HEADER TRANSCRIPTION/DNA 02-APR-15 4Z5C TITLE HIPB-O3 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*CP*GP*TP*AP*GP*AP*GP*CP*GP*GP*AP*TP*AP*A)- COMPND 9 3'); COMPND 10 CHAIN: C; COMPND 11 SYNONYM: OPERATOR 3 OF HIPBA 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*TP*CP*TP*AP*CP*GP*GP*GP*AP*TP*A)-3'); COMPND 16 CHAIN: D; COMPND 17 SYNONYM: OPERATOR 3 OF HIPBA 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 VARIANT: MG1655; SOURCE 6 GENE: HIPB, B1508, JW1501; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)PLYSS-T1; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET15B; SOURCE 12 MOL_ID: 2; SOURCE 13 SYNTHETIC: YES; SOURCE 14 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 15 ORGANISM_TAXID: 32630; SOURCE 16 MOL_ID: 3; SOURCE 17 SYNTHETIC: YES; SOURCE 18 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 19 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 2 27-SEP-23 4Z5C 1 REMARK REVDAT 1 06-JUL-16 4Z5C 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. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.2_1309) 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.91 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.230 REMARK 3 COMPLETENESS FOR RANGE (%) : 87.0 REMARK 3 NUMBER OF REFLECTIONS : 12373 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.196 REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1237 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 49.9202 - 5.1984 0.95 1414 157 0.1694 0.1898 REMARK 3 2 5.1984 - 4.1267 0.96 1382 154 0.1576 0.1758 REMARK 3 3 4.1267 - 3.6053 0.97 1387 160 0.1666 0.2091 REMARK 3 4 3.6053 - 3.2757 0.97 1361 153 0.1759 0.2161 REMARK 3 5 3.2757 - 3.0410 0.95 1350 155 0.2024 0.2580 REMARK 3 6 3.0410 - 2.8617 0.93 1305 142 0.2382 0.3240 REMARK 3 7 2.8617 - 2.7184 0.90 1262 144 0.2642 0.2904 REMARK 3 8 2.7184 - 2.6001 0.80 1122 114 0.2543 0.2706 REMARK 3 9 2.6001 - 2.5000 0.39 553 58 0.2275 0.2519 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.00 REMARK 3 SHRINKAGE RADIUS : 0.70 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.270 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.560 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.25 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 2076 REMARK 3 ANGLE : 1.110 2977 REMARK 3 CHIRALITY : 0.070 344 REMARK 3 PLANARITY : 0.005 235 REMARK 3 DIHEDRAL : 25.527 832 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 4Z5C COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-APR-15. REMARK 100 THE DEPOSITION ID IS D_1000208569. 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 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14130 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 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 (%) : 99.2 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.54 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3 REMARK 200 DATA REDUNDANCY IN SHELL : 4.30 REMARK 200 R MERGE FOR SHELL (I) : 0.67800 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 (%): 65.03 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.52 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.02 M MGCL2, 0.05 M SODIUM CACODYLATE REMARK 280 TRIHYDRATE, PH 6.0, 5% 2-PROPANOL, 0.001 M 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 19.59867 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 39.19733 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 39.19733 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 19.59867 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: 7180 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12490 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 110 LIES ON A SPECIAL POSITION. 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 O HOH B 108 O HOH B 121 1.82 REMARK 500 OP1 DG C 17 O HOH C 101 1.89 REMARK 500 O5' DA C 21 O HOH C 102 1.92 REMARK 500 O HOH A 130 O HOH D 117 1.92 REMARK 500 O3' DA C 21 O HOH C 103 2.00 REMARK 500 C5' DA C 21 O HOH C 102 2.01 REMARK 500 O2 DC C 8 N2 DG D 36 2.02 REMARK 500 OD1 ASN A 48 O HOH A 101 2.02 REMARK 500 O HOH B 101 O HOH B 125 2.05 REMARK 500 O3' DG C 16 O HOH C 101 2.08 REMARK 500 O GLN B 5 O HOH B 101 2.16 REMARK 500 O HOH A 118 O HOH A 123 2.17 REMARK 500 O3' DC C 7 O HOH C 104 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 ASN A 48 58.01 -150.88 REMARK 500 REMARK 500 REMARK: NULL 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: 4Z5D 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 4Z5C A 4 74 UNP P23873 HIPB_ECOLI 4 74 DBREF 4Z5C B 4 74 UNP P23873 HIPB_ECOLI 4 74 DBREF 4Z5C C 1 21 PDB 4Z5C 4Z5C 1 21 DBREF 4Z5C D 22 41 PDB 4Z5C 4Z5C 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 DC DG DT DA DG DA 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 DT DC DT DA SEQRES 2 D 20 DC DG DG DG DA DT DA FORMUL 5 HOH *95(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 109.027 109.027 58.796 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 0.009172 0.005295 0.000000 0.00000 SCALE2 0.000000 0.010591 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017008 0.00000