HEADER DNA BINDING PROTEIN 08-MAY-18 5ZUZ TITLE SOLUTION STRUCTURE OF THE DNA-BINDING DOMAIN OF ROK COMPND MOL_ID: 1; COMPND 2 MOLECULE: ROK; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: DNA-BINDING DOMAIN SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS SUBSP. SUBTILIS STR. 168; SOURCE 3 ORGANISM_TAXID: 224308; SOURCE 4 STRAIN: 168 KEYWDS WINGED HELIX, XENOGENEIC SILENCER, DNA BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR B.XIA,B.DUAN REVDAT 3 01-MAY-24 5ZUZ 1 REMARK REVDAT 2 28-NOV-18 5ZUZ 1 JRNL REVDAT 1 17-OCT-18 5ZUZ 0 JRNL AUTH B.DUAN,P.DING,T.R.HUGHES,W.W.NAVARRE,J.LIU,B.XIA JRNL TITL HOW BACTERIAL XENOGENEIC SILENCER ROK DISTINGUISHES FOREIGN JRNL TITL 2 FROM SELF DNA IN ITS RESIDENT GENOME. JRNL REF NUCLEIC ACIDS RES. V. 46 10514 2018 JRNL REFN ESSN 1362-4962 JRNL PMID 30252102 JRNL DOI 10.1093/NAR/GKY836 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA, AMBER REMARK 3 AUTHORS : GUNTERT, MUMENTHALER AND WUTHRICH (CYANA), CASE, REMARK 3 DARDEN, CHEATHAM III, SIMMERLING, WANG, DUKE, LUO, REMARK 3 ... AND KOLLMAN (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5ZUZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 09-MAY-18. REMARK 100 THE DEPOSITION ID IS D_1300007467. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.0 REMARK 210 IONIC STRENGTH : 50 MM NACL REMARK 210 PRESSURE : AMBIENT BAR REMARK 210 SAMPLE CONTENTS : 1 MM 15N_13C ROK, 90% H2O/10% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D 1H-13C NOESY; 3D 1H-15N NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 950 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : SANE, NMRPIPE REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : 20 STRUCTURES FOR LOWEST ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL 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: 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 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 2 ARG A 108 NE - CZ - NH2 ANGL. DEV. = 3.9 DEGREES REMARK 500 3 ARG A 105 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 3 ARG A 130 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 6 ARG A 106 NE - CZ - NH2 ANGL. DEV. = 3.0 DEGREES REMARK 500 6 ARG A 121 NE - CZ - NH2 ANGL. DEV. = 3.6 DEGREES REMARK 500 7 ARG A 108 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 8 ARG A 105 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 8 ARG A 112 NE - CZ - NH2 ANGL. DEV. = 4.3 DEGREES REMARK 500 9 ARG A 105 NE - CZ - NH2 ANGL. DEV. = 3.2 DEGREES REMARK 500 10 ARG A 105 NE - CZ - NH2 ANGL. DEV. = 3.1 DEGREES REMARK 500 10 ARG A 130 NE - CZ - NH2 ANGL. DEV. = 3.7 DEGREES REMARK 500 11 ARG A 130 NE - CZ - NH2 ANGL. DEV. = 3.7 DEGREES REMARK 500 14 ARG A 107 NE - CZ - NH2 ANGL. DEV. = 3.2 DEGREES REMARK 500 15 ARG A 107 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 15 ARG A 130 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 16 ARG A 105 NE - CZ - NH2 ANGL. DEV. = 3.1 DEGREES REMARK 500 19 ARG A 105 NE - CZ - NH2 ANGL. DEV. = 3.5 DEGREES REMARK 500 19 ARG A 107 NE - CZ - NH2 ANGL. DEV. = 3.9 DEGREES REMARK 500 19 ARG A 130 NE - CZ - NH2 ANGL. DEV. = 3.4 DEGREES REMARK 500 20 ARG A 130 NE - CZ - NH1 ANGL. DEV. = 3.8 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 1 ARG A 174 107.54 -57.24 REMARK 500 1 GLU A 182 49.13 -77.31 REMARK 500 2 THR A 103 -47.54 -143.54 REMARK 500 2 ARG A 174 106.04 -53.63 REMARK 500 2 GLU A 187 -20.72 -148.50 REMARK 500 3 ARG A 174 109.10 -53.10 REMARK 500 3 GLU A 184 46.10 -77.38 REMARK 500 4 ARG A 108 -52.93 -161.77 REMARK 500 4 ARG A 174 109.40 -58.44 REMARK 500 5 ARG A 174 108.03 -56.46 REMARK 500 6 THR A 103 28.57 -69.34 REMARK 500 6 LYS A 171 71.68 -119.24 REMARK 500 7 ARG A 174 107.83 -54.88 REMARK 500 8 THR A 104 35.96 -67.82 REMARK 500 8 ARG A 174 106.66 -49.99 REMARK 500 9 ARG A 105 -140.75 -135.48 REMARK 500 9 HIS A 194 38.04 -99.56 REMARK 500 10 ARG A 174 109.34 -58.19 REMARK 500 11 ARG A 174 104.81 -49.78 REMARK 500 12 THR A 104 25.48 -72.26 REMARK 500 12 ARG A 105 36.79 -75.26 REMARK 500 12 ARG A 174 108.21 -50.45 REMARK 500 13 HIS A 131 72.51 -112.07 REMARK 500 13 ARG A 174 106.91 -58.81 REMARK 500 13 GLU A 187 -38.25 -132.13 REMARK 500 14 LYS A 171 76.89 -119.45 REMARK 500 14 ARG A 174 107.87 -55.44 REMARK 500 15 THR A 104 0.21 -68.26 REMARK 500 15 LYS A 171 72.75 -114.77 REMARK 500 16 ARG A 112 70.04 48.63 REMARK 500 16 ARG A 174 109.46 -52.24 REMARK 500 18 THR A 104 47.17 -71.18 REMARK 500 18 ARG A 174 109.24 -57.89 REMARK 500 19 ARG A 174 107.32 -59.58 REMARK 500 19 HIS A 196 56.86 -142.36 REMARK 500 20 THR A 104 42.10 -67.83 REMARK 500 20 LYS A 171 76.30 -117.61 REMARK 500 20 HIS A 194 45.55 -79.90 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 36187 RELATED DB: BMRB REMARK 900 SOLUTION STRUCTURE OF THE DNA-BINDING DOMAIN OF ROK DBREF 5ZUZ A 97 199 PDB 5ZUZ 5ZUZ 97 199 SEQRES 1 A 103 ALA GLY ILE PRO ASP GLY THR THR ARG ARG ARG ARG GLY SEQRES 2 A 103 THR ALA ARG PRO GLY SER LYS ALA ALA LYS LEU ARG GLU SEQRES 3 A 103 ALA ALA ILE LYS THR LEU LYS ARG HIS ASN ALA ALA ILE SEQRES 4 A 103 LYS SER SER GLU LEU GLN LYS GLU ILE GLU LYS GLU SER SEQRES 5 A 103 GLY LEU GLU ILE PRO ASN MET THR THR PHE MET GLN SER SEQRES 6 A 103 LEU ILE LYS MET TYR PRO GLU VAL LYS LYS PRO TYR ARG SEQRES 7 A 103 GLY GLN TYR ILE LEU GLU GLY GLU ILE GLU SER ALA GLU SEQRES 8 A 103 SER ALA ASN GLU LEU GLU HIS HIS HIS HIS HIS HIS HELIX 1 AA1 ARG A 106 THR A 110 5 5 HELIX 2 AA2 SER A 115 HIS A 131 1 17 HELIX 3 AA3 SER A 137 GLY A 149 1 13 HELIX 4 AA4 ASN A 154 TYR A 166 1 13 HELIX 5 AA5 ASN A 190 HIS A 195 1 6 SHEET 1 AA1 3 ILE A 135 LYS A 136 0 SHEET 2 AA1 3 GLN A 176 LEU A 179 -1 O TYR A 177 N ILE A 135 SHEET 3 AA1 3 VAL A 169 TYR A 173 -1 N LYS A 170 O ILE A 178 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 MODEL 1