HEADER DNA BINDING PROTEIN/DNA 25-FEB-16 2NBJ TITLE DNA-ARCHEAL MC1 PROTEIN COMPLEX STRUCTURE BY NMR COMPND MOL_ID: 1; COMPND 2 MOLECULE: CHROMOSOMAL PROTEIN MC1; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'-D(*AP*AP*AP*AP*AP*CP*AP*CP*AP*CP*AP*CP*CP*CP*A)- COMPND 7 3'); COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: DNA (5'-D(P*TP*GP*GP*GP*TP*GP*TP*GP*TP*GP*TP*TP*TP*TP*T)- COMPND 12 3'); COMPND 13 CHAIN: C; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHANOSARCINA THERMOPHILA CHTI-55; SOURCE 3 ORGANISM_TAXID: 1434121; SOURCE 4 STRAIN: CHTI55; SOURCE 5 GENE: MSTHC_1630; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PET24A-MC1; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 MOL_ID: 3; SOURCE 12 SYNTHETIC: YES KEYWDS DNA-PROTEIN COMPLEX, BENT DNA, ARCHAEA, DNA BINDING PROTEIN-DNA KEYWDS 2 COMPLEX EXPDTA SOLUTION NMR NUMMDL 12 AUTHOR F.PAQUET,K.LOTH,C.LANDON REVDAT 1 01-MAR-17 2NBJ 0 JRNL AUTH F.PAQUET,K.LOTH,C.LANDON JRNL TITL FIRST 3D STRUCTURE OF AN ATYPICAL PROTEIN-DNA COMPLEX JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : HADDOCK, CNS REMARK 3 AUTHORS : ALEXANDRE BONVIN (HADDOCK), BRUNGER, ADAMS, CLORE, REMARK 3 GROS, NILGES AND READ (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2NBJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-MAR-16. REMARK 100 THE RCSB ID CODE IS RCSB104661. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 299 REMARK 210 PH : 6 REMARK 210 IONIC STRENGTH : 100 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.18 MM [U-100% 15N] PROTEIN, REMARK 210 1.18 MM [U-100% 13C; U-100% 15N] REMARK 210 A1-A15 DNA, 10 MM SODIUM REMARK 210 PHOSPHATE, 100 MM SODIUM REMARK 210 CHLORIDE, 1 MM EDTA, 90% H2O/10% REMARK 210 D2O; 0.85 MM [U-100% 15N] REMARK 210 PROTEIN, 0.85 MM [U-100% 13C; U- REMARK 210 100% 15N] A1-A15 DNA, 10 MM REMARK 210 SODIUM PHOSPHATE, 100 MM SODIUM REMARK 210 CHLORIDE, 1 MM EDTA, 10 MG/ML PF1 REMARK 210 PHAGE, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 3D 1H-15N NOESY; REMARK 210 2D 1H-15N HSQC; 2D 1H-13C HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 700 MHZ REMARK 210 SPECTROMETER MODEL : INOVA; AVANCE REMARK 210 SPECTROMETER MANUFACTURER : VARIAN; BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN, VNMR, NMRPIPE, CCPNMR, REMARK 210 HADDOCK REMARK 210 METHOD USED : NULL REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 12 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS 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 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 H2'' DT C 24 H5'' DG C 25 1.31 REMARK 500 H2'' DA B 1 H5'' DA B 2 1.34 REMARK 500 OD1 ASP A 66 HH22 ARG A 71 1.55 REMARK 500 HZ3 LYS A 59 OE2 GLU A 87 1.57 REMARK 500 HZ3 LYS A 85 OE1 GLU A 87 1.58 REMARK 500 OD1 ASP A 66 HZ1 LYS A 69 1.58 REMARK 500 O ILE A 89 HO3' DT C 30 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 5 DA B 15 C3' - C2' - C1' ANGL. DEV. = -5.0 DEGREES REMARK 500 7 DA B 15 C3' - C2' - C1' ANGL. DEV. = -4.9 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 ASP A 10 -124.96 -83.08 REMARK 500 1 HIS A 16 -123.46 -90.06 REMARK 500 1 LYS A 22 -58.57 -157.05 REMARK 500 1 THR A 38 -119.06 -160.28 REMARK 500 1 LYS A 39 -79.96 -70.31 REMARK 500 1 ASN A 41 106.54 174.73 REMARK 500 1 ASP A 66 -169.48 134.59 REMARK 500 1 PRO A 68 104.23 -55.58 REMARK 500 1 LYS A 69 -97.69 -115.94 REMARK 500 1 ALA A 73 -51.92 -27.81 REMARK 500 1 PRO A 76 -143.66 -102.61 REMARK 500 1 GLU A 77 -124.78 54.24 REMARK 500 1 GLU A 87 -70.13 -80.99 REMARK 500 1 ARG A 88 114.33 -168.96 REMARK 500 2 ASN A 2 114.22 -163.35 REMARK 500 2 ASP A 10 -125.50 -81.04 REMARK 500 2 HIS A 16 -126.62 -89.45 REMARK 500 2 THR A 20 55.17 -140.93 REMARK 500 2 LYS A 22 -72.67 -148.11 REMARK 500 2 ALA A 32 2.00 -63.49 REMARK 500 2 THR A 38 -105.33 -172.59 REMARK 500 2 LYS A 39 -85.09 -77.43 REMARK 500 2 ASN A 41 129.27 179.78 REMARK 500 2 THR A 52 -166.37 -127.10 REMARK 500 2 LYS A 53 74.25 -110.68 REMARK 500 2 ASP A 66 -174.04 139.75 REMARK 500 2 PRO A 68 96.10 -46.88 REMARK 500 2 LYS A 69 -120.22 -110.78 REMARK 500 2 ALA A 73 -56.97 -25.80 REMARK 500 2 PRO A 76 -131.48 -102.44 REMARK 500 2 GLU A 77 -127.07 49.24 REMARK 500 2 GLU A 87 -77.67 -83.04 REMARK 500 2 ARG A 88 117.50 -163.78 REMARK 500 3 ASP A 10 -125.81 -88.32 REMARK 500 3 HIS A 16 -126.08 -89.78 REMARK 500 3 LYS A 22 -43.97 -165.96 REMARK 500 3 ALA A 32 0.91 -67.44 REMARK 500 3 THR A 38 -105.55 -170.59 REMARK 500 3 LYS A 39 -87.43 -73.49 REMARK 500 3 ASN A 41 120.47 -172.49 REMARK 500 3 LYS A 53 94.69 -62.46 REMARK 500 3 ASP A 66 -173.19 138.57 REMARK 500 3 PRO A 68 96.80 -55.01 REMARK 500 3 LYS A 69 -123.75 -104.54 REMARK 500 3 ALA A 73 -55.21 -27.60 REMARK 500 3 MET A 75 79.13 -119.68 REMARK 500 3 PRO A 76 -146.79 -103.03 REMARK 500 3 GLU A 77 -122.57 49.13 REMARK 500 3 LYS A 86 102.15 -56.18 REMARK 500 3 GLU A 87 -70.64 -83.96 REMARK 500 REMARK 500 THIS ENTRY HAS 186 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 19957 RELATED DB: BMRB REMARK 900 CHEMICAL SHIFTS ASSIGNMENT OF THE PROTEIN AND THE DNA IN REMARK 900 COMPLEX REMARK 900 RELATED ID: 2KHL RELATED DB: PDB REMARK 900 3D STRUCTURE OF THE FREE MC1 PROTEIN DBREF1 2NBJ A 1 93 UNP A0A0E3KRH5_METTE DBREF2 2NBJ A A0A0E3KRH5 2 94 DBREF 2NBJ B 1 15 PDB 2NBJ 2NBJ 1 15 DBREF 2NBJ C 16 30 PDB 2NBJ 2NBJ 16 30 SEQRES 1 A 93 SER ASN THR ARG ASN PHE VAL LEU ARG ASP GLU ASP GLY SEQRES 2 A 93 ASN GLU HIS GLY VAL PHE THR GLY LYS GLN PRO ARG GLN SEQRES 3 A 93 ALA ALA LEU LYS ALA ALA ASN ARG GLY SER GLY THR LYS SEQRES 4 A 93 ALA ASN PRO ASP ILE ILE ARG LEU ARG GLU ARG GLY THR SEQRES 5 A 93 LYS LYS VAL HIS VAL PHE LYS ALA TRP LYS GLU ILE VAL SEQRES 6 A 93 ASP ALA PRO LYS ASN ARG PRO ALA TRP MET PRO GLU LYS SEQRES 7 A 93 ILE SER LYS PRO PHE VAL LYS LYS GLU ARG ILE GLU LYS SEQRES 8 A 93 LEU GLU SEQRES 1 B 15 DA DA DA DA DA DC DA DC DA DC DA DC DC SEQRES 2 B 15 DC DA SEQRES 1 C 15 DT DG DG DG DT DG DT DG DT DG DT DT DT SEQRES 2 C 15 DT DT HELIX 1 1 GLN A 23 ALA A 32 1 10 HELIX 2 2 ASN A 33 GLY A 35 5 3 SHEET 1 A 5 GLU A 15 GLY A 21 0 SHEET 2 A 5 ARG A 4 ARG A 9 -1 N PHE A 6 O PHE A 19 SHEET 3 A 5 ILE A 44 ARG A 50 -1 O ARG A 50 N ASN A 5 SHEET 4 A 5 VAL A 55 ASP A 66 -1 O PHE A 58 N ILE A 45 SHEET 5 A 5 LYS A 78 LYS A 86 -1 O PHE A 83 N TRP A 61 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