HEADER TRANSCRIPTION REPRESSOR 25-SEP-03 1R1T TITLE CRYSTAL STRUCTURE OF THE CYANOBACTERIAL METALLOTHIONEIN REPRESSOR SMTB TITLE 2 IN THE APO-FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSCRIPTIONAL REPRESSOR SMTB; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNECHOCOCCUS ELONGATUS PCC 7942; SOURCE 3 ORGANISM_TAXID: 1140; SOURCE 4 STRAIN: PCC7942; SOURCE 5 GENE: SMTB; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS ZINC, TRANSCRIPTIONAL REGULATION, WINGED HTH PROTEIN, DNA BINDING, KEYWDS 2 TRANSCRIPTION REPRESSOR EXPDTA X-RAY DIFFRACTION AUTHOR C.EICKEN,M.A.PENNELLA,X.CHEN,K.M.KOSHLAP,M.L.VANZILE,J.C.SACCHETTINI, AUTHOR 2 D.P.GIEDROC REVDAT 3 23-AUG-23 1R1T 1 REMARK REVDAT 2 24-FEB-09 1R1T 1 VERSN REVDAT 1 18-MAY-04 1R1T 0 JRNL AUTH C.EICKEN,M.A.PENNELLA,X.CHEN,K.M.KOSHLAP,M.L.VANZILE, JRNL AUTH 2 J.C.SACCHETTINI,D.P.GIEDROC JRNL TITL A METAL-LIGAND-MEDIATED INTERSUBUNIT ALLOSTERIC SWITCH IN JRNL TITL 2 RELATED SMTB/ARSR ZINC SENSOR PROTEINS. JRNL REF J.MOL.BIOL. V. 333 683 2003 JRNL REFN ISSN 0022-2836 JRNL PMID 14568530 JRNL DOI 10.1016/J.JMB.2003.09.007 REMARK 2 REMARK 2 RESOLUTION. 1.70 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 60.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 90.3 REMARK 3 NUMBER OF REFLECTIONS : 21874 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.216 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 2163 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 : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL 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 : 1556 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 279 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.14000 REMARK 3 B22 (A**2) : 3.15800 REMARK 3 B33 (A**2) : -3.29800 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 2.99900 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) : 0.004 REMARK 3 BOND ANGLES (DEGREES) : 1.038 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) : 1.372 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.137 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.546 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.855 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1R1T COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-SEP-03. REMARK 100 THE DEPOSITION ID IS D_1000020333. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-MAR-01 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 14-BM-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22325 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 60.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.5 REMARK 200 DATA REDUNDANCY : 4.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.02900 REMARK 200 FOR THE DATA SET : 19.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 58.3 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.18500 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: CNS REMARK 200 STARTING MODEL: PDB ENTRY 1SMT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.22 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NA/K PHOSPHATE, HEPES, PH 7.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 34.86100 REMARK 290 SMTRY3 2 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 300 REMARK: THE ASYMMETRIC UNIT CONTAINS THE DIMERIC BIOLOGICAL REMARK 300 ASSEMBLY. 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3770 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10870 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -34.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 1 REMARK 465 THR A 2 REMARK 465 LYS A 3 REMARK 465 PRO A 4 REMARK 465 VAL A 5 REMARK 465 LEU A 6 REMARK 465 GLN A 7 REMARK 465 ASP A 8 REMARK 465 GLY A 9 REMARK 465 GLU A 10 REMARK 465 THR A 11 REMARK 465 VAL A 12 REMARK 465 VAL A 13 REMARK 465 CYS A 14 REMARK 465 GLN A 15 REMARK 465 GLY A 16 REMARK 465 THR A 17 REMARK 465 HIS A 18 REMARK 465 ALA A 19 REMARK 465 ALA A 20 REMARK 465 ILE A 21 REMARK 465 ALA A 22 REMARK 465 SER A 23 REMARK 465 ARG A 122 REMARK 465 MET B 1 REMARK 465 THR B 2 REMARK 465 LYS B 3 REMARK 465 PRO B 4 REMARK 465 VAL B 5 REMARK 465 LEU B 6 REMARK 465 GLN B 7 REMARK 465 ASP B 8 REMARK 465 GLY B 9 REMARK 465 GLU B 10 REMARK 465 THR B 11 REMARK 465 VAL B 12 REMARK 465 VAL B 13 REMARK 465 CYS B 14 REMARK 465 GLN B 15 REMARK 465 GLY B 16 REMARK 465 THR B 17 REMARK 465 HIS B 18 REMARK 465 ALA B 19 REMARK 465 GLN B 119 REMARK 465 GLU B 120 REMARK 465 CYS B 121 REMARK 465 ARG B 122 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 GLU A 120 -142.54 -91.81 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1SMT RELATED DB: PDB REMARK 900 THE SAME PROTEIN STRUCTURE SOLVED TO LOWER RESOLUTION REMARK 900 RELATED ID: 1RIU RELATED DB: PDB REMARK 900 APO-FORM OF CZRA REMARK 900 RELATED ID: 1RIV RELATED DB: PDB REMARK 900 ZN2-FORM OF CZRA REMARK 900 RELATED ID: 1R22 RELATED DB: PDB REMARK 900 THE SAME PROTEIN (C14S/C61S/C121S MUTANT) IN ITS ZN2-FORM REMARK 900 RELATED ID: 1R23 RELATED DB: PDB REMARK 900 SMTB IN THE ZN1-FORM DBREF 1R1T A 1 122 UNP P30340 SMTB_SYNP7 1 122 DBREF 1R1T B 1 122 UNP P30340 SMTB_SYNP7 1 122 SEQRES 1 A 122 MET THR LYS PRO VAL LEU GLN ASP GLY GLU THR VAL VAL SEQRES 2 A 122 CYS GLN GLY THR HIS ALA ALA ILE ALA SER GLU LEU GLN SEQRES 3 A 122 ALA ILE ALA PRO GLU VAL ALA GLN SER LEU ALA GLU PHE SEQRES 4 A 122 PHE ALA VAL LEU ALA ASP PRO ASN ARG LEU ARG LEU LEU SEQRES 5 A 122 SER LEU LEU ALA ARG SER GLU LEU CYS VAL GLY ASP LEU SEQRES 6 A 122 ALA GLN ALA ILE GLY VAL SER GLU SER ALA VAL SER HIS SEQRES 7 A 122 GLN LEU ARG SER LEU ARG ASN LEU ARG LEU VAL SER TYR SEQRES 8 A 122 ARG LYS GLN GLY ARG HIS VAL TYR TYR GLN LEU GLN ASP SEQRES 9 A 122 HIS HIS ILE VAL ALA LEU TYR GLN ASN ALA LEU ASP HIS SEQRES 10 A 122 LEU GLN GLU CYS ARG SEQRES 1 B 122 MET THR LYS PRO VAL LEU GLN ASP GLY GLU THR VAL VAL SEQRES 2 B 122 CYS GLN GLY THR HIS ALA ALA ILE ALA SER GLU LEU GLN SEQRES 3 B 122 ALA ILE ALA PRO GLU VAL ALA GLN SER LEU ALA GLU PHE SEQRES 4 B 122 PHE ALA VAL LEU ALA ASP PRO ASN ARG LEU ARG LEU LEU SEQRES 5 B 122 SER LEU LEU ALA ARG SER GLU LEU CYS VAL GLY ASP LEU SEQRES 6 B 122 ALA GLN ALA ILE GLY VAL SER GLU SER ALA VAL SER HIS SEQRES 7 B 122 GLN LEU ARG SER LEU ARG ASN LEU ARG LEU VAL SER TYR SEQRES 8 B 122 ARG LYS GLN GLY ARG HIS VAL TYR TYR GLN LEU GLN ASP SEQRES 9 B 122 HIS HIS ILE VAL ALA LEU TYR GLN ASN ALA LEU ASP HIS SEQRES 10 B 122 LEU GLN GLU CYS ARG FORMUL 3 HOH *279(H2 O) HELIX 1 1 ALA A 29 ALA A 44 1 16 HELIX 2 2 ASP A 45 ALA A 56 1 12 HELIX 3 3 CYS A 61 GLY A 70 1 10 HELIX 4 4 SER A 72 LEU A 86 1 15 HELIX 5 5 ASP A 104 LEU A 118 1 15 HELIX 6 6 ILE B 21 LEU B 25 5 5 HELIX 7 7 ALA B 29 ALA B 44 1 16 HELIX 8 8 ASP B 45 ALA B 56 1 12 HELIX 9 9 CYS B 61 GLY B 70 1 10 HELIX 10 10 SER B 72 LEU B 86 1 15 HELIX 11 11 ASP B 104 LEU B 118 1 15 SHEET 1 A 2 VAL A 89 GLN A 94 0 SHEET 2 A 2 HIS A 97 LEU A 102 -1 O HIS A 97 N GLN A 94 SHEET 1 B 2 VAL B 89 GLN B 94 0 SHEET 2 B 2 HIS B 97 LEU B 102 -1 O HIS B 97 N GLN B 94 CRYST1 37.240 69.722 43.221 90.00 95.84 90.00 P 1 21 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 0.026853 0.000000 0.002747 0.00000 SCALE2 0.000000 0.014343 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023258 0.00000