HEADER DNA BINDING PROTEIN 16-JUN-99 1QRY TITLE HOMEOBOX PROTEIN VND (VENTRAL NERVOUS SYSTEM DEFECTIVE PROTEIN) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (HOMEOBOX VENTRAL NERVOUS SYSTEM DEFECTIVE COMPND 3 PROTEIN); COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: VND/NK2 HOMEODOMAIN; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DROSOPHILA MELANOGASTER; SOURCE 3 ORGANISM_COMMON: FRUIT FLY; SOURCE 4 ORGANISM_TAXID: 7227; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE)PLYSS; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET-15B KEYWDS HELIX-TURN-HELIX, DNA-BINDING PROTEIN, DNA BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR B.XIANG REVDAT 4 02-MAR-22 1QRY 1 KEYWDS REMARK REVDAT 3 24-FEB-09 1QRY 1 VERSN REVDAT 2 31-MAY-05 1QRY 1 JRNL REMARK COMPND REVDAT 1 06-JUL-99 1QRY 0 JRNL AUTH K.J.HWANG,B.XIANG,J.M.GRUSCHUS,K.Y.NAM,K.T.NO,M.NIRENBERG, JRNL AUTH 2 J.A.FERRETTI JRNL TITL DISTORTION OF THE THREE-DIMENSIONAL STRUCTURE OF THE JRNL TITL 2 VND/NK-2 HOMEODOMAIN BOUND TO DNA INDUCED BY AN JRNL TITL 3 EMBRYONICALLY LETHAL A35T POINT MUTATION. JRNL REF BIOCHEMISTRY V. 42 12522 2003 JRNL REFN ISSN 0006-2960 JRNL PMID 14580198 JRNL DOI 10.1021/BI030116I REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NMRPIPE, X-PLOR REMARK 3 AUTHORS : DELAGLIO (NMRPIPE), BRUNGER (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON 1146 NOE REMARK 3 -DERIVED DISTANCE RESTRAINTS AND 43 DIHEDRAL ANGLE RESTRAINTS. REMARK 4 REMARK 4 1QRY COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-JUN-99. REMARK 100 THE DEPOSITION ID IS D_1000009193. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 308 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.7 MM A35T VND/NK2-DNA COMPLEX; REMARK 210 A35T VND/NK2 IS 15N SINGLE- REMARK 210 LABELED; 90% H2O, 10% D2O; PH REMARK 210 6.8; 0.7 MM A35T VND/NK2-DNA REMARK 210 COMPLEX; A35T VND/NK2 IS 15N/13C REMARK 210 DOUBLE-LABELED; 90% H2O, 10% D2O; REMARK 210 PH 6.8; 0.7 MM A35T VND/NK2-DNA REMARK 210 COMPLEX; A35T VND/NK2 IS 15N/13C REMARK 210 DOUBLE-LABELED; 100% D2O; PH6.8 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 15N-1H HSQC; 3D CBCANH; 3D REMARK 210 CBCA(CO)NH; 3D HBHA(CO)NH; 3D REMARK 210 HNHA; 3D HCCH-TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : X-PLOR REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH ACCEPTABLE REMARK 210 COVALENT GEOMETRY,STRUCTURES REMARK 210 WITH THE LEAST RESTRAINT REMARK 210 VIOLATIONS,STRUCTURES WITH THE REMARK 210 LOWEST ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: 3D 15N EDITED NOESY-HSQC, 4D 15N/13C EDITED HMQC-NOESY REMARK 210 -HSQC, AND 4D 13C/13C EDITED HMQC-NOESY-HSQC WERE USED FOR REMARK 210 OBTAINING NOE RESTRAINTS. 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 HG1 THR A 20 H GLN A 23 1.29 REMARK 500 O HIS A 63 H THR A 67 1.34 REMARK 500 O PHE A 60 H ARG A 64 1.37 REMARK 500 O LEU A 37 HH12 ARG A 42 1.49 REMARK 500 O LEU A 45 H LEU A 48 1.56 REMARK 500 O ARG A 42 H LEU A 45 1.58 REMARK 500 O GLU A 43 OG1 THR A 46 2.15 REMARK 500 O LEU A 45 N LEU A 48 2.16 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 PRO A 40 C - N - CD ANGL. DEV. = -16.5 DEGREES REMARK 500 2 PRO A 40 C - N - CD ANGL. DEV. = -16.0 DEGREES REMARK 500 6 PRO A 40 C - N - CD ANGL. DEV. = -14.9 DEGREES REMARK 500 7 PRO A 40 C - N - CD ANGL. DEV. = -16.2 DEGREES REMARK 500 9 PRO A 40 C - N - CD ANGL. DEV. = -15.6 DEGREES REMARK 500 10 PRO A 40 C - N - CD ANGL. DEV. = -14.4 DEGREES REMARK 500 12 PRO A 40 C - N - CD ANGL. DEV. = -18.3 DEGREES REMARK 500 14 PRO A 40 C - N - CD ANGL. DEV. = -13.9 DEGREES REMARK 500 16 PRO A 40 C - N - CD ANGL. DEV. = -18.2 DEGREES REMARK 500 17 PRO A 40 C - N - CD ANGL. DEV. = -18.2 DEGREES REMARK 500 18 PRO A 40 C - N - CD ANGL. DEV. = -18.8 DEGREES REMARK 500 19 PRO A 40 C - N - CD ANGL. DEV. = -19.9 DEGREES REMARK 500 20 PRO A 40 C - N - CD ANGL. DEV. = -19.2 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 LYS A 12 -164.49 -77.09 REMARK 500 1 ARG A 13 42.29 -101.25 REMARK 500 1 ARG A 15 109.48 167.53 REMARK 500 1 ARG A 16 171.62 -45.44 REMARK 500 1 LEU A 18 -154.16 -148.60 REMARK 500 1 LYS A 21 -16.66 -43.49 REMARK 500 1 GLN A 23 -80.49 -40.55 REMARK 500 1 THR A 24 -35.64 -33.44 REMARK 500 1 TYR A 25 -76.25 -66.33 REMARK 500 1 LEU A 37 140.28 -35.22 REMARK 500 1 SER A 38 -141.60 -123.54 REMARK 500 1 GLU A 43 -61.86 -26.99 REMARK 500 1 THR A 46 -22.40 -36.71 REMARK 500 1 LEU A 48 -90.17 -64.71 REMARK 500 1 ILE A 49 31.86 -98.81 REMARK 500 1 ARG A 50 -2.01 45.27 REMARK 500 1 LEU A 51 95.84 -46.68 REMARK 500 1 THR A 52 129.51 -35.03 REMARK 500 1 PRO A 53 -82.09 -23.57 REMARK 500 1 THR A 67 -15.57 -42.85 REMARK 500 1 GLU A 73 -85.90 -87.47 REMARK 500 1 LYS A 74 -148.85 34.54 REMARK 500 1 GLU A 77 118.90 68.37 REMARK 500 1 HIS A 79 101.48 -172.26 REMARK 500 2 HIS A 3 110.26 51.48 REMARK 500 2 ASP A 6 107.57 56.90 REMARK 500 2 PRO A 9 23.83 -79.59 REMARK 500 2 ASN A 10 -20.39 -147.42 REMARK 500 2 LYS A 11 -42.89 81.50 REMARK 500 2 LYS A 12 143.54 56.54 REMARK 500 2 ARG A 13 43.53 -93.39 REMARK 500 2 LYS A 14 -75.58 55.34 REMARK 500 2 ARG A 16 166.26 -39.53 REMARK 500 2 VAL A 17 150.89 -48.39 REMARK 500 2 LEU A 18 -121.23 -95.59 REMARK 500 2 PHE A 19 149.46 58.27 REMARK 500 2 LYS A 21 -28.65 -36.04 REMARK 500 2 GLN A 23 -87.53 -43.70 REMARK 500 2 THR A 24 -24.94 -32.59 REMARK 500 2 TYR A 25 -75.01 -74.75 REMARK 500 2 ARG A 32 -72.41 -60.59 REMARK 500 2 LEU A 37 138.00 -32.53 REMARK 500 2 SER A 38 -140.06 -125.60 REMARK 500 2 THR A 46 -13.18 -44.07 REMARK 500 2 LEU A 48 -90.14 -70.22 REMARK 500 2 ARG A 50 -14.05 48.04 REMARK 500 2 LEU A 51 103.11 -39.11 REMARK 500 2 THR A 52 147.06 -30.44 REMARK 500 2 PRO A 53 -84.17 -51.74 REMARK 500 2 THR A 67 -15.30 -41.81 REMARK 500 REMARK 500 THIS ENTRY HAS 512 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL DBREF 1QRY A 5 80 UNP P22808 VND_DROME 538 613 SEQRES 1 A 80 GLY SER HIS MET SER ASP GLY LEU PRO ASN LYS LYS ARG SEQRES 2 A 80 LYS ARG ARG VAL LEU PHE THR LYS ALA GLN THR TYR GLU SEQRES 3 A 80 LEU GLU ARG ARG PHE ARG GLN GLN ARG TYR LEU SER ALA SEQRES 4 A 80 PRO GLU ARG GLU HIS LEU THR SER LEU ILE ARG LEU THR SEQRES 5 A 80 PRO THR GLN VAL LYS ILE TRP PHE GLN ASN HIS ARG TYR SEQRES 6 A 80 LYS THR LYS ARG ALA GLN ASN GLU LYS GLY TYR GLU GLY SEQRES 7 A 80 HIS PRO HELIX 1 1 THR A 20 GLN A 34 1 15 HELIX 2 2 SER A 38 LEU A 48 1 11 HELIX 3 3 THR A 52 LYS A 74 1 23 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 MODEL 2 MODEL 3 MODEL 4 MODEL 5 MODEL 6 MODEL 7 MODEL 8 MODEL 9 MODEL 10 MODEL 11 MODEL 12 MODEL 13 MODEL 14 MODEL 15 MODEL 16 MODEL 17 MODEL 18 MODEL 19 MODEL 20