HEADER DNA BINDING PROTEIN/DNA 06-MAY-98 1NK3 TITLE VND/NK-2 HOMEODOMAIN/DNA COMPLEX, NMR, MINIMIZED AVERAGE TITLE 2 STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'- COMPND 3 D(*TP*GP*TP*GP*TP*CP*AP*AP*GP*TP*GP*GP*CP*TP*GP*T)-3'); COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA (5'- COMPND 8 D(*AP*CP*AP*GP*CP*CP*AP*CP*TP*TP*GP*AP*CP*AP*CP*A)-3'); COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: HOMEOBOX PROTEIN VND; COMPND 13 CHAIN: P; COMPND 14 FRAGMENT: HOMEODOMAIN; COMPND 15 SYNONYM: VND/NK-2 HOMEODOMAIN, VENTRAL NERVOUS SYSTEM COMPND 16 DEFECTIVE PROTEIN, HOMEOBOX PROTEIN NK-2; COMPND 17 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: DROSOPHILA MELANOGASTER; SOURCE 7 ORGANISM_COMMON: FRUIT FLY; SOURCE 8 ORGANISM_TAXID: 7227; SOURCE 9 ORGAN: FRUIT; SOURCE 10 GENE: POTENTIAL; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 13 EXPRESSION_SYSTEM_PLASMID: PET11D KEYWDS HOMEODOMAIN, HOMEOBOX, DNA-BINDING PROTEIN, EMBRYONIC KEYWDS 2 DEVELOPMENT, COMPLEX (HOMEODOMAIN/DNA), DNA BINDING KEYWDS 3 PROTEIN/DNA COMPLEX EXPDTA SOLUTION NMR AUTHOR J.M.GRUSCHUS,D.H.H.TSAO,L.-H.WANG,M.NIRENBERG,J.A.FERRETTI REVDAT 3 24-FEB-09 1NK3 1 VERSN REVDAT 2 23-FEB-99 1NK3 3 COMPND REMARK TITLE DBREF REVDAT 2 2 3 HEADER TER ATOM SEQRES REVDAT 2 3 3 JRNL KEYWDS HELIX REVDAT 1 09-DEC-98 1NK3 0 JRNL AUTH J.M.GRUSCHUS,D.H.TSAO,L.H.WANG,M.NIRENBERG, JRNL AUTH 2 J.A.FERRETTI JRNL TITL INTERACTIONS OF THE VND/NK-2 HOMEODOMAIN WITH DNA JRNL TITL 2 BY NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY: BASIS JRNL TITL 3 OF BINDING SPECIFICITY. JRNL REF BIOCHEMISTRY V. 36 5372 1997 JRNL REFN ISSN 0006-2960 JRNL PMID 9154919 JRNL DOI 10.1021/BI9620060 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH J.M.GRUSCHUS,D.H.TSAO,L.H.WANG,M.NIRENBERG, REMARK 1 AUTH 2 J.A.FERRETTI REMARK 1 TITL INTERACTIONS OF THE VND/NK-2 HOMEODOMAIN WITH DNA REMARK 1 TITL 2 BY NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY: BASIS REMARK 1 TITL 3 OF BINDING SPECIFICITY REMARK 1 REF BIOCHEMISTRY V. 36 5372 1997 REMARK 1 REFN ISSN 0006-2960 REMARK 1 REFERENCE 2 REMARK 1 AUTH D.H.TSAO,J.M.GRUSCHUS,L.H.WANG,M.NIRENBERG, REMARK 1 AUTH 2 J.A.FERRETTI REMARK 1 TITL THE THREE-DIMENSIONAL SOLUTION STRUCTURE OF THE REMARK 1 TITL 2 NK-2 HOMEODOMAIN FROM DROSOPHILA REMARK 1 REF J.MOL.BIOL. V. 251 297 1995 REMARK 1 REFN ISSN 0022-2836 REMARK 1 REFERENCE 3 REMARK 1 AUTH D.H.TSAO,J.M.GRUSCHUS,L.H.WANG,M.NIRENBERG, REMARK 1 AUTH 2 J.A.FERRETTI REMARK 1 TITL ELONGATION OF HELIX III OF THE NK-2 HOMEODOMAIN REMARK 1 TITL 2 UPON BINDING TO DNA: A SECONDARY STRUCTURE STUDY REMARK 1 TITL 3 BY NMR REMARK 1 REF BIOCHEMISTRY V. 33 15053 1994 REMARK 1 REFN ISSN 0006-2960 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : INSIGHT II 97 AUTHOR : MSI MSI REMARK 3 AUTHORS : JONES,ZOU,COWAN,KJELDGAARD REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NMR REFINE/INSIGHT II 97 REMARK 4 REMARK 4 1NK3 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) : 308 REMARK 210 PH : 6.0 REMARK 210 IONIC STRENGTH : 60MM REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : H2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 15N-EDITED 3D NOESY H2O, 13C- REMARK 210 EDITED 3D NOESY D2O, 12C- REMARK 210 FILTERED 2D NOESY D2O, 1-1 REMARK 210 SEMISELECTIVE 2D NOESY H2O, REMARK 210 DEUTERIUM EXCHANGE 15N 2D HMQC REMARK 210 H2O, QUANTITATIVE HN-HALPHA J- REMARK 210 COUPLING REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AMX600 REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMR REFINE REFINE REMARK 210 METHOD USED : DISTANCE GEOMETRY/ SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 80 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : LEAST RESTRAINT VIOLATION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: THIS MODEL IS THE AVERAGE STRUCTURE OF THE ENSEMBLE OF REMARK 210 20 STRUCTURES (1NK2). THE UNSTRUCTURED N-TERMINAL AND C- REMARK 210 TERMINAL AMINO ACIDS (P 101-P 107 AND P 171-P 177 IN PDB ENTRY REMARK 210 1NK2) WERE REMOVED PRIOR TO MINIMIZATION OF THE AVERAGE REMARK 210 STRUCTURE BY THE MD_SCHE DULE PROGRAM OF INSIGHTII/NMR REFINE, REMARK 210 SUBJECT TO ALL EXPERIMENTAL RESTRAINTS FOR THE DNA AND REMARK 210 REMAINING PROTEIN RESIDUES. THE REMAINING PROTEIN RESIDUES ARE REMARK 210 RENUMBERED STARTING WITH P 100 SO THAT THE RESIDUE NUMBERING REMARK 210 FOLLOWS THE STANDARD, CANONICAL NUMBER ING SCHEME FOR REMARK 210 HOMEODOMAINS. 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 RES C SSSEQI REMARK 465 ALA P 93 REMARK 465 SER P 94 REMARK 465 ASP P 95 REMARK 465 GLY P 96 REMARK 465 LEU P 97 REMARK 465 PRO P 98 REMARK 465 ASN P 99 REMARK 465 LYS P 163 REMARK 465 GLY P 164 REMARK 465 TYR P 165 REMARK 465 GLU P 166 REMARK 465 GLY P 167 REMARK 465 HIS P 168 REMARK 465 PRO P 169 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 DT A 1 C2' DT A 1 C1' 0.060 REMARK 500 DG A 9 C6 DG A 9 N1 0.046 REMARK 500 DG A 11 C6 DG A 11 N1 0.046 REMARK 500 DC A 13 C4 DC A 13 C5 0.049 REMARK 500 DG A 15 C6 DG A 15 N1 0.042 REMARK 500 DC B 18 C4 DC B 18 C5 0.049 REMARK 500 DA B 32 O3' DA B 32 C3' -0.038 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 DT A 1 O4' - C4' - C3' ANGL. DEV. = -2.6 DEGREES REMARK 500 DG A 2 C5 - C6 - N1 ANGL. DEV. = -3.9 DEGREES REMARK 500 DG A 2 N1 - C6 - O6 ANGL. DEV. = 4.8 DEGREES REMARK 500 DT A 1 C3' - O3' - P ANGL. DEV. = 10.8 DEGREES REMARK 500 DT A 3 P - O5' - C5' ANGL. DEV. = -16.9 DEGREES REMARK 500 DG A 4 C5 - C6 - N1 ANGL. DEV. = -4.4 DEGREES REMARK 500 DG A 4 C6 - C5 - N7 ANGL. DEV. = -3.7 DEGREES REMARK 500 DG A 4 N1 - C6 - O6 ANGL. DEV. = 5.8 DEGREES REMARK 500 DT A 5 N3 - C4 - O4 ANGL. DEV. = 3.7 DEGREES REMARK 500 DT A 5 C4 - C5 - C7 ANGL. DEV. = -4.1 DEGREES REMARK 500 DC A 6 C2 - N3 - C4 ANGL. DEV. = 3.2 DEGREES REMARK 500 DA A 8 P - O5' - C5' ANGL. DEV. = -12.3 DEGREES REMARK 500 DA A 8 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 DA A 8 C6 - N1 - C2 ANGL. DEV. = 4.1 DEGREES REMARK 500 DA A 8 C2 - N3 - C4 ANGL. DEV. = -3.1 DEGREES REMARK 500 DA A 8 C5 - C6 - N6 ANGL. DEV. = 5.3 DEGREES REMARK 500 DG A 9 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 DG A 9 C5 - C6 - N1 ANGL. DEV. = -4.4 DEGREES REMARK 500 DG A 9 N1 - C6 - O6 ANGL. DEV. = 5.6 DEGREES REMARK 500 DG A 9 C8 - N9 - C1' ANGL. DEV. = 8.5 DEGREES REMARK 500 DG A 9 C4 - N9 - C1' ANGL. DEV. = -8.0 DEGREES REMARK 500 DG A 11 C5 - C6 - N1 ANGL. DEV. = -3.1 DEGREES REMARK 500 DG A 11 N1 - C6 - O6 ANGL. DEV. = 4.2 DEGREES REMARK 500 DG A 12 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 DG A 12 C5 - C6 - N1 ANGL. DEV. = -4.9 DEGREES REMARK 500 DG A 12 N1 - C6 - O6 ANGL. DEV. = 4.8 DEGREES REMARK 500 DC A 13 C4 - C5 - C6 ANGL. DEV. = -3.4 DEGREES REMARK 500 DG A 15 O4' - C1' - N9 ANGL. DEV. = -6.6 DEGREES REMARK 500 DG A 15 C5 - C6 - N1 ANGL. DEV. = -4.4 DEGREES REMARK 500 DG A 15 N1 - C6 - O6 ANGL. DEV. = 4.3 DEGREES REMARK 500 DT A 16 O4' - C4' - C3' ANGL. DEV. = -4.3 DEGREES REMARK 500 DT A 16 C4 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 DT A 16 C6 - C5 - C7 ANGL. DEV. = 3.9 DEGREES REMARK 500 DA B 17 O4' - C1' - N9 ANGL. DEV. = -5.0 DEGREES REMARK 500 DA B 17 C3' - O3' - P ANGL. DEV. = 7.8 DEGREES REMARK 500 DA B 19 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DG B 20 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES REMARK 500 DG B 20 C5 - C6 - N1 ANGL. DEV. = -4.5 DEGREES REMARK 500 DG B 20 N1 - C6 - O6 ANGL. DEV. = 3.9 DEGREES REMARK 500 DC B 21 C2 - N3 - C4 ANGL. DEV. = 3.0 DEGREES REMARK 500 DC B 21 C3' - O3' - P ANGL. DEV. = 8.6 DEGREES REMARK 500 DA B 23 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 DA B 23 C6 - N1 - C2 ANGL. DEV. = 3.7 DEGREES REMARK 500 DC B 24 C6 - N1 - C2 ANGL. DEV. = 2.7 DEGREES REMARK 500 DC B 24 C2 - N1 - C1' ANGL. DEV. = -8.0 DEGREES REMARK 500 DT B 25 N3 - C4 - O4 ANGL. DEV. = 3.8 DEGREES REMARK 500 DT B 26 N3 - C4 - O4 ANGL. DEV. = 3.6 DEGREES REMARK 500 DT B 26 C4 - C5 - C7 ANGL. DEV. = -5.5 DEGREES REMARK 500 DT B 26 C6 - C5 - C7 ANGL. DEV. = 4.9 DEGREES REMARK 500 DG B 27 C5 - C6 - N1 ANGL. DEV. = -3.8 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 63 ANGLE DEVIATIONS. 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 P 102 51.16 -92.36 REMARK 500 LYS P 103 66.82 31.84 REMARK 500 ARG P 139 22.87 85.47 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 DG A 4 0.06 SIDE_CHAIN REMARK 500 DG A 9 0.06 SIDE_CHAIN REMARK 500 DT B 26 0.12 SIDE_CHAIN REMARK 500 DA B 28 0.09 SIDE_CHAIN REMARK 500 PHE P 149 0.09 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1NK2 RELATED DB: PDB REMARK 900 ENSEMBLE OF 20 STRUCTURES DBREF 1NK3 P 100 162 UNP P22808 VND_DROME 68 130 DBREF 1NK3 A 1 16 PDB 1NK3 1NK3 1 16 DBREF 1NK3 B 17 32 PDB 1NK3 1NK3 17 32 SEQRES 1 A 16 DT DG DT DG DT DC DA DA DG DT DG DG DC SEQRES 2 A 16 DT DG DT SEQRES 1 B 16 DA DC DA DG DC DC DA DC DT DT DG DA DC SEQRES 2 B 16 DA DC DA SEQRES 1 P 77 ALA SER ASP GLY LEU PRO ASN LYS LYS ARG LYS ARG ARG SEQRES 2 P 77 VAL LEU PHE THR LYS ALA GLN THR TYR GLU LEU GLU ARG SEQRES 3 P 77 ARG PHE ARG GLN GLN ARG TYR LEU SER ALA PRO GLU ARG SEQRES 4 P 77 GLU HIS LEU ALA SER LEU ILE ARG LEU THR PRO THR GLN SEQRES 5 P 77 VAL LYS ILE TRP PHE GLN ASN HIS ARG TYR LYS THR LYS SEQRES 6 P 77 ARG ALA GLN ASN GLU LYS GLY TYR GLU GLY HIS PRO HELIX 1 I LYS P 110 GLN P 122 1 13 HELIX 2 II ALA P 128 ILE P 138 1 11 HELIX 3 III PRO P 142 GLU P 162 1 21 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 MASTER 242 0 0 3 0 0 0 6 0 0 0 10 END