10 20 30 40 50 60 70 80 1GCC - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER TRANSCRIPTION/DNA 13-MAR-98 1GCC
TITLE SOLUTION NMR STRUCTURE OF THE COMPLEX OF GCC-BOX BINDING TITLE 2 DOMAIN OF ATERF1 AND GCC-BOX DNA, MINIMIZED AVERAGE TITLE 3 STRUCTURE
COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*TP*AP*GP*CP*CP*GP*CP*CP*AP*GP*C)-3'); COMPND 3 CHAIN: B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'-D(*GP*CP*TP*GP*GP*CP*GP*GP*CP*TP*A)-3'); COMPND 7 CHAIN: C; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: ETHYLENE RESPONSIVE ELEMENT BINDING FACTOR 1; COMPND 11 CHAIN: A; COMPND 12 FRAGMENT: GCC-BOX BINDING DOMAIN; COMPND 13 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES; SOURCE 5 MOL_ID: 3; SOURCE 6 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; SOURCE 7 ORGANISM_COMMON: THALE CRESS; SOURCE 8 ORGANISM_TAXID: 3702; SOURCE 9 CELL_LINE: BL21; SOURCE 10 GENE: ATERF1; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 12 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 13 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 14 EXPRESSION_SYSTEM_PLASMID: PAF104; SOURCE 15 OTHER_DETAILS: DNA-BINDING DOMAIN OF ATERF1;
KEYWDS TRANSCRIPTION FACTOR, PROTEIN-DNA COMPLEX, ETHYLENE KEYWDS 2 INDUCIBLE, COMPLEX (TRANSCRIPTION FACTOR/DNA), KEYWDS 3 TRANSCRIPTION/DNA COMPLEX
EXPDTA SOLUTION NMR
AUTHOR K.YAMASAKI,M.D.ALLEN,M.OHME-TAKAGI,M.TATENO,M.SUZUKI
REVDAT 2 24-FEB-09 1GCC 1 VERSN REVDAT 1 23-MAR-99 1GCC 0
JRNL AUTH M.D.ALLEN,K.YAMASAKI,M.OHME-TAKAGI,M.TATENO, JRNL AUTH 2 M.SUZUKI JRNL TITL A NOVEL MODE OF DNA RECOGNITION BY A BETA-SHEET JRNL TITL 2 REVEALED BY THE SOLUTION STRUCTURE OF THE GCC-BOX JRNL TITL 3 BINDING DOMAIN IN COMPLEX WITH DNA. JRNL REF EMBO J. V. 17 5484 1998 JRNL REFN ISSN 0261-4189 JRNL PMID 9736626 JRNL DOI 10.1093/EMBOJ/17.18.5484
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: SEE REMARK 210 OTHER PROGRAMS USED: REMARK 3 AMBER 4.1 AUTHORS: PEARLMAN,CASE,CALDWELL,ROSS,CHEATHAM III, REMARK 3 FERGUSON,SEIBEL,SINGH,WEINER,KOLLMAN
REMARK 4 REMARK 4 1GCC COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.0 REMARK 210 IONIC STRENGTH : 90 MM REMARK 210 PRESSURE : 1 ATMOSPHERE ATM REMARK 210 SAMPLE CONTENTS : POTASIUM PHOSPHATE REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY, TOCSY, DQF-COSY, 1H- REMARK 210 15N HSQC, 3D 1H-15N NOESY- REMARK 210 HMQC, 3D 1H-15N TOCSY-HMQC, REMARK 210 13C, 15N-FILTERED NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 750 MHZ, 500 MHZ REMARK 210 SPECTROMETER MODEL : DMX750, DMX500 REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : X-PLOR 3.1, AMBER 4.1 REMARK 210 METHOD USED : SIMULATED ANNEALING PROTOCOL REMARK 210 IN X-PLOR 3.1 WAS CARRIED OUT REMARK 210 TO OBTAIN 25 STRUCTURES. REMARK 210 MINIMIZED MEAN STRUCTURE OF REMARK 210 THEM WAS FURTHER REVISED BY A REMARK 210 300 PS RESTRAINED MOLECULAR REMARK 210 DYNAMICAL CALCULATION IN THE REMARK 210 PRESENCE OF APPROXIMATELY 5000 REMARK 210 TIP3P WATER MOLSCULES, USING REMARK 210 CORNELL FORCE FIELD IN AMBER REMARK 210 4.1. THE MEAN CO-ORDINATE OF REMARK 210 200 STRUCTURES OBTAINED AFTER REMARK 210 THE EQUILIBRIUM (100 PS) WAS REMARK 210 ENERGY-MINIMIZED. REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 1 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: SIGNALS DUE TO PROTEINS WERE OBTAINED BY NOESY, TOCSY, REMARK 210 DQF-COSY FOR UNLABELED SAMPLE AND 1H-15N HSQC, 3D 1H-15N NOESY REMARK 210 -HMQC AND 3D 1H-15N TOCSY-HMQC FOR THE SAMPLE WITH 15N-LABELED REMARK 210 PROTEIN. SIGNALS DUE TO DNA WERE OBTAINED BY NOESY, TOCSY, AND REMARK 210 DQF-COSY FOR UNLABELED SAMPLE AND 13C,15N-FILTERED NOESY FOR REMARK 210 SAMPLE WITH 13C, 15N-LABELED PROTEIN. INTERMOLECULAR NOES WERE REMARK 210 IDENTIFIED USING NOESY SPECTRA INCLUDING THOSE WITH AND REMARK 210 WITHOUT 13C- OR 15N-DECOUPLING FOR SAMPLE WITH 13C,15N-LABELED REMARK 210 PROTEIN.
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 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 DC B 6 O4' - C4' - C3' ANGL. DEV. = 3.7 DEGREES REMARK 500 DC B 10 O4' - C4' - C3' ANGL. DEV. = 3.7 DEGREES REMARK 500 DC C 15 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DT C 16 O4' - C4' - C3' ANGL. DEV. = 4.0 DEGREES REMARK 500 DG C 18 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 DG C 20 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 DC C 22 O4' - C4' - C3' ANGL. DEV. = 3.7 DEGREES REMARK 500 ARG A 147 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 ARG A 150 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG A 150 NE - CZ - NH2 ANGL. DEV. = -3.4 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 ARG A 197 74.04 51.83 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 DC B 7 0.07 SIDE_CHAIN REMARK 500 DT C 16 0.07 SIDE_CHAIN REMARK 500 DG C 17 0.06 SIDE_CHAIN REMARK 500 DC C 19 0.09 SIDE_CHAIN REMARK 500 DC C 22 0.07 SIDE_CHAIN REMARK 500 ARG A 147 0.14 SIDE_CHAIN REMARK 500 ARG A 170 0.08 SIDE_CHAIN REMARK 500 TYR A 186 0.10 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL
DBREF 1GCC A 144 206 UNP O80337 ERF1A_ARATH 144 206 DBREF 1GCC B 3 13 PDB 1GCC 1GCC 3 13 DBREF 1GCC C 14 24 PDB 1GCC 1GCC 14 24
SEQRES 1 B 11 DT DA DG DC DC DG DC DC DA DG DC SEQRES 1 C 11 DG DC DT DG DG DC DG DG DC DT DA SEQRES 1 A 63 LYS HIS TYR ARG GLY VAL ARG GLN ARG PRO TRP GLY LYS SEQRES 2 A 63 PHE ALA ALA GLU ILE ARG ASP PRO ALA LYS ASN GLY ALA SEQRES 3 A 63 ARG VAL TRP LEU GLY THR PHE GLU THR ALA GLU ASP ALA SEQRES 4 A 63 ALA LEU ALA TYR ASP ARG ALA ALA PHE ARG MET ARG GLY SEQRES 5 A 63 SER ARG ALA LEU LEU ASN PHE PRO LEU ARG VAL
HELIX 1 1 ALA A 179 ARG A 194 1 16
SHEET 1 A 3 VAL A 149 ARG A 152 0 SHEET 2 A 3 LYS A 156 ASP A 163 -1 N ALA A 158 O ARG A 150 SHEET 3 A 3 ALA A 169 PHE A 176 -1 N PHE A 176 O PHE A 157
LINK N HIS A 145 C LYS A 144 1555 1555 1.34 LINK C HIS A 145 N TYR A 146 1555 1555 1.34
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