 EXPRESSION TAG SEQADV 6TRI SER B 0 UNP O48504 EXPRESSION TAG SEQRES 1 A 95 MET GLN THR ASP THR SER ASN ARG LEU LYS GLN ILE MET SEQRES 2 A 95 ALA GLU ARG ASN LEU LYS GLN VAL ASP ILE LEU ASN LEU SEQRES 3 A 95 SER ILE PRO PHE GLN LYS LYS PHE GLY ILE LYS LEU SER SEQRES 4 A 95 LYS SER THR LEU SER GLN TYR VAL ASN SER VAL GLN SER SEQRES 5 A 95 PRO ASP GLN ASN ARG ILE TYR LEU LEU ALA LYS THR LEU SEQRES 6 A 95 GLY VAL SER GLU ALA TRP LEU MET GLY PHE ASP VAL PRO SEQRES 7 A 95 MET VAL GLU SER SER LYS ILE GLU ASN ASP SER HIS HIS SEQRES 8 A 95 HIS HIS HIS HIS SEQRES 1 B 74 GLY SER MET SER TYR ASP TYR SER SER LEU LEU GLY LYS SEQRES 2 B 74 ILE THR GLU LYS CYS GLY THR GLN TYR ASN PHE ALA ILE SEQRES 3 B 74 ALA MET GLY LEU SER GLU ARG THR VAL SER LEU LYS LEU SEQRES 4 B 74 ASN ASP LYS VAL THR TRP LYS ASP ASP GLU ILE LEU LYS SEQRES 5 B 74 ALA VAL HIS VAL LEU GLU LEU ASN PRO GLN ASP ILE PRO SEQRES 6 B 74 LYS TYR PHE PHE ASN ALA LYS VAL HIS HET SO4 A 101 5 HET SO4 B 101 5 HETNAM SO4 SULFATE ION FORMUL 3 SO4 2(O4 S 2-) FORMUL 5 HOH *20(H2 O) HELIX 1 AA1 ASP A 4 ARG A 16 1 13 HELIX 2 AA2 LYS A 19 GLY A 35 1 17 HELIX 3 AA3 SER A 39 ASN A 48 1 10 HELIX 4 AA4 ASP A 54 GLY A 66 1 13 HELIX 5 AA5 SER A 68 MET A 73 1 6 HELIX 6 AA6 TYR B 5 CYS B 16 1 12 HELIX 7 AA7 THR B 18 GLY B 27 1 10 HELIX 8 AA8 SER B 29 ASN B 38 1 10 HELIX 9 AA9 LYS B 44 GLU B 56 1 13 HELIX 10 AB1 ASN B 58 GLN B 60 5 3 HELIX 11 AB2 ASP B 61 PHE B 67 1 7 SITE 1 AC1 5 GLN A 20 LYS A 40 ASN A 56 LYS B 40 SITE 2 AC1 5 THR B 42 SITE 1 AC2 1 ARG B 31 CRYST1 94.405 94.405 30.558 90.00 90.00 120.00 P 3 2 1 6 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 0.010593 0.006116 0.000000 0.00000 SCALE2 0.000000 0.012231 0.000000 0.00000 SCALE3 0.000000 0.000000 0.032725 0.00000