HEADER TRANSCRIPTION 21-DEC-12 3ZHI TITLE N-TERMINAL DOMAIN OF THE CI REPRESSOR FROM BACTERIOPHAGE TP901-1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CI; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: N-TERMINAL DOMAIN, RESIDUES 2-74; COMPND 5 SYNONYM: CI REPRESSOR; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LACTOCOCCUS PHAGE TP901-1; SOURCE 3 ORGANISM_TAXID: 35345; SOURCE 4 CELL: LACTOCOCCUS LACTIS; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: M15; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PQE-70 KEYWDS TRANSCRIPTION, TRANSCRIPTION REGULATION EXPDTA X-RAY DIFFRACTION AUTHOR K.H.FRANDSEN,K.K.RASMUSSEN,J.N.POULSEN,L.LO LEGGIO REVDAT 1 25-DEC-13 3ZHI 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. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VICENT 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 18.609 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.01 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.63 REMARK 3 NUMBER OF REFLECTIONS : 12594 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.1374 REMARK 3 R VALUE (WORKING SET) : 0.1351 REMARK 3 FREE R VALUE : 0.1826 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.0 REMARK 3 FREE R VALUE TEST SET COUNT : 628 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 18.6106 - 2.5383 0.98 3094 163 0.1387 0.1815 REMARK 3 2 2.5383 - 2.0155 0.98 2971 153 0.1261 0.1710 REMARK 3 3 2.0155 - 1.7610 0.99 2941 155 0.1279 0.1956 REMARK 3 4 1.7610 - 1.6001 1.00 2960 157 0.1484 0.2062 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) : 0.11 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.54 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.35 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 : 0.010 613 REMARK 3 ANGLE : 1.164 833 REMARK 3 CHIRALITY : 0.061 100 REMARK 3 PLANARITY : 0.005 103 REMARK 3 DIHEDRAL : 13.325 245 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 3ZHI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 23-DEC-12. REMARK 100 THE PDBE ID CODE IS EBI-55260. 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 : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97625 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12874 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.60 REMARK 200 RESOLUTION RANGE LOW (A) : 18.60 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.0 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 5.1 REMARK 200 R MERGE (I) : 0.04 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 26.49 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.70 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : 5.1 REMARK 200 R MERGE FOR SHELL (I) : 0.34 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.90 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.23 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.42 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.1M SODIUM CITRATE 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 14.81000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 35.75000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.79500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 35.75000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 14.81000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 21.79500 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 MET A 0 REMARK 465 LEU A 1 REMARK 465 ARG A 75 REMARK 465 SER A 76 REMARK 465 HIS A 77 REMARK 465 HIS A 78 REMARK 465 HIS A 79 REMARK 465 HIS A 80 REMARK 465 HIS A 81 REMARK 465 HIS A 82 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3ZHM RELATED DB: PDB REMARK 900 N-TERMINAL DOMAIN OF THE CI REPRESSOR FROM REMARK 900 BACTERIOPHAGE TP901-1 IN COMPLEX WITH THE OL2 OPERATOR REMARK 900 HALF-SITE DBREF 3ZHI A 2 74 UNP O48503 O48503_9CAUD 2 74 SEQADV 3ZHI MET A 0 UNP O48503 EXPRESSION TAG SEQADV 3ZHI LEU A 1 UNP O48503 EXPRESSION TAG SEQADV 3ZHI ARG A 75 UNP O48503 EXPRESSION TAG SEQADV 3ZHI SER A 76 UNP O48503 EXPRESSION TAG SEQADV 3ZHI HIS A 77 UNP O48503 EXPRESSION TAG SEQADV 3ZHI HIS A 78 UNP O48503 EXPRESSION TAG SEQADV 3ZHI HIS A 79 UNP O48503 EXPRESSION TAG SEQADV 3ZHI HIS A 80 UNP O48503 EXPRESSION TAG SEQADV 3ZHI HIS A 81 UNP O48503 EXPRESSION TAG SEQADV 3ZHI HIS A 82 UNP O48503 EXPRESSION TAG SEQADV 3ZHI ALA A 45 UNP O48503 GLN 45 ENGINEERED MUTATION SEQADV 3ZHI ALA A 48 UNP O48503 ASN 48 ENGINEERED MUTATION SEQRES 1 A 83 MET LEU LYS THR ASP THR SER ASN ARG LEU LYS GLN ILE SEQRES 2 A 83 MET ALA GLU ARG ASN LEU LYS GLN VAL ASP ILE LEU ASN SEQRES 3 A 83 LEU SER ILE PRO PHE GLN LYS LYS PHE GLY ILE LYS LEU SEQRES 4 A 83 SER LYS SER THR LEU SER ALA TYR VAL ALA SER VAL GLN SEQRES 5 A 83 SER PRO ASP GLN ASN ARG ILE TYR LEU LEU ALA LYS THR SEQRES 6 A 83 LEU GLY VAL SER GLU ALA TRP LEU MET GLY ARG SER HIS SEQRES 7 A 83 HIS HIS HIS HIS HIS FORMUL 2 HOH *106(H2 O) HELIX 1 1 THR A 3 ASN A 17 1 15 HELIX 2 2 LYS A 19 GLY A 35 1 17 HELIX 3 3 SER A 39 ALA A 48 1 10 HELIX 4 4 ASP A 54 GLY A 66 1 13 HELIX 5 5 SER A 68 GLY A 74 1 7 CRYST1 29.620 43.590 71.500 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 0.033761 0.000000 0.000000 0.00000 SCALE2 0.000000 0.022941 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013986 0.00000