PDB Short entry for 2K1N HEADER TRANSCRIPTION/DNA 10-MAR-08 2K1N TITLE DNA BOUND STRUCTURE OF THE N-TERMINAL DOMAIN OF ABRB COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (25-MER); COMPND 3 CHAIN: E; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA (25-MER); COMPND 8 CHAIN: F; COMPND 9 ENGINEERED: YES; COMPND 10 MUTATION: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: ABRB FAMILY TRANSCRIPTIONAL REGULATOR; COMPND 13 CHAIN: A, B, C, D; COMPND 14 FRAGMENT: SEQUENCE DATABASE RESIDUES 3-57; COMPND 15 SYNONYM: ABRB/MAZE/SPOVT FAMILY DNA-BINDING DOMAIN-CONTAINING COMPND 16 PROTEIN,TRANSCRIPTIONAL REGULATOR FOR TRANSITION STATEPROTEIN, COMPND 17 TRANSITION STATE REGULATORY PROTEIN ABRB; COMPND 18 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 8 ORGANISM_TAXID: 32630; SOURCE 9 MOL_ID: 3; SOURCE 10 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS; SOURCE 11 ORGANISM_TAXID: 1423; SOURCE 12 GENE: B4122_4520, B4417_1778, DFO69_4335, FAL52_19720, SOURCE 13 SC09_CONTIG28ORF00381; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 16 EXPRESSION_SYSTEM_STRAIN: BL21DE3; SOURCE 17 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 18 EXPRESSION_SYSTEM_VECTOR: PET24B KEYWDS ABRB, ABRB8, DNA BOUND, TRANSITION STATE REGULATOR, DNA BINDING KEYWDS 2 PROTEIN, ACTIVATOR, DNA-BINDING, REPRESSOR, SPORULATION, KEYWDS 3 TRANSCRIPTION, TRANSCRIPTION REGULATION, TRANSCRIPTION-DNA COMPLEX EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR J.CAVANAGH,B.G.BOBAY,D.M.SULLIVAN,R.J.THOMPSON REVDAT 4 16-MAR-22 2K1N 1 COMPND SOURCE REMARK DBREF REVDAT 3 24-FEB-09 2K1N 1 VERSN REVDAT 2 25-NOV-08 2K1N 1 JRNL REVDAT 1 11-NOV-08 2K1N 0 JRNL AUTH D.M.SULLIVAN,B.G.BOBAY,D.J.KOJETIN,R.J.THOMPSON,M.RANCE, JRNL AUTH 2 M.A.STRAUCH,J.CAVANAGH JRNL TITL INSIGHTS INTO THE NATURE OF DNA BINDING OF ABRB-LIKE JRNL TITL 2 TRANSCRIPTION FACTORS JRNL REF STRUCTURE V. 16 1702 2008 JRNL REFN ISSN 0969-2126 JRNL PMID 19000822 JRNL DOI 10.1016/J.STR.2008.08.014 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NMRPIPE, HADDOCK 1.3 REMARK 3 AUTHORS : DELAGLIO, GRZESIEK, VUISTER, ZHU, PFEIFER AND BAX REMARK 3 (NMRPIPE), CYRIL DOMINGUEZ, ROLF BOELENS AND REMARK 3 ALEXANDRE M.J.J. BONVIN (HADDOCK) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2K1N COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-MAR-08. REMARK 100 THE DEPOSITION ID IS D_1000100562. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 305 REMARK 210 PH : 5.5 REMARK 210 IONIC STRENGTH : 10 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.5 MM [U-99% 15N] ABRBN55, 90% REMARK 210 H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRVIEW REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 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: HEXAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: E, F, A, B, C, D 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 H22 DG E 17 O2 DC F 9 1.58 REMARK 500 HZ2 LYS B 9 OD1 ASP B 11 1.58 REMARK 500 OE2 GLU D 35 HZ2 LYS D 46 1.58 REMARK 500 H22 DG E 18 O2 DC F 8 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 1 DG F 3 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 2 DC F 9 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 3 DG F 3 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 4 DG F 3 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 4 DG F 17 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 5 DG F 3 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 6 DG F 3 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 7 DC E 22 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 7 DG F 3 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 8 DA F 14 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES REMARK 500 8 DG F 17 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 9 DA F 10 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 9 DA F 14 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 10 DT F 6 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 10 DA F 14 O4' - C1' - N9 ANGL. DEV. = 1.9 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 VAL A 10 -157.77 -112.16 REMARK 500 1 ARG A 15 83.04 44.92 REMARK 500 1 GLU A 30 53.85 -93.29 REMARK 500 1 ASP A 32 -164.72 -126.35 REMARK 500 1 ASP A 40 -83.86 65.80 REMARK 500 1 LYS A 49 81.51 -160.05 REMARK 500 1 MET A 52 35.47 -150.93 REMARK 500 1 LYS B 2 -156.55 -92.47 REMARK 500 1 ILE B 6 -66.21 175.12 REMARK 500 1 ASP B 32 -57.25 175.41 REMARK 500 1 ASP B 40 -79.44 66.03 REMARK 500 1 PRO B 50 -71.83 -60.80 REMARK 500 1 THR C 4 103.13 -59.55 REMARK 500 1 ASP C 11 -158.05 -98.34 REMARK 500 1 LEU C 13 -105.66 -145.25 REMARK 500 1 ASP C 32 -161.59 -78.04 REMARK 500 1 ASP C 40 -77.16 69.68 REMARK 500 1 SER D 3 45.83 -86.58 REMARK 500 1 VAL D 10 -95.93 -84.40 REMARK 500 1 LYS D 31 30.41 -148.67 REMARK 500 1 ASP D 32 -158.90 -103.98 REMARK 500 1 ASP D 40 -86.16 69.44 REMARK 500 2 ASP A 40 -97.03 63.98 REMARK 500 2 THR A 53 40.43 -89.26 REMARK 500 2 CYS A 54 87.34 67.62 REMARK 500 2 LYS B 2 86.77 60.18 REMARK 500 2 PRO B 19 103.47 -58.52 REMARK 500 2 ALA B 29 -70.00 -98.63 REMARK 500 2 GLU B 30 14.39 -160.18 REMARK 500 2 ASP B 40 -99.98 62.34 REMARK 500 2 ASN B 51 105.97 59.09 REMARK 500 2 LYS C 2 74.34 -161.10 REMARK 500 2 SER C 3 45.89 -86.15 REMARK 500 2 ASP C 11 141.98 177.33 REMARK 500 2 GLU C 12 47.22 -80.84 REMARK 500 2 LEU C 13 -61.32 -160.50 REMARK 500 2 PRO C 19 125.14 -33.91 REMARK 500 2 LEU C 26 -82.63 -72.45 REMARK 500 2 ALA C 29 18.55 -170.50 REMARK 500 2 ASP C 32 -79.08 -121.75 REMARK 500 2 ASP C 40 -74.73 68.04 REMARK 500 2 GLU C 41 -32.68 -132.75 REMARK 500 2 LYS C 47 -78.43 -76.27 REMARK 500 2 TYR C 48 147.93 178.53 REMARK 500 2 VAL D 10 -76.09 -81.89 REMARK 500 2 ASP D 11 -166.92 -179.20 REMARK 500 2 VAL D 16 96.53 -69.88 REMARK 500 2 ASP D 40 -81.10 64.99 REMARK 500 2 GLU D 41 20.64 -146.80 REMARK 500 2 LYS D 47 -72.13 -127.57 REMARK 500 REMARK 500 THIS ENTRY HAS 245 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1Z0R RELATED DB: PDB REMARK 900 STRUCTURE OF THE N-TERMINAL DOMAIN OF ABRB DBREF 2K1N E 1 25 PDB 2K1N 2K1N 1 25 DBREF 2K1N F 1 25 PDB 2K1N 2K1N 1 25 DBREF1 2K1N A 1 55 UNP A0A063X7Z2_BACIU DBREF2 2K1N A A0A063X7Z2 1 55 DBREF1 2K1N B 1 55 UNP A0A063X7Z2_BACIU DBREF2 2K1N B A0A063X7Z2 1 55 DBREF1 2K1N C 1 55 UNP A0A063X7Z2_BACIU DBREF2 2K1N C A0A063X7Z2 1 55 DBREF1 2K1N D 1 55 UNP A0A063X7Z2_BACIU DBREF2 2K1N D A0A063X7Z2 1 55 SEQRES 1 E 25 DA DT DG DA DT DT DG DA DC DA DA DT DT SEQRES 2 E 25 DA DT DT DG DG DA DA DA DC DC DT DT SEQRES 1 F 25 DA DA DG DG DT DT DT DC DC DA DA DT DA SEQRES 2 F 25 DA DT DT DG DT DC DA DA DT DC DA DT SEQRES 1 A 55 MET LYS SER THR GLY ILE VAL ARG LYS VAL ASP GLU LEU SEQRES 2 A 55 GLY ARG VAL VAL ILE PRO ILE GLU LEU ARG ARG THR LEU SEQRES 3 A 55 GLY ILE ALA GLU LYS ASP ALA LEU GLU ILE TYR VAL ASP SEQRES 4 A 55 ASP GLU LYS ILE ILE LEU LYS LYS TYR LYS PRO ASN MET SEQRES 5 A 55 THR CYS GLN SEQRES 1 B 55 MET LYS SER THR GLY ILE VAL ARG LYS VAL ASP GLU LEU SEQRES 2 B 55 GLY ARG VAL VAL ILE PRO ILE GLU LEU ARG ARG THR LEU SEQRES 3 B 55 GLY ILE ALA GLU LYS ASP ALA LEU GLU ILE TYR VAL ASP SEQRES 4 B 55 ASP GLU LYS ILE ILE LEU LYS LYS TYR LYS PRO ASN MET SEQRES 5 B 55 THR CYS GLN SEQRES 1 C 55 MET LYS SER THR GLY ILE VAL ARG LYS VAL ASP GLU LEU SEQRES 2 C 55 GLY ARG VAL VAL ILE PRO ILE GLU LEU ARG ARG THR LEU SEQRES 3 C 55 GLY ILE ALA GLU LYS ASP ALA LEU GLU ILE TYR VAL ASP SEQRES 4 C 55 ASP GLU LYS ILE ILE LEU LYS LYS TYR LYS PRO ASN MET SEQRES 5 C 55 THR CYS GLN SEQRES 1 D 55 MET LYS SER THR GLY ILE VAL ARG LYS VAL ASP GLU LEU SEQRES 2 D 55 GLY ARG VAL VAL ILE PRO ILE GLU LEU ARG ARG THR LEU SEQRES 3 D 55 GLY ILE ALA GLU LYS ASP ALA LEU GLU ILE TYR VAL ASP SEQRES 4 D 55 ASP GLU LYS ILE ILE LEU LYS LYS TYR LYS PRO ASN MET SEQRES 5 D 55 THR CYS GLN HELIX 1 1 PRO A 19 GLY A 27 1 9 HELIX 2 2 LYS A 49 THR A 53 5 5 HELIX 3 3 PRO B 19 LEU B 26 1 8 HELIX 4 4 PRO C 19 GLY C 27 1 9 HELIX 5 5 PRO D 19 GLY D 27 1 9 SHEET 1 A 6 ILE A 6 LYS A 9 0 SHEET 2 A 6 ALA B 33 ASP B 39 -1 O ILE B 36 N ILE A 6 SHEET 3 A 6 LYS B 42 LYS B 47 -1 O ILE B 44 N TYR B 37 SHEET 4 A 6 LYS A 42 LYS A 46 -1 N ILE A 43 O LEU B 45 SHEET 5 A 6 ALA A 33 ASP A 39 -1 N ASP A 39 O LYS A 42 SHEET 6 A 6 ILE B 6 LYS B 9 -1 O ARG B 8 N LEU A 34 SHEET 1 B 6 ILE C 6 LYS C 9 0 SHEET 2 B 6 ALA D 33 ASP D 39 -1 O ILE D 36 N ILE C 6 SHEET 3 B 6 LYS D 42 LYS D 46 -1 O ILE D 44 N TYR D 37 SHEET 4 B 6 LYS C 42 LYS C 46 -1 N LEU C 45 O ILE D 43 SHEET 5 B 6 ALA C 33 ASP C 39 -1 N TYR C 37 O ILE C 44 SHEET 6 B 6 THR D 4 LYS D 9 -1 O ILE D 6 N ILE C 36 SSBOND 1 CYS A 54 CYS C 54 1555 1555 2.03 SSBOND 2 CYS B 54 CYS D 54 1555 1555 2.03 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