HEADER TRANSCRIPTION/DNA 02-APR-15 4Z5D TITLE HIPB-O4 21MER COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: ANTITOXIN HIPB; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 4-74; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA (5'- COMPND 8 D(*TP*TP*TP*AP*TP*CP*CP*GP*CP*GP*AP*TP*CP*GP*CP*GP*GP*AP*TP*AP*A)- COMPND 9 3'); COMPND 10 CHAIN: C; COMPND 11 SYNONYM: OPERATOR 4 OF HIBA OPERON, TOP STRAND; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: DNA (5'- COMPND 15 D(*TP*TP*TP*AP*TP*CP*CP*GP*CP*GP*AP*TP*CP*GP*CP*GP*GP*AP*TP*A)-3'); COMPND 16 CHAIN: D; COMPND 17 SYNONYM: OPERATOR 4 OF HIBA OPERON, BOTTOM STRAND; COMPND 18 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 GENE: HIPB, B1508, JW1501; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)PLYSS-T1; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET15B; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 14 ORGANISM_TAXID: 32630; SOURCE 15 MOL_ID: 3; SOURCE 16 SYNTHETIC: YES; SOURCE 17 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 18 ORGANISM_TAXID: 32630 KEYWDS HTH MOTIF, TRANSCRIPTION REPRESSOR, HIPA SEQUESTERING, TRANSCRIPTION- KEYWDS 2 DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.MIN,R.G.BRENNAN,M.A.SCHUMACHER REVDAT 3 27-SEP-23 4Z5D 1 REMARK REVDAT 2 22-NOV-17 4Z5D 1 REMARK REVDAT 1 06-JUL-16 4Z5D 0 JRNL AUTH J.MIN,A.WANG,R.G.BRENNAN,M.A.SCHUMACHER JRNL TITL MOLECULAR MECHANISM ON HIPBA GENE REGULATION. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.15 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.1_1168) 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) : 2.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.03 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.230 REMARK 3 COMPLETENESS FOR RANGE (%) : 89.3 REMARK 3 NUMBER OF REFLECTIONS : 19767 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.179 REMARK 3 FREE R VALUE : 0.183 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.040 REMARK 3 FREE R VALUE TEST SET COUNT : 1984 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 47.0381 - 5.1831 0.99 1483 163 0.1687 0.1754 REMARK 3 2 5.1831 - 4.1148 0.99 1418 165 0.1512 0.1408 REMARK 3 3 4.1148 - 3.5948 0.99 1427 156 0.1524 0.1378 REMARK 3 4 3.5948 - 3.2662 0.98 1398 154 0.1568 0.1541 REMARK 3 5 3.2662 - 3.0322 0.97 1384 150 0.1758 0.1722 REMARK 3 6 3.0322 - 2.8534 0.96 1351 147 0.2029 0.2098 REMARK 3 7 2.8534 - 2.7105 0.96 1353 155 0.2058 0.2174 REMARK 3 8 2.7105 - 2.5926 0.95 1347 157 0.2024 0.2122 REMARK 3 9 2.5926 - 2.4928 0.95 1349 151 0.2001 0.2387 REMARK 3 10 2.4928 - 2.4068 0.93 1289 144 0.2038 0.2181 REMARK 3 11 2.4068 - 2.3315 0.92 1298 145 0.2101 0.2055 REMARK 3 12 2.3315 - 2.2649 0.88 1228 138 0.2101 0.2589 REMARK 3 13 2.2649 - 2.2052 0.75 1049 116 0.2080 0.2237 REMARK 3 14 2.2052 - 2.1500 0.29 409 43 0.1878 0.2550 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.090 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.02 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 : 0.012 2076 REMARK 3 ANGLE : 1.186 2977 REMARK 3 CHIRALITY : 0.094 344 REMARK 3 PLANARITY : 0.006 235 REMARK 3 DIHEDRAL : 23.396 832 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 4Z5D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-APR-15. REMARK 100 THE DEPOSITION ID IS D_1000208577. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-JAN-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU FR-E+ SUPERBRIGHT REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : RIGAKU VARIMAX REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000, DENZO REMARK 200 DATA SCALING SOFTWARE : HKL-3000, SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22157 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.150 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.100 REMARK 200 R MERGE (I) : 0.04800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.19 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.2 REMARK 200 DATA REDUNDANCY IN SHELL : 4.30 REMARK 200 R MERGE FOR SHELL (I) : 0.60200 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: PDB ENTRY 4Z52 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 64.99 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.51 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.02M MGCL2, 0.05M SODIUM CACODYLATE REMARK 280 TRIHYDRATE, PH 6.0, 5~30% 2-PROPANOL, 0.001M SPERMINE, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 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+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 19.72967 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 39.45933 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 39.45933 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 19.72967 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: 7130 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12620 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -56.0 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 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 HOH B 117 LIES ON A SPECIAL POSITION. REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4Z5A RELATED DB: PDB REMARK 900 RELATED ID: 4Z5B RELATED DB: PDB REMARK 900 RELATED ID: 4Z5C RELATED DB: PDB REMARK 900 RELATED ID: 4Z5E RELATED DB: PDB REMARK 900 RELATED ID: 4Z5F RELATED DB: PDB REMARK 900 RELATED ID: 4Z5G RELATED DB: PDB REMARK 900 RELATED ID: 4Z5H RELATED DB: PDB REMARK 900 RELATED ID: 4Z5I RELATED DB: PDB REMARK 900 RELATED ID: 4Z5J RELATED DB: PDB REMARK 900 RELATED ID: 4Z5K RELATED DB: PDB REMARK 900 RELATED ID: 4Z5L RELATED DB: PDB REMARK 900 RELATED ID: 4Z5M RELATED DB: PDB REMARK 900 RELATED ID: 4Z5N RELATED DB: PDB REMARK 900 RELATED ID: 4Z5O RELATED DB: PDB REMARK 900 RELATED ID: 4Z52 RELATED DB: PDB REMARK 900 RELATED ID: 4Z56 RELATED DB: PDB REMARK 900 RELATED ID: 4Z57 RELATED DB: PDB REMARK 900 RELATED ID: 4Z58 RELATED DB: PDB REMARK 900 RELATED ID: 4Z59 RELATED DB: PDB DBREF 4Z5D A 4 74 UNP P23873 HIPB_ECOLI 4 74 DBREF 4Z5D B 4 74 UNP P23873 HIPB_ECOLI 4 74 DBREF 4Z5D C 1 21 PDB 4Z5D 4Z5D 1 21 DBREF 4Z5D D 22 41 PDB 4Z5D 4Z5D 22 41 SEQRES 1 A 71 PHE GLN LYS ILE TYR SER PRO THR GLN LEU ALA ASN ALA SEQRES 2 A 71 MET LYS LEU VAL ARG GLN GLN ASN GLY TRP THR GLN SER SEQRES 3 A 71 GLU LEU ALA LYS LYS ILE GLY ILE LYS GLN ALA THR ILE SEQRES 4 A 71 SER ASN PHE GLU ASN ASN PRO ASP ASN THR THR LEU THR SEQRES 5 A 71 THR PHE PHE LYS ILE LEU GLN SER LEU GLU LEU SER MET SEQRES 6 A 71 THR LEU CYS ASP ALA LYS SEQRES 1 B 71 PHE GLN LYS ILE TYR SER PRO THR GLN LEU ALA ASN ALA SEQRES 2 B 71 MET LYS LEU VAL ARG GLN GLN ASN GLY TRP THR GLN SER SEQRES 3 B 71 GLU LEU ALA LYS LYS ILE GLY ILE LYS GLN ALA THR ILE SEQRES 4 B 71 SER ASN PHE GLU ASN ASN PRO ASP ASN THR THR LEU THR SEQRES 5 B 71 THR PHE PHE LYS ILE LEU GLN SER LEU GLU LEU SER MET SEQRES 6 B 71 THR LEU CYS ASP ALA LYS SEQRES 1 C 21 DT DT DT DA DT DC DC DG DC DG DA DT DC SEQRES 2 C 21 DG DC DG DG DA DT DA DA SEQRES 1 D 20 DT DT DT DA DT DC DC DG DC DG DA DT DC SEQRES 2 D 20 DG DC DG DG DA DT DA FORMUL 5 HOH *270(H2 O) HELIX 1 AA1 SER A 9 ASN A 24 1 16 HELIX 2 AA2 THR A 27 GLY A 36 1 10 HELIX 3 AA3 LYS A 38 ASN A 48 1 11 HELIX 4 AA4 PRO A 49 THR A 52 5 4 HELIX 5 AA5 THR A 53 LEU A 64 1 12 HELIX 6 AA6 SER B 9 ASN B 24 1 16 HELIX 7 AA7 THR B 27 GLY B 36 1 10 HELIX 8 AA8 LYS B 38 ASN B 48 1 11 HELIX 9 AA9 PRO B 49 THR B 52 5 4 HELIX 10 AB1 THR B 53 LEU B 64 1 12 SHEET 1 AA1 3 LYS B 6 ILE B 7 0 SHEET 2 AA1 3 LEU A 66 ASP A 72 -1 N MET A 68 O ILE B 7 SHEET 3 AA1 3 LEU B 66 ASP B 72 -1 O SER B 67 N CYS A 71 CRYST1 108.604 108.604 59.189 90.00 90.00 120.00 P 31 2 1 12 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 0.009208 0.005316 0.000000 0.00000 SCALE2 0.000000 0.010632 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016895 0.00000