HEADER DNA BINDING PROTEIN/DNA 24-APR-98 1BBX TITLE NON-SPECIFIC PROTEIN-DNA INTERACTIONS IN THE SSO7D-DNA COMPLEX, NMR, 1 TITLE 2 STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*CP*TP*AP*GP*CP*GP*CP*GP*CP*TP*AP*G)-3'); COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA-BINDING PROTEIN 7D; COMPND 7 CHAIN: C, D; COMPND 8 SYNONYM: SSO7D; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 ORGANISM_SCIENTIFIC: SULFOLOBUS SOLFATARICUS; SOURCE 5 ORGANISM_TAXID: 2287; SOURCE 6 CELL_LINE: BL21; SOURCE 7 ATCC: DSM 1616; SOURCE 8 COLLECTION: DSM 1616; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 10 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 11 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 12 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS PROTEIN-DNA INTERACTION, NONSPECIFIC PROTEIN-DNA INTERACTION, COMPLEX KEYWDS 2 (DNA-BINDING PROTEIN-DNA), DNA BINDING PROTEIN-DNA COMPLEX EXPDTA SOLUTION NMR AUTHOR P.AGBACK,H.BAUMANN,S.KNAPP,R.LADENSTEIN,T.HARD REVDAT 4 22-MAY-24 1BBX 1 REMARK REVDAT 3 16-FEB-22 1BBX 1 REMARK SEQADV REVDAT 2 24-FEB-09 1BBX 1 VERSN REVDAT 1 14-OCT-98 1BBX 0 JRNL AUTH P.AGBACK,H.BAUMANN,S.KNAPP,R.LADENSTEIN,T.HARD JRNL TITL ARCHITECTURE OF NONSPECIFIC PROTEIN-DNA INTERACTIONS IN THE JRNL TITL 2 SSO7D-DNA COMPLEX JRNL REF NAT.STRUCT.BIOL. V. 5 579 1998 JRNL REFN ISSN 1072-8368 JRNL PMID 9665172 JRNL DOI 10.1038/836 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH H.BAUMANN,S.KNAPP,A.KARSHIKOFF,R.LADENSTEIN,T.HARD REMARK 1 TITL DNA-BINDING SURFACE OF THE SSO7D PROTEIN FROM SULFOLOBUS REMARK 1 TITL 2 SOLFATARICUS REMARK 1 REF J.MOL.BIOL. V. 247 840 1995 REMARK 1 REFN ISSN 0022-2836 REMARK 1 REFERENCE 2 REMARK 1 AUTH H.BAUMANN,S.KNAPP,T.LUNDBACK,R.LADENSTEIN,T.HARD REMARK 1 TITL SOLUTION STRUCTURE AND DNA-BINDING PROPERTIES OF A REMARK 1 TITL 2 THERMOSTABLE PROTEIN FROM THE ARCHAEON SULFOLOBUS REMARK 1 TITL 3 SOLFATARICUS REMARK 1 REF NAT.STRUCT.BIOL. V. 1 808 1994 REMARK 1 REFN ISSN 1072-8368 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REFINEMENT DETAILS CAN BE FOUND IN THE REMARK 3 JRNL CITATION ABOVE. REMARK 4 REMARK 4 1BBX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000171570. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 323 REMARK 210 PH : 5.0 REMARK 210 IONIC STRENGTH : 60 MM REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : H2O:D2O 9:1 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : HNCO; CBCA(CO)NNH; HNCACB; HCCH REMARK 210 -TOCSY; HCC-TOCSY; 13C; 15N REMARK 210 DOUBLE HALF-FILTERED 2D NOESY; REMARK 210 15N-EDITED 3D NOE-HSQC; 13C- REMARK 210 EDITED 3D NOE-HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : UNITY REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : VNMR, ANSIG, XPLOR REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : LOWEST RESTRAINT ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR REMARK 210 SPECTROSCOPY ON 13C, 15N-LABELLED SSO7D AND NON-LABELLED DNA REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS 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 H5'' DT A 10 OP2 DA A 11 1.49 REMARK 500 H5'' DT B 22 OP2 DA B 23 1.50 REMARK 500 O SER C 46 H ASP C 49 1.53 REMARK 500 O SER D 46 H ASP D 49 1.54 REMARK 500 O TYR D 7 H GLY D 9 1.56 REMARK 500 O TYR C 7 H GLY C 9 1.56 REMARK 500 O LEU D 54 H MET D 57 1.59 REMARK 500 O LEU C 54 H MET C 57 1.59 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 DT A 2 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 DA A 3 N7 - C8 - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 DG A 4 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 DG A 4 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 DG A 6 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 DG A 8 N7 - C8 - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 DT A 10 C6 - C5 - C7 ANGL. DEV. = -4.3 DEGREES REMARK 500 DA A 11 N7 - C8 - N9 ANGL. DEV. = 4.0 DEGREES REMARK 500 DG A 12 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 DG A 12 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 DT B 14 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 DA B 15 N7 - C8 - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 DG B 16 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 DG B 16 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 DG B 18 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 DG B 20 N7 - C8 - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 DT B 22 C6 - C5 - C7 ANGL. DEV. = -4.3 DEGREES REMARK 500 DA B 23 N7 - C8 - N9 ANGL. DEV. = 4.0 DEGREES REMARK 500 DG B 24 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 DG B 24 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES 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 PHE C 5 -156.75 178.05 REMARK 500 LYS C 8 -59.22 66.96 REMARK 500 LYS C 20 -53.36 -165.33 REMARK 500 TRP C 23 -163.89 -111.20 REMARK 500 ARG C 24 101.28 -167.46 REMARK 500 MET C 28 -112.85 -174.83 REMARK 500 SER C 30 97.75 -50.64 REMARK 500 GLU C 35 33.92 -155.39 REMARK 500 LYS C 39 51.88 -95.37 REMARK 500 THR C 40 -70.80 64.01 REMARK 500 LEU C 54 -53.08 -136.98 REMARK 500 GLN C 61 -102.40 -91.89 REMARK 500 PHE D 5 -156.85 178.03 REMARK 500 LYS D 8 -59.17 66.88 REMARK 500 LYS D 20 -53.40 -165.46 REMARK 500 TRP D 23 -164.06 -111.25 REMARK 500 ARG D 24 101.38 -167.38 REMARK 500 MET D 28 -111.72 -174.82 REMARK 500 SER D 30 97.67 -50.72 REMARK 500 GLU D 35 33.91 -155.44 REMARK 500 LYS D 39 52.00 -95.50 REMARK 500 THR D 40 -70.84 63.92 REMARK 500 LEU D 54 -53.13 -137.02 REMARK 500 GLN D 61 -102.55 -91.86 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG C 24 0.18 SIDE CHAIN REMARK 500 ARG C 42 0.13 SIDE CHAIN REMARK 500 ARG D 24 0.18 SIDE CHAIN REMARK 500 ARG D 42 0.13 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 1BBX C 1 63 UNP P39476 DN72_SULSO 1 63 DBREF 1BBX D 1 63 UNP P39476 DN72_SULSO 1 63 DBREF 1BBX A 1 12 PDB 1BBX 1BBX 1 12 DBREF 1BBX B 13 24 PDB 1BBX 1BBX 13 24 SEQADV 1BBX GLN C 13 UNP P39476 GLU 13 CONFLICT SEQADV 1BBX GLN D 13 UNP P39476 GLU 13 CONFLICT SEQRES 1 A 12 DC DT DA DG DC DG DC DG DC DT DA DG SEQRES 1 B 12 DC DT DA DG DC DG DC DG DC DT DA DG SEQRES 1 C 63 ALA THR VAL LYS PHE LYS TYR LYS GLY GLU GLU LYS GLN SEQRES 2 C 63 VAL ASP ILE SER LYS ILE LYS LYS VAL TRP ARG VAL GLY SEQRES 3 C 63 LYS MET ILE SER PHE THR TYR ASP GLU GLY GLY GLY LYS SEQRES 4 C 63 THR GLY ARG GLY ALA VAL SER GLU LYS ASP ALA PRO LYS SEQRES 5 C 63 GLU LEU LEU GLN MET LEU GLU LYS GLN LYS LYS SEQRES 1 D 63 ALA THR VAL LYS PHE LYS TYR LYS GLY GLU GLU LYS GLN SEQRES 2 D 63 VAL ASP ILE SER LYS ILE LYS LYS VAL TRP ARG VAL GLY SEQRES 3 D 63 LYS MET ILE SER PHE THR TYR ASP GLU GLY GLY GLY LYS SEQRES 4 D 63 THR GLY ARG GLY ALA VAL SER GLU LYS ASP ALA PRO LYS SEQRES 5 D 63 GLU LEU LEU GLN MET LEU GLU LYS GLN LYS LYS HELIX 1 1 ILE C 16 LYS C 18 5 3 HELIX 2 2 LEU C 55 LYS C 60 1 6 HELIX 3 3 ILE D 16 LYS D 18 5 3 HELIX 4 4 LEU D 55 LYS D 60 1 6 SHEET 1 A 2 VAL C 3 TYR C 7 0 SHEET 2 A 2 GLU C 10 VAL C 14 -1 N VAL C 14 O VAL C 3 SHEET 1 B 2 VAL D 3 TYR D 7 0 SHEET 2 B 2 GLU D 10 VAL D 14 -1 N VAL D 14 O VAL D 3 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000