HEADER TRANSCRIPTION/DNA 13-JUL-98 3HDD TITLE ENGRAILED HOMEODOMAIN DNA COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*TP*TP*TP*TP*GP*CP*CP*AP*TP*GP*TP*AP*AP*TP*TP*AP*CP*CP COMPND 3 *TP*AP*A)-3'; COMPND 4 CHAIN: C; COMPND 5 FRAGMENT: HOMEODOMAIN; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: 5'-D(*AP*TP*TP*AP*GP*GP*TP*AP*AP*TP*TP*AP*CP*AP*TP*GP*GP*CP COMPND 9 *AP*AP*A)-3'; COMPND 10 CHAIN: D; COMPND 11 FRAGMENT: HOMEODOMAIN; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: ENGRAILED HOMEODOMAIN; COMPND 15 CHAIN: A, B; COMPND 16 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: HOMEODOMAIN SEQUENCE FROM DROSOPHILA MELANOGASTER SOURCE 4 (FRUIT FLY); SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 OTHER_DETAILS: HOMEODOMAIN SEQUENCE FROM DROSOPHILA MELANOGASTER SOURCE 8 (FRUIT FLY); SOURCE 9 MOL_ID: 3; SOURCE 10 ORGANISM_SCIENTIFIC: DROSOPHILA MELANOGASTER; SOURCE 11 ORGANISM_COMMON: FRUIT FLY; SOURCE 12 ORGANISM_TAXID: 7227; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DNA BINDING, COMPLEX (DNA BINDING PROTEIN-DNA), TRANSCRIPTION-DNA KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR E.FRAENKEL,M.A.ROULD,K.A.CHAMBERS,C.O.PABO REVDAT 3 02-AUG-23 3HDD 1 REMARK REVDAT 2 24-FEB-09 3HDD 1 VERSN REVDAT 1 11-NOV-98 3HDD 0 JRNL AUTH E.FRAENKEL,M.A.ROULD,K.A.CHAMBERS,C.O.PABO JRNL TITL ENGRAILED HOMEODOMAIN-DNA COMPLEX AT 2.2 A RESOLUTION: A JRNL TITL 2 DETAILED VIEW OF THE INTERFACE AND COMPARISON WITH OTHER JRNL TITL 3 ENGRAILED STRUCTURES. JRNL REF J.MOL.BIOL. V. 284 351 1998 JRNL REFN ISSN 0022-2836 JRNL PMID 9813123 JRNL DOI 10.1006/JMBI.1998.2147 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 10000000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 93.7 REMARK 3 NUMBER OF REFLECTIONS : 17663 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.204 REMARK 3 FREE R VALUE : 0.232 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1760 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.006 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.34 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 75.60 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2002 REMARK 3 BIN R VALUE (WORKING SET) : 0.3500 REMARK 3 BIN FREE R VALUE : 0.3260 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 198 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.023 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 956 REMARK 3 NUCLEIC ACID ATOMS : 855 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 53 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 39.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 56.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.48000 REMARK 3 B22 (A**2) : 0.11000 REMARK 3 B33 (A**2) : 0.37000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.66000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.31 REMARK 3 ESD FROM SIGMAA (A) : 0.42 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.33 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.37 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 19.20 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.210 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 2.110 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 3.520 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 3.890 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 6.470 ; 2.500 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PARNDBX.DNA REMARK 3 PARAMETER FILE 2 : PARHCSDX.PRO REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPNDBX.DNA REMARK 3 TOPOLOGY FILE 2 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 3HDD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY NDB. REMARK 100 THE DEPOSITION ID IS D_1000178998. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JUL-95 REMARK 200 TEMPERATURE (KELVIN) : 123 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NI MIRROR AND NI FILTER REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IIC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18176 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.0 REMARK 200 DATA REDUNDANCY : 2.600 REMARK 200 R MERGE (I) : 0.04200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 25.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.30 REMARK 200 COMPLETENESS FOR SHELL (%) : 70.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.20000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: PDB ENTRY 1HDD REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.41 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: COMPLEX WAS CRYSTALLIZED BY HANGING REMARK 280 DROP VAPOR DIFFUSION OVER 0.26M AMOAC AND 1% PEG400., PH 7.0, REMARK 280 VAPOR DIFFUSION - HANGING DROP, VAPOR DIFFUSION, HANGING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 65.31000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.76000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 65.31000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 22.76000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D, A, B 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLU A 1 REMARK 465 LYS A 2 REMARK 465 ARG A 3 REMARK 465 PRO A 4 REMARK 465 THR A 60 REMARK 465 GLU B 1 REMARK 465 LYS B 2 REMARK 465 SER B 59 REMARK 465 THR B 60 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 ASN A 23 108.31 -161.16 REMARK 500 LYS A 58 72.32 -100.12 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 C 217 0.07 SIDE CHAIN REMARK 500 DC C 218 0.06 SIDE CHAIN REMARK 500 DG D 327 0.05 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 3HDD A 1 60 UNP P02836 HMEN_DROME 454 513 DBREF 3HDD B 1 60 UNP P02836 HMEN_DROME 454 513 DBREF 3HDD C 201 221 PDB 3HDD 3HDD 201 221 DBREF 3HDD D 322 342 PDB 3HDD 3HDD 322 342 SEQRES 1 C 21 DT DT DT DT DG DC DC DA DT DG DT DA DA SEQRES 2 C 21 DT DT DA DC DC DT DA DA SEQRES 1 D 21 DA DT DT DA DG DG DT DA DA DT DT DA DC SEQRES 2 D 21 DA DT DG DG DC DA DA DA SEQRES 1 A 60 GLU LYS ARG PRO ARG THR ALA PHE SER SER GLU GLN LEU SEQRES 2 A 60 ALA ARG LEU LYS ARG GLU PHE ASN GLU ASN ARG TYR LEU SEQRES 3 A 60 THR GLU ARG ARG ARG GLN GLN LEU SER SER GLU LEU GLY SEQRES 4 A 60 LEU ASN GLU ALA GLN ILE LYS ILE TRP PHE GLN ASN LYS SEQRES 5 A 60 ARG ALA LYS ILE LYS LYS SER THR SEQRES 1 B 60 GLU LYS ARG PRO ARG THR ALA PHE SER SER GLU GLN LEU SEQRES 2 B 60 ALA ARG LEU LYS ARG GLU PHE ASN GLU ASN ARG TYR LEU SEQRES 3 B 60 THR GLU ARG ARG ARG GLN GLN LEU SER SER GLU LEU GLY SEQRES 4 B 60 LEU ASN GLU ALA GLN ILE LYS ILE TRP PHE GLN ASN LYS SEQRES 5 B 60 ARG ALA LYS ILE LYS LYS SER THR FORMUL 5 HOH *53(H2 O) HELIX 1 1 SER A 10 GLU A 22 1SEE REMARK 650 13 HELIX 2 2 GLU A 28 LEU A 38 1 11 HELIX 3 3 GLU A 42 LYS A 57 1 16 HELIX 4 4 SER B 10 GLU B 22 1SEE REMARK 650 13 HELIX 5 5 GLU B 28 LEU B 38 1 11 HELIX 6 6 GLU B 42 LYS B 57 1 16 CRYST1 130.620 45.520 72.930 90.00 118.32 90.00 C 1 2 1 8 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 0.007656 0.000000 0.004126 0.00000 SCALE2 0.000000 0.021968 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015576 0.00000