HEADER DNA BINDING PROTEIN 28-JUN-22 7YB4 TITLE SOLUTION STRUCTURE OF HOMEODOMAIN OF EXTRADENTICLE COMPND MOL_ID: 1; COMPND 2 MOLECULE: HOMEOBOX PROTEIN EXTRADENTICLE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DPBX; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DROSOPHILA MELANOGASTER; SOURCE 3 ORGANISM_COMMON: FRUIT FLY; SOURCE 4 ORGANISM_TAXID: 7227; SOURCE 5 GENE: EXD, CG8933; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS TRANSCRIPTION FACTOR, HOMEOTIC PROTEIN, DNA BINDING DOMAIN, DNA KEYWDS 2 BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR B.ACHARYA,A.J.BASAK,W.LEE,S.DE REVDAT 2 15-MAY-24 7YB4 1 REMARK REVDAT 1 26-JUL-23 7YB4 0 JRNL AUTH B.ACHARYA,A.J.BASAK,W.LEE,S.DE JRNL TITL SOLUTION STRUCTURE OF HOMEODOMAIN OF EXTRADENTICLE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PONDEROSA-C/S REMARK 3 AUTHORS : LEE, STARK AND MARKLEY REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7YB4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 29-JUN-22. REMARK 100 THE DEPOSITION ID IS D_1300030546. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 5.5 REMARK 210 IONIC STRENGTH : 50 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.6 MM [U-13C; U-15N] HOMEOBOX REMARK 210 PROTEIN EXTRADENTICLE, 90% H2O/ REMARK 210 10% D2O; 0.6 MM [U-13C; U-15N] REMARK 210 HOMEOBOX PROTEIN EXTRADENTICLE, REMARK 210 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D 1H-15N NOESY; 3D HBHA(CO)NH; REMARK 210 3D 1H-13C NOESY ALIPHATIC; 3D 1H- REMARK 210 13C NOESY AROMATIC; 3D HCCH- REMARK 210 TOCSY; 3D 1H-15N TOCSY; 3D H(CCO) REMARK 210 NH; 3D HNCO; 3D HN(CO)CA; 3D REMARK 210 CBCA(CO)NH; 3D HNCACB REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : ASCENDTM REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN, NMRPIPE, NMRFAM-SPARKY REMARK 210 METHOD USED : DGSA-DISTANCE GEOMETRY SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 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: 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: 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 19 PHE A 289 CB - CG - CD2 ANGL. DEV. = 5.3 DEGREES REMARK 500 19 PHE A 289 CB - CG - CD1 ANGL. DEV. = -5.1 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 241 139.63 62.31 REMARK 500 1 ASN A 244 177.29 -58.78 REMARK 500 1 PHE A 245 -171.49 65.91 REMARK 500 1 SER A 246 -179.04 82.71 REMARK 500 1 LYS A 297 152.33 60.99 REMARK 500 1 ASN A 299 151.22 59.80 REMARK 500 2 ARG A 243 -175.10 49.65 REMARK 500 2 PHE A 245 25.11 -175.26 REMARK 500 3 LYS A 241 157.34 49.62 REMARK 500 3 ARG A 243 176.08 -60.00 REMARK 500 3 ASN A 244 174.00 -52.57 REMARK 500 3 LYS A 297 177.07 63.20 REMARK 500 4 HIS A 236 -59.50 -122.14 REMARK 500 4 ARG A 242 -66.95 -100.77 REMARK 500 4 ARG A 243 -74.03 -178.33 REMARK 500 5 ARG A 243 -97.15 -59.52 REMARK 500 5 ASN A 244 72.60 -170.08 REMARK 500 5 PHE A 245 82.87 -152.55 REMARK 500 5 LYS A 297 -105.68 57.79 REMARK 500 6 HIS A 236 89.68 63.78 REMARK 500 6 ALA A 238 55.93 -150.16 REMARK 500 6 ARG A 242 -177.59 48.84 REMARK 500 6 PHE A 245 -23.79 -179.07 REMARK 500 6 TYR A 296 -70.83 -104.89 REMARK 500 6 LYS A 297 169.02 58.67 REMARK 500 7 TYR A 296 -63.90 -100.29 REMARK 500 7 LYS A 298 52.01 -173.36 REMARK 500 8 ARG A 242 151.73 57.24 REMARK 500 8 PHE A 245 40.18 -175.36 REMARK 500 8 ASN A 299 -85.46 -134.13 REMARK 500 9 ARG A 243 34.21 159.87 REMARK 500 9 ASN A 244 -158.21 56.29 REMARK 500 9 LYS A 297 104.32 56.09 REMARK 500 10 SER A 235 91.94 53.70 REMARK 500 10 ARG A 240 -64.79 -95.51 REMARK 500 10 LYS A 241 124.13 57.90 REMARK 500 10 PHE A 245 23.42 -153.36 REMARK 500 11 SER A 235 100.76 56.13 REMARK 500 11 ARG A 242 -38.19 -138.35 REMARK 500 11 LYS A 297 38.72 -88.03 REMARK 500 12 HIS A 236 105.35 58.80 REMARK 500 12 ARG A 242 148.07 -38.71 REMARK 500 12 PHE A 245 45.13 178.56 REMARK 500 12 LYS A 297 137.17 62.78 REMARK 500 13 ARG A 239 179.52 70.58 REMARK 500 14 MET A 237 -69.56 70.31 REMARK 500 14 ALA A 238 115.29 59.64 REMARK 500 14 ARG A 240 70.82 -113.25 REMARK 500 14 LYS A 241 160.57 48.19 REMARK 500 14 ARG A 243 -106.25 85.75 REMARK 500 REMARK 500 THIS ENTRY HAS 76 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 51157 RELATED DB: BMRB DBREF 7YB4 A 238 300 UNP P40427 EXD_DROME 238 300 SEQADV 7YB4 GLY A 234 UNP P40427 EXPRESSION TAG SEQADV 7YB4 SER A 235 UNP P40427 EXPRESSION TAG SEQADV 7YB4 HIS A 236 UNP P40427 EXPRESSION TAG SEQADV 7YB4 MET A 237 UNP P40427 EXPRESSION TAG SEQRES 1 A 67 GLY SER HIS MET ALA ARG ARG LYS ARG ARG ASN PHE SER SEQRES 2 A 67 LYS GLN ALA SER GLU ILE LEU ASN GLU TYR PHE TYR SER SEQRES 3 A 67 HIS LEU SER ASN PRO TYR PRO SER GLU GLU ALA LYS GLU SEQRES 4 A 67 GLU LEU ALA ARG LYS CYS GLY ILE THR VAL SER GLN VAL SEQRES 5 A 67 SER ASN TRP PHE GLY ASN LYS ARG ILE ARG TYR LYS LYS SEQRES 6 A 67 ASN ILE HELIX 1 AA1 PHE A 245 HIS A 260 1 16 HELIX 2 AA2 SER A 267 GLY A 279 1 13 HELIX 3 AA3 THR A 281 LYS A 297 1 17 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 TER 1121 ILE A 300 ENDMDL MODEL 2 TER 1121 ILE A 300 ENDMDL MODEL 3 TER 1121 ILE A 300 ENDMDL MODEL 4 TER 1121 ILE A 300 ENDMDL MODEL 5 TER 1121 ILE A 300 ENDMDL MODEL 6 TER 1121 ILE A 300 ENDMDL MODEL 7 TER 1121 ILE A 300 ENDMDL MODEL 8 TER 1121 ILE A 300 ENDMDL MODEL 9 TER 1121 ILE A 300 ENDMDL MODEL 10 TER 1121 ILE A 300 ENDMDL MODEL 11 TER 1121 ILE A 300 ENDMDL MODEL 12 TER 1121 ILE A 300 ENDMDL MODEL 13 TER 1121 ILE A 300 ENDMDL MODEL 14 TER 1121 ILE A 300 ENDMDL MODEL 15 TER 1121 ILE A 300 ENDMDL MODEL 16 TER 1121 ILE A 300 ENDMDL MODEL 17 TER 1121 ILE A 300 ENDMDL MODEL 18 TER 1121 ILE A 300 ENDMDL MODEL 19 TER 1121 ILE A 300 ENDMDL MODEL 20 TER 1121 ILE A 300 ENDMDL MASTER 167 0 0 3 0 0 0 6 561 1 0 6 END