HEADER DNA BINDING PROTEIN 13-SEP-06 2ICT TITLE CRYSTAL STRUCTURE OF THE BACTERIAL ANTITOXIN HIGA FROM ESCHERICHIA TITLE 2 COLI AT PH 8.5. NORTHEAST STRUCTURAL GENOMICS TARGET ER390. COMPND MOL_ID: 1; COMPND 2 MOLECULE: ANTITOXIN HIGA; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PUTATIVE HTH-TYPE TRANSCRIPTIONAL REGULATOR YDDM; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 199310; SOURCE 4 STRAIN: CFT073; SOURCE 5 GENE: HIGA; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)+ MAGIC; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28-HIGA KEYWDS HELIX-TURN-HELIX, STRUCTURAL GENOMICS, PSI-2, PROTEIN STRUCTURE KEYWDS 2 INITIATIVE, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM, NESG, DNA KEYWDS 3 BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.A.ARBING,M.ABASHIDZE,J.M.HURLEY,L.ZHAO,H.JANJUA,K.CUNNINGHAM, AUTHOR 2 L.C.MA,R.XIAO,J.LIU,M.C.BARAN,T.B.ACTON,B.ROST,M.INOUYE,N.A.WOYCHIK, AUTHOR 3 G.T.MONTELIONE,J.F.HUNT,NORTHEAST STRUCTURAL GENOMICS CONSORTIUM AUTHOR 4 (NESG) REVDAT 5 18-OCT-17 2ICT 1 REMARK REVDAT 4 13-JUL-11 2ICT 1 VERSN REVDAT 3 18-AUG-10 2ICT 1 JRNL REVDAT 2 24-FEB-09 2ICT 1 VERSN REVDAT 1 26-SEP-06 2ICT 0 JRNL AUTH M.A.ARBING,S.K.HANDELMAN,A.P.KUZIN,G.VERDON,C.WANG,M.SU, JRNL AUTH 2 F.P.ROTHENBACHER,M.ABASHIDZE,M.LIU,J.M.HURLEY,R.XIAO, JRNL AUTH 3 T.ACTON,M.INOUYE,G.T.MONTELIONE,N.A.WOYCHIK,J.F.HUNT JRNL TITL CRYSTAL STRUCTURES OF PHD-DOC, HIGA, AND YEEU ESTABLISH JRNL TITL 2 MULTIPLE EVOLUTIONARY LINKS BETWEEN MICROBIAL JRNL TITL 3 GROWTH-REGULATING TOXIN-ANTITOXIN SYSTEMS. JRNL REF STRUCTURE V. 18 996 2010 JRNL REFN ISSN 0969-2126 JRNL PMID 20696400 JRNL DOI 10.1016/J.STR.2010.04.018 REMARK 2 REMARK 2 RESOLUTION. 1.63 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.63 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1360.0 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 82.3 REMARK 3 NUMBER OF REFLECTIONS : 9805 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.198 REMARK 3 FREE R VALUE : 0.201 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.200 REMARK 3 FREE R VALUE TEST SET COUNT : 506 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.63 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.69 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 580 REMARK 3 BIN R VALUE (WORKING SET) : 0.2470 REMARK 3 BIN FREE R VALUE : 0.3400 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 23 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 727 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 96 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.01 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.32100 REMARK 3 B22 (A**2) : -3.60100 REMARK 3 B33 (A**2) : 0.28000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -2.39000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.013 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 36.82 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2ICT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-SEP-06. REMARK 100 THE DEPOSITION ID IS D_1000039422. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-JUL-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97941 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11696 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.630 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 5.700 REMARK 200 R MERGE (I) : 0.23700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.63 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.66 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.80200 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: COMO 1.2 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.59 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.26 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 5 MM MGSO4, 50 MM TRIS PH 8.5, 35% 1,6 REMARK 280 -HEXANEDIOL, UNDER OIL., TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 45.26750 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 13.18200 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 45.26750 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 13.18200 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 3240 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10610 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -24.0 KCAL/MOL 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 90.53500 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 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 SER A 62 -165.32 64.96 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2ICP RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE BACTERIAL ANTITOXIN HIGA FROM ESCHERICHIA REMARK 900 COLI AT PH 4.0 REMARK 900 RELATED ID: ER390 RELATED DB: TARGETDB DBREF 2ICT A 1 94 UNP P67699 YDDM_ECOLI 1 94 SEQRES 1 A 94 MSE LYS MSE ALA ASN HIS PRO ARG PRO GLY ASP ILE ILE SEQRES 2 A 94 GLN GLU SER LEU ASP GLU LEU ASN VAL SER LEU ARG GLU SEQRES 3 A 94 PHE ALA ARG ALA MSE GLU ILE ALA PRO SER THR ALA SER SEQRES 4 A 94 ARG LEU LEU THR GLY LYS ALA ALA LEU THR PRO GLU MSE SEQRES 5 A 94 ALA ILE LYS LEU SER VAL VAL ILE GLY SER SER PRO GLN SEQRES 6 A 94 MSE TRP LEU ASN LEU GLN ASN ALA TRP SER LEU ALA GLU SEQRES 7 A 94 ALA GLU LYS THR VAL ASP VAL SER ARG LEU ARG ARG LEU SEQRES 8 A 94 VAL THR GLN MODRES 2ICT MSE A 1 MET SELENOMETHIONINE MODRES 2ICT MSE A 3 MET SELENOMETHIONINE MODRES 2ICT MSE A 31 MET SELENOMETHIONINE MODRES 2ICT MSE A 52 MET SELENOMETHIONINE MODRES 2ICT MSE A 66 MET SELENOMETHIONINE HET MSE A 1 8 HET MSE A 3 8 HET MSE A 31 8 HET MSE A 52 8 HET MSE A 66 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 5(C5 H11 N O2 SE) FORMUL 2 HOH *96(H2 O) HELIX 1 1 ARG A 8 ASN A 21 1 14 HELIX 2 2 SER A 23 GLU A 32 1 10 HELIX 3 3 ALA A 34 THR A 43 1 10 HELIX 4 4 THR A 49 ILE A 60 1 12 HELIX 5 5 SER A 63 LYS A 81 1 19 LINK C MSE A 1 N LYS A 2 1555 1555 1.33 LINK C LYS A 2 N MSE A 3 1555 1555 1.33 LINK C MSE A 3 N ALA A 4 1555 1555 1.33 LINK C ALA A 30 N MSE A 31 1555 1555 1.33 LINK C MSE A 31 N GLU A 32 1555 1555 1.33 LINK C GLU A 51 N MSE A 52 1555 1555 1.33 LINK C MSE A 52 N ALA A 53 1555 1555 1.33 LINK C GLN A 65 N MSE A 66 1555 1555 1.33 LINK C MSE A 66 N TRP A 67 1555 1555 1.33 CRYST1 90.535 26.364 39.485 90.00 91.51 90.00 C 1 2 1 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 0.011045 0.000000 0.000291 0.00000 SCALE2 0.000000 0.037931 0.000000 0.00000 SCALE3 0.000000 0.000000 0.025335 0.00000 HETATM 1 N MSE A 1 57.965 2.424 12.018 1.00 63.28 N HETATM 2 CA MSE A 1 57.084 3.587 11.703 1.00 64.07 C HETATM 3 C MSE A 1 56.365 4.086 12.952 1.00 59.65 C HETATM 4 O MSE A 1 55.784 3.300 13.699 1.00 58.88 O HETATM 5 CB MSE A 1 56.047 3.194 10.645 1.00 74.64 C HETATM 6 CG MSE A 1 55.064 4.304 10.281 1.00 83.94 C HETATM 7 SE MSE A 1 53.696 3.714 9.038 1.00 93.00 SE HETATM 8 CE MSE A 1 54.671 3.845 7.388 1.00102.02 C