HEADER TRANSCRIPTION 22-DEC-12 3ZHM TITLE N-TERMINAL DOMAIN OF THE CI REPRESSOR FROM BACTERIOPHAGE TP901-1 IN TITLE 2 COMPLEX WITH THE OL2 OPERATOR HALF-SITE COMPND MOL_ID: 1; COMPND 2 MOLECULE: CI; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 2-74; COMPND 5 SYNONYM: CI REPRESSOR; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: 5'-D(*AP*GP*TP*TP*CP*AP*CP*GP*TP*TP*CP*AP*AP*GP COMPND 9 *TP*GP*CP*A)-3'; COMPND 10 CHAIN: B; COMPND 11 SYNONYM: OL2 OPERATOR HALF-SITE; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: 5'-D(*AP*CP*GP*TP*GP*AP*AP*CP*TP*TP*GP*CP*AP*CP COMPND 15 *TP*TP*GP*A)-3'; COMPND 16 CHAIN: C; COMPND 17 SYNONYM: OL2 OPERATOR HALF-SITE; COMPND 18 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LACTOCOCCUS PHAGE TP901-1; SOURCE 3 ORGANISM_TAXID: 35345; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: M15; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PQE-70; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: LACTOCOCCUS PHAGE TP901-1; SOURCE 11 ORGANISM_TAXID: 35345; SOURCE 12 MOL_ID: 3; SOURCE 13 SYNTHETIC: YES; SOURCE 14 ORGANISM_SCIENTIFIC: LACTOCOCCUS PHAGE TP901-1; SOURCE 15 ORGANISM_TAXID: 35345 KEYWDS TRANSCRIPTION, TRANSCRIPTION FACTOR, TRANSCRIPTION REGULATION EXPDTA X-RAY DIFFRACTION AUTHOR K.H.FRANDSEN,K.K.RASMUSSEN,J.N.POULSEN,L.LO LEGGIO REVDAT 3 20-DEC-23 3ZHM 1 REMARK REVDAT 2 01-APR-15 3ZHM 1 REMARK REVDAT 1 25-DEC-13 3ZHM 0 JRNL AUTH K.H.FRANDSEN,K.K.RASMUSSEN,M.R.JENSEN,K.HAMMER,M.PEDERSEN, JRNL AUTH 2 J.N.POULSEN,L.ARLETH,L.LO LEGGIO JRNL TITL BINDING OF THE N-TERMINAL DOMAIN OF THE LACTOCOCCAL JRNL TITL 2 BACTERIOPHAGE TP901-1 CI REPRESSOR TO ITS TARGET DNA: A JRNL TITL 3 CRYSTALLOGRAPHY, SMALL ANGLE SCATTERING, AND NUCLEAR JRNL TITL 4 MAGNETIC RESONANCE STUDY. JRNL REF BIOCHEMISTRY V. 52 6892 2013 JRNL REFN ISSN 0006-2960 JRNL PMID 24047404 JRNL DOI 10.1021/BI400439Y REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.91 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 4332 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.201 REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.218 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.370 REMARK 3 FREE R VALUE TEST SET COUNT : 445 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 33.9129 - 3.7491 1.00 1345 152 0.1726 0.1873 REMARK 3 2 3.7491 - 2.9763 1.00 1282 145 0.1992 0.2289 REMARK 3 3 2.9763 - 2.6002 1.00 1260 148 0.2548 0.2658 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) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.900 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.41 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 : 0.002 1057 REMARK 3 ANGLE : 0.671 1496 REMARK 3 CHIRALITY : 0.039 169 REMARK 3 PLANARITY : 0.002 127 REMARK 3 DIHEDRAL : 21.816 421 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 3ZHM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 22-DEC-12. REMARK 100 THE DEPOSITION ID IS D_1290055261. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.87 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4365 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 33.910 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.360 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 4.400 REMARK 200 R MERGE (I) : 0.16000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.74 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.60 REMARK 200 R MERGE FOR SHELL (I) : 0.49000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.700 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: PDB ENTRY 2R1J REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 7 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 14.93000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 33.91000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.03500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 33.91000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 14.93000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.03500 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2210 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7180 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -18.7 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 DT B 40 REMARK 465 DC B 41 REMARK 465 DA B 42 REMARK 465 DA B 43 REMARK 465 DG B 44 REMARK 465 DT B 45 REMARK 465 DG B 46 REMARK 465 DC B 47 REMARK 465 DA B 48 REMARK 465 DT C 11 REMARK 465 DG C 12 REMARK 465 DC C 13 REMARK 465 DA C 14 REMARK 465 DC C 15 REMARK 465 DT C 16 REMARK 465 DT C 17 REMARK 465 DG C 18 REMARK 465 DA C 19 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 DT C 10 C7 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 OH TYR A 46 OP1 DG C 4 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3ZHI RELATED DB: PDB REMARK 900 N-TERMINAL DOMAIN OF THE CI REPRESSOR FROM BACTERIOPHAGE TP901-1 REMARK 999 REMARK 999 SEQUENCE REMARK 999 OLIGONUCLEOTIDES WERE PURCHASED FROM TAG COPENHAGEN DBREF 3ZHM A 2 74 UNP O48503 O48503_9CAUD 2 74 DBREF 3ZHM B 31 48 PDB 3ZHM 3ZHM 31 48 DBREF 3ZHM C 2 19 PDB 3ZHM 3ZHM 2 19 SEQADV 3ZHM ARG A 75 UNP O48503 EXPRESSION TAG SEQADV 3ZHM SER A 76 UNP O48503 EXPRESSION TAG SEQADV 3ZHM HIS A 77 UNP O48503 EXPRESSION TAG SEQADV 3ZHM HIS A 78 UNP O48503 EXPRESSION TAG SEQADV 3ZHM HIS A 79 UNP O48503 EXPRESSION TAG SEQADV 3ZHM HIS A 80 UNP O48503 EXPRESSION TAG SEQRES 1 A 79 LYS THR ASP THR SER ASN ARG LEU LYS GLN ILE MET ALA SEQRES 2 A 79 GLU ARG ASN LEU LYS GLN VAL ASP ILE LEU ASN LEU SER SEQRES 3 A 79 ILE PRO PHE GLN LYS LYS PHE GLY ILE LYS LEU SER LYS SEQRES 4 A 79 SER THR LEU SER GLN TYR VAL ASN SER VAL GLN SER PRO SEQRES 5 A 79 ASP GLN ASN ARG ILE TYR LEU LEU ALA LYS THR LEU GLY SEQRES 6 A 79 VAL SER GLU ALA TRP LEU MET GLY ARG SER HIS HIS HIS SEQRES 7 A 79 HIS SEQRES 1 B 18 DA DG DT DT DC DA DC DG DT DT DC DA DA SEQRES 2 B 18 DG DT DG DC DA SEQRES 1 C 18 DA DC DG DT DG DA DA DC DT DT DG DC DA SEQRES 2 C 18 DC DT DT DG DA FORMUL 4 HOH *56(H2 O) HELIX 1 1 THR A 3 ARG A 16 1 14 HELIX 2 2 LYS A 19 GLY A 35 1 17 HELIX 3 3 SER A 39 ASN A 48 1 10 HELIX 4 4 ASP A 54 GLY A 66 1 13 HELIX 5 5 SER A 68 MET A 73 1 6 CRYST1 29.860 64.070 67.820 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 0.033490 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015608 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014745 0.00000