HEADER DNA BINDING PROTEIN 08-OCT-10 2L4M TITLE SOLUTION STRUCTURE OF THE ZBETA DOMAIN OF HUMAN DAI AND ITS BINDING TITLE 2 MODES TO B- AND Z-DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: UNCHARACTERIZED PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 103-166; COMPND 5 SYNONYM: DAI, DNA-DEPENDENT ACTIVATOR OF IFN-REGULATORY FACTORS; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: ZBP1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PET28A KEYWDS ZBETA, Z-DNA BINDING PROTEIN, BENT ALPHA HELIX, ALPHA+BETA HELIX- KEYWDS 2 TURN-HELIX, B-Z TRANSITION, DNA BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR K.KIM,B.I.KHAYRUTDINOV,Y.H.JEON,K.K.KIM REVDAT 2 01-MAY-24 2L4M 1 REMARK SEQADV REVDAT 1 13-APR-11 2L4M 0 JRNL AUTH K.KIM,B.KHAYRUTDINOV,C.-K.LEE,H.-K.CHEONG,S.KANG,H.PARK, JRNL AUTH 2 S.LEE,Y.-G.KIM,J.-G.JEE,A.RICH,K.K.KIM,Y.H.JEON JRNL TITL SOLUTION STRUCTURE OF THE ZBETA DOMAIN OF HUMAN JRNL TITL 2 DNA-DEPENDENT ACTIVATOR OF IFN-REGULATORY FACTORS AND ITS JRNL TITL 3 BINDING MODES TO B- AND Z-DNA JRNL REF PROC.NATL.ACAD.SCI.USA 2011 JRNL REFN ESSN 1091-6490 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER A. T. ET.AL. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2L4M COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-OCT-10. REMARK 100 THE DEPOSITION ID IS D_1000101950. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 308 REMARK 210 PH : 5.5 REMARK 210 IONIC STRENGTH : 10 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 2 MM [U-99% 13C; U-99% 15N] REMARK 210 ZBETADAI-1, 90% H2O, 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 2D 1H-1H TOCSY; 2D 1H-1H NOESY; REMARK 210 3D CBCA(CO)NH; 3D C(CO)NH; 3D REMARK 210 HNCO; 3D HNCA; 3D HNCACB; 3D REMARK 210 HN(CO)CA; 3D HCCH-TOCSY; 3D HCCH- REMARK 210 COSY; 3D 1H-15N NOESY; 3D 1H-15N REMARK 210 TOCSY; 3D 1H-13C NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 900 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 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: 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 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 1 ARG A 115 CD - NE - CZ ANGL. DEV. = 8.7 DEGREES REMARK 500 1 ARG A 115 NE - CZ - NH1 ANGL. DEV. = 4.8 DEGREES REMARK 500 1 ARG A 146 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 2 ARG A 146 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 3 ARG A 150 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 4 ARG A 109 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 5 ARG A 150 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 6 ARG A 150 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 7 ARG A 150 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 8 ARG A 146 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 9 ARG A 150 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 10 ARG A 109 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 10 ARG A 146 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 14 ARG A 146 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 14 ARG A 150 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 16 ARG A 146 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 16 ARG A 150 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 17 ARG A 150 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 18 ARG A 146 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 20 ARG A 115 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 20 ARG A 115 NE - CZ - NH2 ANGL. DEV. = -3.2 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 HIS A 151 38.51 71.85 REMARK 500 1 TYR A 165 91.65 -66.88 REMARK 500 2 HIS A 151 39.22 71.32 REMARK 500 2 SER A 159 14.53 -148.83 REMARK 500 2 TYR A 165 92.75 -66.43 REMARK 500 3 HIS A 151 39.21 72.02 REMARK 500 3 TYR A 165 89.60 -66.41 REMARK 500 4 HIS A 151 38.52 71.84 REMARK 500 4 SER A 159 10.75 -143.96 REMARK 500 4 TYR A 165 89.17 -67.99 REMARK 500 5 HIS A 99 170.70 60.42 REMARK 500 5 HIS A 151 39.05 72.43 REMARK 500 5 SER A 159 18.90 -143.74 REMARK 500 5 TYR A 165 98.01 -67.87 REMARK 500 6 HIS A 151 38.68 71.49 REMARK 500 6 SER A 159 18.01 -143.62 REMARK 500 6 TYR A 165 89.25 -68.33 REMARK 500 7 HIS A 151 40.00 71.54 REMARK 500 7 SER A 159 16.45 -148.20 REMARK 500 7 TYR A 165 96.10 -66.84 REMARK 500 8 TYR A 165 89.62 -68.03 REMARK 500 9 TYR A 165 88.65 -66.15 REMARK 500 10 HIS A 99 165.67 62.34 REMARK 500 10 HIS A 151 38.60 71.44 REMARK 500 10 TYR A 165 92.46 -66.80 REMARK 500 11 HIS A 151 37.14 70.83 REMARK 500 11 SER A 159 10.19 -141.26 REMARK 500 11 TYR A 165 88.81 -64.00 REMARK 500 12 HIS A 151 38.02 72.48 REMARK 500 12 SER A 159 10.40 -141.31 REMARK 500 12 TYR A 165 86.80 -67.37 REMARK 500 13 HIS A 151 37.92 71.42 REMARK 500 13 TYR A 165 86.83 -67.74 REMARK 500 14 HIS A 151 36.71 73.26 REMARK 500 14 SER A 159 11.26 -142.00 REMARK 500 14 TYR A 165 89.42 -65.10 REMARK 500 15 SER A 102 153.70 65.29 REMARK 500 15 HIS A 151 38.43 72.02 REMARK 500 15 SER A 159 13.13 -144.21 REMARK 500 15 TYR A 165 90.56 -68.27 REMARK 500 16 HIS A 151 39.27 71.64 REMARK 500 16 SER A 159 16.70 -150.13 REMARK 500 16 TYR A 165 88.01 -69.10 REMARK 500 17 SER A 102 146.89 63.07 REMARK 500 17 HIS A 151 38.51 72.06 REMARK 500 17 TYR A 165 90.35 -67.43 REMARK 500 18 ALA A 101 166.58 58.13 REMARK 500 18 HIS A 151 38.46 72.77 REMARK 500 18 SER A 159 15.12 -140.64 REMARK 500 19 SER A 102 -53.12 -121.65 REMARK 500 REMARK 500 THIS ENTRY HAS 57 RAMACHANDRAN OUTLIERS. 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 4 ARG A 109 0.08 SIDE CHAIN REMARK 500 11 ARG A 150 0.10 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 2L4M A 103 166 UNP C9J523 C9J523_HUMAN 103 166 SEQADV 2L4M SER A 98 UNP C9J523 EXPRESSION TAG SEQADV 2L4M HIS A 99 UNP C9J523 EXPRESSION TAG SEQADV 2L4M MET A 100 UNP C9J523 EXPRESSION TAG SEQADV 2L4M ALA A 101 UNP C9J523 EXPRESSION TAG SEQADV 2L4M SER A 102 UNP C9J523 EXPRESSION TAG SEQRES 1 A 69 SER HIS MET ALA SER PRO GLN PHE SER GLN GLN ARG GLU SEQRES 2 A 69 GLU ASP ILE TYR ARG PHE LEU LYS ASP ASN GLY PRO GLN SEQRES 3 A 69 ARG ALA LEU VAL ILE ALA GLN ALA LEU GLY MET ARG THR SEQRES 4 A 69 ALA LYS ASP VAL ASN ARG ASP LEU TYR ARG MET LYS SER SEQRES 5 A 69 ARG HIS LEU LEU ASP MET ASP GLU GLN SER LYS ALA TRP SEQRES 6 A 69 THR ILE TYR ARG HELIX 1 1 GLN A 107 GLY A 121 1 15 HELIX 2 2 ALA A 125 GLY A 133 1 9 HELIX 3 3 THR A 136 SER A 149 1 14 SHEET 1 A 3 GLN A 123 ARG A 124 0 SHEET 2 A 3 ALA A 161 ILE A 164 -1 O TRP A 162 N GLN A 123 SHEET 3 A 3 LEU A 153 MET A 155 -1 N ASP A 154 O THR A 163 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