HEADER TRANSCRIPTION, DNA BINDING PROTEIN/DNA 31-MAY-12 2LTT TITLE SOLUTION NMR STRUCTURE OF YDBC:DT19G1 COMPLEX. NORTHEAST STRUCTURAL TITLE 2 GENOMICS CONSORTIUM (NESG) TARGET KR150 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE UNCHARACTERIZED PROTEIN YDBC; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'- COMPND 7 D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3'); COMPND 8 CHAIN: C; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LACTOCOCCUS LACTIS SUBSP. LACTIS; SOURCE 3 ORGANISM_TAXID: 272623; SOURCE 4 STRAIN: IL1403; SOURCE 5 GENE: YDBC, LL0313, L114363; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PET21_NESG; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES KEYWDS STRUCTURAL GENOMICS, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM, NESG, KEYWDS 2 PSI-BIOLOGY, PROTEIN STRUCTURE INITIATIVE, TRANSCRIPTION, DNA KEYWDS 3 BINDING PROTEIN-DNA COMPLEX EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR P.ROSSI,C.M.BARBIERI,J.A.ARAMINI,E.BINI,H.LEE,H.JANJUA,C.CICCOSANTI, AUTHOR 2 H.WANG,T.B.ACTON,R.XIAO,J.K.EVERETT,G.T.MONTELIONE,NORTHEAST AUTHOR 3 STRUCTURAL GENOMICS CONSORTIUM (NESG) REVDAT 4 06-MAR-13 2LTT 1 JRNL REVDAT 3 30-JAN-13 2LTT 1 JRNL REVDAT 2 16-JAN-13 2LTT 1 JRNL REVDAT 1 20-JUN-12 2LTT 0 JRNL AUTH P.ROSSI,C.M.BARBIERI,J.M.ARAMINI,E.BINI,H.W.LEE,H.JANJUA, JRNL AUTH 2 R.XIAO,T.B.ACTON,G.T.MONTELIONE JRNL TITL STRUCTURES OF APO- AND SSDNA-BOUND YDBC FROM LACTOCOCCUS JRNL TITL 2 LACTIS UNCOVER THE FUNCTION OF PROTEIN DOMAIN FAMILY DUF2128 JRNL TITL 3 AND EXPAND THE SINGLE-STRANDED DNA-BINDING DOMAIN PROTEOME. JRNL REF NUCLEIC ACIDS RES. V. 41 2756 2013 JRNL REFN ISSN 0305-1048 JRNL PMID 23303792 JRNL DOI 10.1093/NAR/GKS1348 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS, CYANA 3.0, HADDOCK REMARK 3 AUTHORS : BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ (CNS) REMARK 3 , GUNTERT, MUMENTHALER AND WUTHRICH (CYANA), BONVIN REMARK 3 A. M. J. J. (HADDOCK) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: RESTRAINED MD IN WATER BATH, OPLSX, NCS REMARK 3 SYMMETRY, C2 SYMMETRY WITHIN HADDOCK INTERFACE REMARK 4 REMARK 4 2LTT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-JUN-12. REMARK 100 THE RCSB ID CODE IS RCSB102824. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.5 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.6 MM [U-100% 13C; U-100% 15N] REMARK 210 KR150.020, 0.02 % NAN3, 10 MM DTT, 100 MM NACL, 10 % D2O, 50 UM REMARK 210 DSS, 10 MM TRIS-HCL, 0.3 MM DNA (5'-D(*TP*TP*TP*TP*TP*TP*TP*TP* REMARK 210 TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*G)-3'), 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D HNCO; 3D HNCA; 3D 1H-13C NOESY ALIPHATIC; 3D 1H-13C NOESY REMARK 210 AROMATIC; 3D 1H-15N NOESY; 3D-13C,15N_X-FILT-13C,15N-EDITEDNOESY; REMARK 210 3D HN(CA)CO; 1H-15N HETNOE; 1D T1; 1D T2(CPMG); 2D 1H-1H NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CNS, CYANA 3.0, NMRPIPE, REMARK 210 TOPSPIN, VNMRJ, PINE, SPARKY, REMARK 210 TALOS+, PALES, PSVS, HADDOCK REMARK 210 METHOD USED : RESTRAINED MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE 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: 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-20 REMARK 465 RES C SSSEQI REMARK 465 HIS A 75 REMARK 465 HIS A 76 REMARK 465 HIS A 77 REMARK 465 HIS A 78 REMARK 465 HIS A 79 REMARK 465 HIS A 80 REMARK 465 HIS B 75 REMARK 465 HIS B 76 REMARK 465 HIS B 77 REMARK 465 HIS B 78 REMARK 465 HIS B 79 REMARK 465 HIS B 80 REMARK 465 DT C 8 REMARK 465 DT C 9 REMARK 465 DT C 10 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 OE1 GLU B 36 HZ3 LYS B 38 1.55 REMARK 500 OE1 GLU A 36 HZ2 LYS A 38 1.58 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 LEU A 13 -74.76 -99.99 REMARK 500 1 LEU A 16 -80.36 -91.02 REMARK 500 1 SER A 17 -177.42 175.51 REMARK 500 1 ASN A 19 -166.40 -113.38 REMARK 500 1 TRP A 23 107.07 -52.95 REMARK 500 1 ALA A 35 -76.80 -121.64 REMARK 500 1 LEU B 13 -71.42 -103.87 REMARK 500 1 LEU B 16 -80.54 -88.24 REMARK 500 1 SER B 17 -178.01 175.25 REMARK 500 1 ASN B 19 -164.01 -112.77 REMARK 500 1 TRP B 23 107.62 -53.59 REMARK 500 1 ALA B 35 -78.41 -113.74 REMARK 500 2 LEU A 13 -74.84 -105.93 REMARK 500 2 LEU A 16 -80.85 -88.85 REMARK 500 2 SER A 17 -171.94 -175.67 REMARK 500 2 ALA A 35 -79.15 -102.60 REMARK 500 2 LEU B 13 -73.15 -108.96 REMARK 500 2 LEU B 16 -80.80 -85.70 REMARK 500 2 SER B 17 -171.61 -179.21 REMARK 500 2 ALA B 35 -81.35 -100.35 REMARK 500 3 LEU A 13 -75.17 -109.28 REMARK 500 3 LEU A 16 -79.85 -92.24 REMARK 500 3 SER A 17 -167.33 179.09 REMARK 500 3 ALA A 35 -88.27 -106.62 REMARK 500 3 LEU B 13 -74.66 -112.00 REMARK 500 3 LEU B 16 -81.29 -92.06 REMARK 500 3 SER B 17 -167.71 -179.18 REMARK 500 3 ALA B 35 -89.77 -103.04 REMARK 500 4 LEU A 13 -73.74 -112.12 REMARK 500 4 LEU A 16 -82.12 -85.81 REMARK 500 4 SER A 17 -166.34 -174.97 REMARK 500 4 ALA A 35 -80.09 -107.92 REMARK 500 4 LEU B 16 -81.86 -87.04 REMARK 500 4 SER B 17 -167.75 -177.26 REMARK 500 4 ALA B 35 -78.17 -116.24 REMARK 500 5 LEU A 13 -75.29 -104.24 REMARK 500 5 LEU A 16 -81.05 -93.89 REMARK 500 5 SER A 17 -169.78 -177.76 REMARK 500 5 ALA A 35 -77.43 -123.50 REMARK 500 5 LEU B 13 -70.46 -111.02 REMARK 500 5 LEU B 16 -81.85 -92.73 REMARK 500 5 SER B 17 -170.45 -178.34 REMARK 500 5 ALA B 35 -70.70 -125.06 REMARK 500 6 LEU A 13 -75.66 -98.95 REMARK 500 6 LEU A 16 -80.65 -90.78 REMARK 500 6 SER A 17 -167.62 -175.17 REMARK 500 6 ALA A 35 -91.58 -108.69 REMARK 500 6 LEU B 13 -72.91 -102.97 REMARK 500 6 LEU B 16 -80.34 -90.67 REMARK 500 6 SER B 17 -167.18 -177.06 REMARK 500 REMARK 500 THIS ENTRY HAS 181 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2LTD RELATED DB: PDB REMARK 900 RELATED ID: 18496 RELATED DB: BMRB REMARK 900 RELATED ID: NESG-KR150 RELATED DB: TARGETTRACK DBREF 2LTT A 1 72 UNP Q9CIP3 Q9CIP3_LACLA 1 72 DBREF 2LTT B 1 72 UNP Q9CIP3 Q9CIP3_LACLA 1 72 DBREF 2LTT C 1 17 PDB 2LTT 2LTT 1 17 SEQADV 2LTT LEU A 73 UNP Q9CIP3 EXPRESSION TAG SEQADV 2LTT GLU A 74 UNP Q9CIP3 EXPRESSION TAG SEQADV 2LTT HIS A 75 UNP Q9CIP3 EXPRESSION TAG SEQADV 2LTT HIS A 76 UNP Q9CIP3 EXPRESSION TAG SEQADV 2LTT HIS A 77 UNP Q9CIP3 EXPRESSION TAG SEQADV 2LTT HIS A 78 UNP Q9CIP3 EXPRESSION TAG SEQADV 2LTT HIS A 79 UNP Q9CIP3 EXPRESSION TAG SEQADV 2LTT HIS A 80 UNP Q9CIP3 EXPRESSION TAG SEQADV 2LTT LEU B 73 UNP Q9CIP3 EXPRESSION TAG SEQADV 2LTT GLU B 74 UNP Q9CIP3 EXPRESSION TAG SEQADV 2LTT HIS B 75 UNP Q9CIP3 EXPRESSION TAG SEQADV 2LTT HIS B 76 UNP Q9CIP3 EXPRESSION TAG SEQADV 2LTT HIS B 77 UNP Q9CIP3 EXPRESSION TAG SEQADV 2LTT HIS B 78 UNP Q9CIP3 EXPRESSION TAG SEQADV 2LTT HIS B 79 UNP Q9CIP3 EXPRESSION TAG SEQADV 2LTT HIS B 80 UNP Q9CIP3 EXPRESSION TAG SEQRES 1 A 80 MET ALA ASP LYS LEU LYS PHE GLU ILE ILE GLU GLU LEU SEQRES 2 A 80 ILE VAL LEU SER GLU ASN ALA LYS GLY TRP ARG LYS GLU SEQRES 3 A 80 LEU ASN ARG VAL SER TRP ASN ASP ALA GLU PRO LYS TYR SEQRES 4 A 80 ASP ILE ARG THR TRP SER PRO ASP HIS GLU LYS MET GLY SEQRES 5 A 80 LYS GLY ILE THR LEU SER GLU GLU GLU PHE GLY VAL LEU SEQRES 6 A 80 LEU LYS GLU LEU GLY ASN LYS LEU GLU HIS HIS HIS HIS SEQRES 7 A 80 HIS HIS SEQRES 1 B 80 MET ALA ASP LYS LEU LYS PHE GLU ILE ILE GLU GLU LEU SEQRES 2 B 80 ILE VAL LEU SER GLU ASN ALA LYS GLY TRP ARG LYS GLU SEQRES 3 B 80 LEU ASN ARG VAL SER TRP ASN ASP ALA GLU PRO LYS TYR SEQRES 4 B 80 ASP ILE ARG THR TRP SER PRO ASP HIS GLU LYS MET GLY SEQRES 5 B 80 LYS GLY ILE THR LEU SER GLU GLU GLU PHE GLY VAL LEU SEQRES 6 B 80 LEU LYS GLU LEU GLY ASN LYS LEU GLU HIS HIS HIS HIS SEQRES 7 B 80 HIS HIS SEQRES 1 C 17 DT DT DT DT DT DT DT DT DT DT DT DT DT SEQRES 2 C 17 DT DT DT DT HELIX 1 1 SER A 58 LEU A 73 1 16 HELIX 2 2 ASN B 33 ALA B 35 5 3 HELIX 3 3 SER B 58 LEU B 73 1 16 SHEET 1 A 4 PHE A 7 SER A 17 0 SHEET 2 A 4 ARG A 24 TRP A 32 -1 O ARG A 29 N GLU A 11 SHEET 3 A 4 GLU A 36 TRP A 44 -1 O GLU A 36 N TRP A 32 SHEET 4 A 4 ILE A 55 LEU A 57 -1 O LEU A 57 N TYR A 39 SHEET 1 B 4 GLU B 11 SER B 17 0 SHEET 2 B 4 ARG B 24 TRP B 32 -1 O ARG B 29 N GLU B 11 SHEET 3 B 4 GLU B 36 TRP B 44 -1 O GLU B 36 N TRP B 32 SHEET 4 B 4 ILE B 55 LEU B 57 -1 O LEU B 57 N TYR B 39 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