HEADER TRANSCRIPTION REGULATOR/DNA 23-JUN-11 2LEV TITLE STRUCTURE OF THE DNA COMPLEX OF THE C-TERMINAL DOMAIN OF LER COMPND MOL_ID: 1; COMPND 2 MOLECULE: LER; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SEQUENCE DATABASE RESIDUES 56-102; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA (5'-D(*GP*CP*GP*AP*TP*AP*AP*TP*TP*GP*AP*TP*AP*GP*G)- COMPND 8 3'); COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: DNA (5'-D(*CP*CP*TP*AP*TP*CP*AP*AP*TP*TP*AP*TP*CP*GP*C)- COMPND 13 3'); COMPND 14 CHAIN: C; COMPND 15 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: LER; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR: PHAT2; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 MOL_ID: 3; SOURCE 11 SYNTHETIC: YES KEYWDS TRANSCRIPTION REGULATOR-DNA COMPLEX, ARGININE-MINOR-GROOVE KEYWDS 2 RECOGNITION, HORIZONTAL GENE TRANSFER, INDIRECT READOUT, NUCLEOID KEYWDS 3 ASSOCIATED PROTEIN EXPDTA SOLUTION NMR; SOLUTION SCATTERING NUMMDL 20 AUTHOR T.N.CORDEIRO,H.SCHIMDT,C.MADRID,A.JUAREZ,P.BERNADO,C.GRISIENGER, AUTHOR 2 J.GARCIA,M.PONS REVDAT 1 07-DEC-11 2LEV 0 JRNL AUTH T.N.CORDEIRO,H.SCHMIDT,C.MADRID,A.JUAREZ,P.BERNADO, JRNL AUTH 2 C.GRIESINGER,J.GARCIA,M.PONS JRNL TITL INDIRECT DNA READOUT BY AN H-NS RELATED PROTEIN: STRUCTURE JRNL TITL 2 OF THE DNA COMPLEX OF THE C-TERMINAL DOMAIN OF LER. JRNL REF PLOS PATHOG. V. 7 02380 2011 JRNL REFN ISSN 1553-7366 JRNL PMID 22114557 JRNL DOI 10.1371/JOURNAL.PPAT.1002380 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA, CNS, AMBER, HADDOCK, CRYSOL, PROCHECK REMARK 3 AUTHORS : GUNTERT, MUMENTHALER AND WUTHRICH (CYANA), REMARK 3 BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ (CNS), REMARK 3 CASE, DARDEN, CHEATHAM, III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, AND KOLLM (AMBER), ALEXANDRE BONVIN REMARK 3 (HADDOCK), SVERGUN D.I., BARBERATO C. AND KOCH REMARK 3 M.H.J. (CRYSOL), LASKOWSKI AND MACARTHUR (PROCHECK) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: PROTEIN STRUCTURE CALCULATION WAS REMARK 3 PERFORMED WITH CYANA 2.1, THE 20 LOWEST-ENERGY CT-LER CONFORMERS REMARK 3 WERE FURTHER ENERGY-REFINED IN EXPLICIT SOLVENT USING USING CNS, REMARK 3 DNA (LEEH) WAS DEFINED AS B-DNA FOLLOWED BY MD WATER REFINEMENT, REMARK 3 INCLUDING NMR RESTRAINTS. THE 20 LOWEST-ENERGY PROTEIN STRUCTURES REMARK 3 WERE SELECTED AND DOCKED ONTO LEEH USING INTERMOLECULAR NOES AND REMARK 3 AIRS, FINAL SCORING AGAINST EXPERIMENTAL NMR AND SAXS DATA. REMARK 3 PACKING, RAMACHANDRAN APPREARANCE. REFINEMENT AGAINST SMALL-ANGLE REMARK 3 X-RAY SCATTERING (SAXS) DATA, QUALITY ASSESSMENT. REMARK 4 REMARK 4 2LEV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-JUN-11. REMARK 100 THE RCSB ID CODE IS RCSB102306. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 5.7 REMARK 210 IONIC STRENGTH : 150 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM [U-100% 13C; U-100% 15N] CT REMARK 210 -LER, 2 MM LEEH A, 2 MM LEEH B, REMARK 210 20 MM SODIUM PHOSPHATE, 20 MM REMARK 210 SODIUM CHLORIDE, 0.01 %(W/V) REMARK 210 SODIUM AZIDE, 0.2 MM EDTA, 90% REMARK 210 H2O/10% D2O; 1 MM [U-100% 13C; U- REMARK 210 100% 15N] CT-LER, 2 MM LEEH A, 2 REMARK 210 MM LEEH B, 20 MM SODIUM REMARK 210 PHOSPHATE, 150 MM SODIUM REMARK 210 CHLORIDE, 0.01 %(W/V) SODIUM REMARK 210 AZIDE, 0.2 MM EDTA, 100% D2O; 1 REMARK 210 MM [U-10% 13C; U-100% 15N] CT- REMARK 210 LER, 2 MM LEEH A, 2 MM LEEH B, 20 REMARK 210 MM SODIUM PHOSPHATE, 150 MM REMARK 210 SODIUM CHLORIDE, 0.01 % (W/V) REMARK 210 SODIUM AZIDE, 0.2 MM EDTA, 90% REMARK 210 H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC REMARK 210 ALIPHATIC; 3D HNCACB; 3D CBCA(CO) REMARK 210 NH; 3D H(CCO)NH; 3D HCCH-TOCSY; REMARK 210 3D HNHA; 3D 1H-15N TOCSY; 3D 1H- REMARK 210 15N NOESY; 3D 1H-13C NOESY REMARK 210 ALIPHATIC; 2D 1H-1H (13C-ED) REMARK 210 NOESY; 2D 1H-1H NOESY; 2D 1H-1H REMARK 210 (13C-FIL) NOESY; 2D 1H-1H (15N/ REMARK 210 13C-FIL) NOESY; 3D 15N/13C-FIL/ REMARK 210 13C-ED- NOESY; 2D 1H-1H (13C-FIL) REMARK 210 TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 700 MHZ; 800 MHZ; 900 REMARK 210 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE, TOPSPIN, CYANA, CNS, REMARK 210 CARA, TALOS, CRYSOL, HADDOCK, REMARK 210 AMBER, PROCHECK REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS, REMARK 210 SIMULATED ANNEALING, MOLECULAR REMARK 210 DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 400 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION 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 265 REMARK 265 EXPERIMENTAL DETAILS REMARK 265 REMARK 265 EXPERIMENT TYPE : SMALL ANGLE X-RAY SCATTERING REMARK 265 DATA ACQUISITION REMARK 265 RADIATION/NEUTRON SOURCE : DESY-EMBL HAMBURG REMARK 265 OUTSTATION REMARK 265 SYNCHROTRON (Y/N) : N REMARK 265 BEAMLINE TYPE : X33 REMARK 265 BEAMLINE INSTRUMENT : NULL REMARK 265 DETECTOR TYPE : 2D PHOTON COUNTING REMARK 265 PILATUS 1M PIXEL REMARK 265 DETECTOR MANUFACTURER DETAILS : NULL REMARK 265 TEMPERATURE (KELVIN) : 298 REMARK 265 PH : 5.7 REMARK 265 NUMBER OF TIME FRAMES USED : 4 REMARK 265 PROTEIN CONCENTRATION RANGE (MG/ML) : 3.6 - 7.3 REMARK 265 SAMPLE BUFFER : 20MM SODIUM REMARK 265 PHOSPHATE, 150MM NACL, REMARK 265 0.2MM EDTA, 0.01%NAN3 REMARK 265 DATA REDUCTION SOFTWARE : PRIMUS, GNOM, CRYSOL REMARK 265 GUINIER MEAN RADIUS OF GYRATION (NM) : 1.82 REMARK 265 SIGMA MEAN RADIUS OF GYRATION : 0.01 REMARK 265 R(XS-1) MEAN CROSS SECTIONAL RADII (NM) : NULL REMARK 265 R(XS-1) SIGMA MEAN CROSS SECTIONAL RADII : NULL REMARK 265 R(XS-2) MEAN CROSS SECTIONAL RADII (NM) : NULL REMARK 265 R(XS-2) SIGMA MEAN CROSS SECTIONAL RADII : NULL REMARK 265 P(R) PROTEIN LENGTH (NM) : 5.3 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 H62 DA B 7 O4 DT C 24 1.55 REMARK 500 H22 DG B 14 O2 DC C 17 1.57 REMARK 500 H62 DA B 6 O4 DT C 25 1.59 REMARK 500 O2 DC B 2 H22 DG C 29 1.60 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 HIS A -4 -10.92 68.57 REMARK 500 1 SER A -2 -62.16 -101.34 REMARK 500 1 MET A -1 176.94 55.45 REMARK 500 1 SER A 2 -39.82 -151.36 REMARK 500 2 MET A -1 -168.94 49.64 REMARK 500 3 HIS A -7 88.53 65.92 REMARK 500 3 HIS A -4 104.79 -58.17 REMARK 500 3 LYS A 4 -171.64 -54.06 REMARK 500 3 ARG A 21 -162.08 43.63 REMARK 500 4 HIS A -7 40.38 -109.37 REMARK 500 4 HIS A -5 -70.37 -59.15 REMARK 500 4 HIS A -4 -10.24 68.39 REMARK 500 4 SER A -2 -61.18 -95.07 REMARK 500 4 MET A -1 -165.43 48.60 REMARK 500 4 SER A 2 -2.87 -143.94 REMARK 500 5 HIS A -7 101.74 63.19 REMARK 500 5 SER A 3 154.81 -49.71 REMARK 500 5 LYS A 4 -171.16 -47.73 REMARK 500 5 ARG A 21 -162.55 43.80 REMARK 500 6 HIS A -4 -3.61 70.60 REMARK 500 6 HIS A -3 28.77 43.93 REMARK 500 6 SER A -2 -60.05 -101.52 REMARK 500 6 MET A -1 -166.54 49.16 REMARK 500 6 SER A 2 -54.67 -151.74 REMARK 500 6 SER A 3 46.59 -88.05 REMARK 500 7 HIS A -7 93.67 64.08 REMARK 500 7 HIS A -3 86.58 -158.47 REMARK 500 7 ASN A 1 -100.72 -129.98 REMARK 500 7 LYS A 4 -173.98 -53.81 REMARK 500 7 ARG A 21 -163.88 43.78 REMARK 500 8 HIS A -4 -4.36 65.65 REMARK 500 8 SER A -2 -61.11 -101.24 REMARK 500 8 MET A -1 -175.48 53.10 REMARK 500 8 SER A 2 -25.91 -143.22 REMARK 500 8 SER A 3 37.91 -92.00 REMARK 500 9 HIS A -4 -9.81 69.35 REMARK 500 9 MET A -1 -172.84 54.31 REMARK 500 9 SER A 2 -50.69 -122.75 REMARK 500 10 HIS A -7 151.07 71.35 REMARK 500 10 ASN A 1 63.32 -103.65 REMARK 500 10 LYS A 4 -172.50 -53.28 REMARK 500 10 ARG A 21 -162.82 50.09 REMARK 500 10 GLU A 45 66.63 60.54 REMARK 500 11 HIS A -7 -174.51 65.19 REMARK 500 11 ASN A 1 -125.49 -129.74 REMARK 500 11 SER A 3 143.08 -39.95 REMARK 500 11 LYS A 4 -172.31 -54.62 REMARK 500 11 ARG A 21 -162.23 43.64 REMARK 500 11 GLU A 45 68.89 38.98 REMARK 500 12 HIS A -7 132.81 69.58 REMARK 500 REMARK 500 THIS ENTRY HAS 90 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 17729 RELATED DB: BMRB DBREF 2LEV A 1 47 UNP E9N650 E9N650_ECOLX 56 102 DBREF 2LEV B 1 15 PDB 2LEV 2LEV 1 15 DBREF 2LEV C 16 30 PDB 2LEV 2LEV 16 30 SEQADV 2LEV SER A -9 UNP E9N650 EXPRESSION TAG SEQADV 2LEV HIS A -8 UNP E9N650 EXPRESSION TAG SEQADV 2LEV HIS A -7 UNP E9N650 EXPRESSION TAG SEQADV 2LEV HIS A -6 UNP E9N650 EXPRESSION TAG SEQADV 2LEV HIS A -5 UNP E9N650 EXPRESSION TAG SEQADV 2LEV HIS A -4 UNP E9N650 EXPRESSION TAG SEQADV 2LEV HIS A -3 UNP E9N650 EXPRESSION TAG SEQADV 2LEV SER A -2 UNP E9N650 EXPRESSION TAG SEQADV 2LEV MET A -1 UNP E9N650 EXPRESSION TAG SEQADV 2LEV GLY A 0 UNP E9N650 EXPRESSION TAG SEQRES 1 A 57 SER HIS HIS HIS HIS HIS HIS SER MET GLY ASN SER SER SEQRES 2 A 57 LYS GLY VAL TYR TYR ARG ASN GLU GLU GLY GLN THR TRP SEQRES 3 A 57 SER GLY VAL GLY ARG GLN PRO ARG TRP LEU LYS GLU ALA SEQRES 4 A 57 LEU LEU ASN GLY MET LYS LYS GLU ASP PHE LEU VAL LYS SEQRES 5 A 57 ASP THR GLU GLU GLU SEQRES 1 B 15 DG DC DG DA DT DA DA DT DT DG DA DT DA SEQRES 2 B 15 DG DG SEQRES 1 C 15 DC DC DT DA DT DC DA DA DT DT DA DT DC SEQRES 2 C 15 DG DC HELIX 1 1 PRO A 23 ASN A 32 1 10 HELIX 2 2 LYS A 35 ASP A 38 5 4 SHEET 1 A 3 THR A 15 TRP A 16 0 SHEET 2 A 3 VAL A 6 ARG A 9 -1 N TYR A 8 O TRP A 16 SHEET 3 A 3 LEU A 40 LYS A 42 -1 O VAL A 41 N TYR A 7 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