PDB Short entry for 1YUI HEADER DNA BINDING PROTEIN/DNA 31-DEC-96 1YUI TITLE SOLUTION NMR STRUCTURE OF THE GAGA FACTOR/DNA COMPLEX, REGULARIZED TITLE 2 MEAN STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*GP*CP*CP*GP*AP*GP*AP*GP*TP*AP*C)-3'); COMPND 3 CHAIN: B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'-D(*GP*TP*AP*CP*TP*CP*TP*CP*GP*GP*C)-3'); COMPND 7 CHAIN: C; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: GAGA-FACTOR; COMPND 11 CHAIN: A; COMPND 12 FRAGMENT: DNA BINDING DOMAIN, RESIDUES 310 - 372 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: DROSOPHILA MELANOGASTER; SOURCE 7 ORGANISM_COMMON: FRUIT FLY; SOURCE 8 ORGANISM_TAXID: 7227 KEYWDS COMPLEX (DNA-BINDING PROTEIN-DNA), CHROMATIN REMODELING, DNA BINDING KEYWDS 2 PROTEIN-DNA COMPLEX EXPDTA SOLUTION NMR AUTHOR G.M.CLORE,J.G.OMICHINSKI,A.M.GRONENBORN REVDAT 3 02-MAR-22 1YUI 1 REMARK LINK REVDAT 2 24-FEB-09 1YUI 1 VERSN REVDAT 1 31-DEC-97 1YUI 0 JRNL AUTH J.G.OMICHINSKI,P.V.PEDONE,G.FELSENFELD,A.M.GRONENBORN, JRNL AUTH 2 G.M.CLORE JRNL TITL THE SOLUTION STRUCTURE OF A SPECIFIC GAGA FACTOR-DNA COMPLEX JRNL TITL 2 REVEALS A MODULAR BINDING MODE. JRNL REF NAT.STRUCT.BIOL. V. 4 122 1997 JRNL REFN ISSN 1072-8368 JRNL PMID 9033593 JRNL DOI 10.1038/NSB0297-122 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER (X-PLOR (SEE ABOVE)), BRUNGER (X-PLOR (SEE REMARK 3 ABOVE)) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 THE 3D STRUCTURE OF THE GAGA FACTOR/DNA COMPLEX WAS SOLVED REMARK 3 BY MULTI-DIMENSIONAL HETERONUCLEAR-EDITED AND -FILTERED REMARK 3 NMR AND IS BASED ON 1475 EXPERIMENTAL NMR RESTRAINTS: REMARK 3 (A) INTRAPROTEIN: 188 SEQUENTIAL (|I- J|=1), 134 MEDIUM REMARK 3 RANGE (1 < |I-J| <=5) AND 95 LONG RANGE (|I-J| >5) REMARK 3 INTERRESIDUES AND 275 INTRARESIDUE APPROXIMATE INTERPROTON REMARK 3 DISTANCE RESTRAINTS; 140 TORSION ANGLE RESTRAINTS; 33 REMARK 3 THREE-BOND HN-HA COUPLING CONSTANT RESTRAINTS; AND 94 REMARK 3 (48 CALPHA AND 46 CBETA) 13C SHIFT RESTRAINTS. (NUMBERS REMARK 3 OF RESIDUES 10 - 61) REMARK 3 (B) INTRA-DNA: 124 INTRARESIDUE, 112 SEQUENTIAL REMARK 3 INTRASTRAND, 21 INTERSTRAND INTERPROTON DISTANCE REMARK 3 RESTRAINTS; 102 TORSION ANGLE RESTRAINTS (FOR ALPHA, BETA, REMARK 3 GAMMA, DELTA, EPSILON AND AND ZETA BACKBONE TORSION REMARK 3 ANGLES). REMARK 3 (C) INTERMOLECULAR: 75 INTERPROTON DISTANCE RESTRAINTS. REMARK 3 THE EXPERIMENTAL NMR RESTRAINTS ARE SUPPLEMENTED BY REMARK 3 HYDROGEN BONDING RESTRAINTS: 24 DISTANCES FOR 12 BACKBONE REMARK 3 HYDROGEN BONDS WITHIN THE PROTEIN, 58 DISTANCES FOR REMARK 3 WATSON-CRICK BASE-PAIRING WITHIN THE DNA, AND 10 AMBIGUOUS REMARK 3 DISTANCE RESTRAINTS BETWEEN THE PROTEIN AND THE DNA. THE REMARK 3 RESTRAINTS HAVE BEEN DEPOSITED. REMARK 3 REMARK 3 THE STRUCTURES WERE CALCULATED USING THE SIMULATED REMARK 3 ANNEALING PROTOCOL OF NILGES ET AL. (1988) FEBS LETT. 229, REMARK 3 129-136 USING THE PROGRAM X-PLOR 3.1 (BRUNGER) MODIFIED REMARK 3 TO INCORPORATE COUPLING CONSTANT (GARRETT ET AL. (1984) J. REMARK 3 MAGN. RESON. SERIES B 104, 99-103) AND CARBON CHEMICAL REMARK 3 SHIFT (KUSZEWSKI ET AL. (1995) J. MAGN. RESON. SERIES B REMARK 3 106, 92-96) RESTRAINTS, AND A CONFORMATIONAL DATABASE REMARK 3 POTENTIAL (KUSZEWSKI ET AL.(1996) PROTEIN SCI. 5, 1067-1080 REMARK 3 REMARK 3 THE RESTRAINED REGULARIZED MEAN STRUCTURE IS PRESENTED IN REMARK 3 THIS ENTRY AND 50 STRUCTURES ARE PRESENTED IN ENTRY 1YUJ. REMARK 3 IN THE RESTRAINED REGULARIZED MEAN COORDINATES THE LAST REMARK 3 COLUMN REPRESENTS THE AVERAGE RMS DIFFERENCE BETWEEN THE REMARK 3 INDIVIDUAL SIMULATED ANNEALING STRUCTURES AND THE MEAN REMARK 3 COORDINATE POSITIONS. THE LAST COLUMN IN THE INDIVIDUAL SA REMARK 3 STRUCTURES HAS NO MEANING. BEST FITTING TO GENERATE THE REMARK 3 AVERAGE STRUCTURE IS WITH RESPECT TO RESIDUES 14 - 58 OF REMARK 3 THE PROTEIN AND BASE PAIRS 1 - 11 OF THE DNA (RESIDUES 10 - REMARK 3 13 AND 59 - 61 ARE DISORDERED IN SOLUTION). RESIDUE 10 REMARK 3 CORRESPONDS TO RESIDUE 319 OF THE NATURAL SEQUENCE. NOTE REMARK 3 THE OCCUPANCY FIELD HAS NO MEANING. REMARK 4 REMARK 4 1YUI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000177448. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303.50 REMARK 210 PH : 6.00 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : TRIPLE RESONANCE REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AMX500; AMX600 REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : REGULARIZED MEAN STRUCTURE REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: TRIPLE RESONANCE FOR ASSIGNMENT OF PROTEIN 12C- FILTERED REMARK 210 NOE, 12C-FILTERED HOHAHA AND 1H-1H NOE FOR DNA. QUANTITATIVE J REMARK 210 CORRELATION FOR COUPLING CONSTANTS 3D 15N- SEPARATED, 3D 13C- REMARK 210 SEPARATED, 3D 12C-FILTERED 3D 13C- SEPARATED/12C-FILTERED, AND REMARK 210 2D 1H-1H NOE EXPERIMENTS. 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: B, C, 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: 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 DG B 101 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 DC B 102 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 DC B 103 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 DG B 104 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 DA B 105 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 DG B 106 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 DA B 107 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 DG B 108 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 DT B 109 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 DA B 110 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 DC B 111 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 DG C 112 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 DT C 113 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 DT C 113 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 DA C 114 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 DC C 115 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 DT C 116 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DC C 117 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 DT C 118 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 DC C 119 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 DG C 120 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 DG C 121 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 DC C 122 O4' - C1' - N1 ANGL. DEV. = 2.0 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 ALA A 12 76.32 -159.26 REMARK 500 LYS A 23 76.45 -104.38 REMARK 500 PRO A 33 152.93 -37.70 REMARK 500 TYR A 40 17.58 52.98 REMARK 500 HIS A 57 -73.20 -152.68 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 64 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 36 SG REMARK 620 2 CYS A 39 SG 107.3 REMARK 620 3 HIS A 52 NE2 106.2 107.5 REMARK 620 4 HIS A 57 NE2 107.3 121.4 106.3 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 64 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1YUJ RELATED DB: PDB REMARK 900 ENSEMBLE OF 50 STRUCTURES DBREF 1YUI A 10 63 UNP Q08605 GAGA_DROME 319 372 DBREF 1YUI B 101 111 PDB 1YUI 1YUI 101 111 DBREF 1YUI C 112 122 PDB 1YUI 1YUI 112 122 SEQRES 1 B 11 DG DC DC DG DA DG DA DG DT DA DC SEQRES 1 C 11 DG DT DA DC DT DC DT DC DG DG DC SEQRES 1 A 54 PRO LYS ALA LYS ARG ALA LYS HIS PRO PRO GLY THR GLU SEQRES 2 A 54 LYS PRO ARG SER ARG SER GLN SER GLU GLN PRO ALA THR SEQRES 3 A 54 CYS PRO ILE CYS TYR ALA VAL ILE ARG GLN SER ARG ASN SEQRES 4 A 54 LEU ARG ARG HIS LEU GLU LEU ARG HIS PHE ALA LYS PRO SEQRES 5 A 54 GLY VAL HET ZN A 64 1 HETNAM ZN ZINC ION FORMUL 4 ZN ZN 2+ HELIX 1 1 ARG A 25 SER A 28 1 4 HELIX 2 2 SER A 46 ARG A 56 1 11 SHEET 1 A 2 ALA A 34 THR A 35 0 SHEET 2 A 2 VAL A 42 ILE A 43 -1 N ILE A 43 O ALA A 34 LINK SG CYS A 36 ZN ZN A 64 1555 1555 2.30 LINK SG CYS A 39 ZN ZN A 64 1555 1555 2.31 LINK NE2 HIS A 52 ZN ZN A 64 1555 1555 2.00 LINK NE2 HIS A 57 ZN ZN A 64 1555 1555 2.01 SITE 1 AC1 4 CYS A 36 CYS A 39 HIS A 52 HIS A 57 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