PDB Short entry for 1FJL HEADER TRANSCRIPTION/DNA 17-DEC-95 1FJL TITLE HOMEODOMAIN FROM THE DROSOPHILA PAIRED PROTEIN BOUND TO A DNA TITLE 2 OLIGONUCLEOTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PAIRED PROTEIN; COMPND 3 CHAIN: A, B, C; COMPND 4 FRAGMENT: HOMEODOMAIN; COMPND 5 SYNONYM: PRD, PAIRED PROTEIN; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: DNA (5'-D(*AP*AP*TP*AP*AP*TP*CP*TP*GP*AP*TP*TP*AP*C)-3'); COMPND 10 CHAIN: D; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: DNA (5'-D(*TP*GP*TP*AP*AP*TP*CP*AP*GP*AP*TP*TP*AP*T)-3'); COMPND 14 CHAIN: E; COMPND 15 ENGINEERED: YES; COMPND 16 MOL_ID: 4; COMPND 17 MOLECULE: DNA (5'-D(*TP*GP*TP*AP*AP*TP*CP*TP*GP*AP*TP*TP*AP*C)-3'); COMPND 18 CHAIN: F; COMPND 19 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 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 SYNTHETIC: YES; SOURCE 9 MOL_ID: 3; SOURCE 10 SYNTHETIC: YES; SOURCE 11 MOL_ID: 4; SOURCE 12 SYNTHETIC: YES KEYWDS DNA-BINDING PROTEIN, DNA, PAIRED BOX, TRANSCRIPTION REGULATION, KEYWDS 2 TRANSCRIPTION-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR D.S.WILSON,B.GUENTHER,C.DESPLAN,J.KURIYAN REVDAT 4 07-FEB-24 1FJL 1 REMARK REVDAT 3 03-NOV-21 1FJL 1 SEQADV REVDAT 2 24-FEB-09 1FJL 1 VERSN REVDAT 1 20-JUN-96 1FJL 0 JRNL AUTH D.S.WILSON,B.GUENTHER,C.DESPLAN,J.KURIYAN JRNL TITL HIGH RESOLUTION CRYSTAL STRUCTURE OF A PAIRED (PAX) CLASS JRNL TITL 2 COOPERATIVE HOMEODOMAIN DIMER ON DNA. JRNL REF CELL(CAMBRIDGE,MASS.) V. 82 709 1995 JRNL REFN ISSN 0092-8674 JRNL PMID 7671301 JRNL DOI 10.1016/0092-8674(95)90468-9 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : NULL REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.198 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1530 REMARK 3 NUCLEIC ACID ATOMS : 966 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 243 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.018 REMARK 3 BOND ANGLES (DEGREES) : 2.800 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE FOLLOWING SIDE CHAINS HAVE REMARK 3 BEEN OMITTED FROM THE MODEL BECAUSE THEIR CONFORMATION REMARK 3 WAS NOT EVIDENT FROM ELECTRON DENSITY MAPS: REMARK 3 HOMEODOMAIN NO. 1: RESIDUES 122, 133, 158. REMARK 3 HOMEODOMAIN NO. 2: RESIDUES 233, 236, 239, 255, 258. REMARK 3 HOMEODOMAIN NO. 3: RESIDUES 300, 324, 357, 358. REMARK 3 REMARK 3 DUE TO THE TWO-FOLD AVERAGING OF THE DNA DUPLEXES, REMARK 3 ALTERNATE SIDE CHAIN IDENTITIES HAVE BEEN MODELED IN THE REMARK 3 FOLLOWING WAY: REMARK 3 REMARK 3 ALTERNATE SIDE CHAIN FOR RESIDUE A D 1A: REMARK 3 RESIDUE T D 1B REMARK 3 REMARK 3 ALTERNATE SIDE CHAIN FOR RESIDUE T D 8A: REMARK 3 RESIDUE A D 8B REMARK 3 REMARK 3 ALTERNATE SIDE CHAIN FOR RESIDUE T E 1A: REMARK 3 RESIDUE A E 1B REMARK 3 REMARK 3 ALTERNATE SIDE CHAIN FOR RESIDUE A E 8A: REMARK 3 RESIDUE T E 8B REMARK 3 REMARK 3 ALTERNATE SIDE CHAIN FOR RESIDUE T F 1A: REMARK 3 RESIDUE A F 1B REMARK 3 REMARK 3 ALTERNATE SIDE CHAIN FOR RESIDUE T F 8A: REMARK 3 RESIDUE A F 8B REMARK 3 REMARK 3 TWO OF THE WATER MOLECULES ARE EXCLUDED BY ONE OF THE TWO REMARK 3 ALTERNATE SIDE CHAINS AT DNA RESIDUES NO. 408 AND 508, AS REMARK 3 FOLLOWS: REMARK 3 REMARK 3 WATER RESIDUE NO. 941 IS PRESENT WITH THE ALTERNATE SIDE REMARK 3 CHAIN REPRESENTED BY RESIDUE 508 BUT NOT 528. REMARK 3 REMARK 3 WATER RESIDUE NO. 942 IS PRESENT WITH THE ALTERNATE SIDE REMARK 3 CHAIN REPRESENTED BY RESIDUE 428 BUT NOT 408. REMARK 4 REMARK 4 1FJL 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_1000173310. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : NULL REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.09 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.42 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 38.61500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 38.61500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 36.10500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 73.44500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 36.10500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 73.44500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 38.61500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 36.10500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 73.44500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 38.61500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 36.10500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 73.44500 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 300 REMARK: A COMPLEX OF TWO HOMEODOMAINS (THE PROTEIN COMPONENT) REMARK 300 BOUND TO ONE 14 BASE PAIR DNA DUPLEX IS THE MOLECULAR REMARK 300 SPECIES ANALYZED IN THIS STUDY. EACH OF THE DNA DUPLEX AND REMARK 300 THE COMPLEX HAS PSEUDO TWO-FOLD SYMMETRY ABOUT ITS CENTER. REMARK 300 THE ASYMMETRIC UNIT CONTAINS 1.5 COMPLEXES, ONE OF WHICH IS REMARK 300 COMPLETELY CONTAINED WITHIN THE ASYMMETRIC UNIT AND THE REMARK 300 OTHER OF IS BISECTED AT ITS CENTER OF SYMMETRY BY A REMARK 300 CRYSTALLOGRAPHIC TWO-FOLD AXIS. THE TWO-FOLD AVERAGED REMARK 300 COMPLEX WAS MODELED AS A COMPLETE SINGLE HOMEODOMAIN AND A REMARK 300 COMPLETE SINGLE STRAND OF THE DUPLEX. THEREFORE, THE MODEL REMARK 300 CONTAINS THREE HOMEODOMAINS AND THREE DNA STRANDS. 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: A, B, D, E 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, F 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 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 146.89000 REMARK 350 BIOMT3 2 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 -16 REMARK 465 ASP A -15 REMARK 465 ILE A -14 REMARK 465 SER A -13 REMARK 465 ASP A -12 REMARK 465 CYS A -11 REMARK 465 GLU A -10 REMARK 465 SER A -9 REMARK 465 GLU A -8 REMARK 465 PRO A -7 REMARK 465 GLY A -6 REMARK 465 ILE A -5 REMARK 465 ALA A -4 REMARK 465 LEU A -3 REMARK 465 LYS A -2 REMARK 465 ARG A -1 REMARK 465 GLU B -16 REMARK 465 ASP B -15 REMARK 465 ILE B -14 REMARK 465 SER B -13 REMARK 465 ASP B -12 REMARK 465 CYS B -11 REMARK 465 GLU B -10 REMARK 465 SER B -9 REMARK 465 GLU B -8 REMARK 465 PRO B -7 REMARK 465 GLY B -6 REMARK 465 ILE B -5 REMARK 465 ALA B -4 REMARK 465 LEU B -3 REMARK 465 LYS B -2 REMARK 465 ARG B -1 REMARK 465 LYS B 0 REMARK 465 GLN B 59 REMARK 465 HIS B 60 REMARK 465 THR B 61 REMARK 465 SER B 62 REMARK 465 VAL B 63 REMARK 465 SER B 64 REMARK 465 GLU C -16 REMARK 465 ASP C -15 REMARK 465 ILE C -14 REMARK 465 SER C -13 REMARK 465 ASP C -12 REMARK 465 CYS C -11 REMARK 465 GLU C -10 REMARK 465 SER C -9 REMARK 465 GLU C -8 REMARK 465 PRO C -7 REMARK 465 GLY C -6 REMARK 465 ILE C -5 REMARK 465 ALA C -4 REMARK 465 LEU C -3 REMARK 465 LYS C -2 REMARK 465 ARG C -1 REMARK 465 GLN C 59 REMARK 465 HIS C 60 REMARK 465 THR C 61 REMARK 465 SER C 62 REMARK 465 VAL C 63 REMARK 465 SER C 64 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG A 22 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 33 CG CD OE1 OE2 REMARK 470 GLN A 36 CD OE1 NE2 REMARK 470 ASN A 39 CG OD1 ND2 REMARK 470 LYS A 58 CG CD CE NZ REMARK 470 GLU B 33 CD OE1 OE2 REMARK 470 GLN B 36 CD OE1 NE2 REMARK 470 ASN B 39 OD1 ND2 REMARK 470 ARG B 55 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 58 O CD CE NZ REMARK 470 LYS C 0 CB CG CD CE NZ REMARK 470 GLN C 24 CD OE1 NE2 REMARK 470 ARG C 57 CG CD NE CZ NH1 NH2 REMARK 470 LYS C 58 CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OP1 DA D 8 O HOH A 858 6565 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 DA D 1 N9 DA D 1 C4 -0.040 REMARK 500 DT D 1 C5 DT D 1 C7 0.038 REMARK 500 DA D 2 C5' DA D 2 C4' 0.071 REMARK 500 DT D 3 O3' DT D 3 C3' -0.043 REMARK 500 DT D 6 C5 DT D 6 C7 0.055 REMARK 500 DC D 7 O3' DA D 8 P -0.261 REMARK 500 DA D 8 C5' DA D 8 C4' 0.049 REMARK 500 DG D 9 C4' DG D 9 C3' -0.062 REMARK 500 DT E 1 C5 DT E 1 C7 0.038 REMARK 500 DA E 1 O3' DG E 2 P -0.103 REMARK 500 DT E 3 C5 DT E 3 C7 0.048 REMARK 500 DA E 4 N3 DA E 4 C4 0.059 REMARK 500 DC E 7 C5' DC E 7 C4' 0.048 REMARK 500 DC E 7 O3' DT E 8 P 0.160 REMARK 500 DT E 8 C5 DT E 8 C7 0.059 REMARK 500 DT E 8 O3' DG E 9 P -0.074 REMARK 500 DA E 10 N3 DA E 10 C4 0.036 REMARK 500 DA E 10 N9 DA E 10 C4 0.040 REMARK 500 DA F 1 C5' DA F 1 C4' 0.052 REMARK 500 DA F 1 O3' DG F 2 P -0.091 REMARK 500 DG F 2 C6 DG F 2 N1 -0.062 REMARK 500 DA F 4 N3 DA F 4 C4 0.042 REMARK 500 DT F 6 C5 DT F 6 C7 0.058 REMARK 500 DC F 7 O3' DA F 8 P 0.177 REMARK 500 DT F 8 C5 DT F 8 C7 0.036 REMARK 500 DA F 8 O3' DG F 9 P 0.149 REMARK 500 DA F 13 O3' DA F 13 C3' -0.057 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 ARG B 3 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 DA D 1 O4' - C1' - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 DA D 1 N1 - C2 - N3 ANGL. DEV. = 3.3 DEGREES REMARK 500 DT D 1 N1 - C2 - N3 ANGL. DEV. = 4.0 DEGREES REMARK 500 DT D 1 C3' - O3' - P ANGL. DEV. = -19.6 DEGREES REMARK 500 DA D 2 O3' - P - OP2 ANGL. DEV. = 11.6 DEGREES REMARK 500 DA D 2 O4' - C1' - N9 ANGL. DEV. = -6.2 DEGREES REMARK 500 DT D 3 C4 - C5 - C6 ANGL. DEV. = 4.3 DEGREES REMARK 500 DT D 3 C5 - C6 - N1 ANGL. DEV. = -3.9 DEGREES REMARK 500 DT D 3 N3 - C2 - O2 ANGL. DEV. = -3.9 DEGREES REMARK 500 DA D 5 O4' - C4' - C3' ANGL. DEV. = 3.8 DEGREES REMARK 500 DT D 6 C4 - C5 - C7 ANGL. DEV. = 4.8 DEGREES REMARK 500 DT D 6 C6 - C5 - C7 ANGL. DEV. = -5.9 DEGREES REMARK 500 DC D 7 N3 - C4 - C5 ANGL. DEV. = -2.4 DEGREES REMARK 500 DC D 7 C3' - O3' - P ANGL. DEV. = 27.3 DEGREES REMARK 500 DA D 8 O4' - C1' - N9 ANGL. DEV. = -9.0 DEGREES REMARK 500 DG D 9 O3' - P - O5' ANGL. DEV. = 29.9 DEGREES REMARK 500 DG D 9 O3' - P - OP1 ANGL. DEV. = -30.0 DEGREES REMARK 500 DG D 9 C5' - C4' - O4' ANGL. DEV. = 7.3 DEGREES REMARK 500 DG D 9 O4' - C1' - N9 ANGL. DEV. = 7.7 DEGREES REMARK 500 DG D 9 N3 - C4 - C5 ANGL. DEV. = -3.3 DEGREES REMARK 500 DG D 9 N9 - C4 - C5 ANGL. DEV. = 2.5 DEGREES REMARK 500 DG D 9 N1 - C6 - O6 ANGL. DEV. = -4.2 DEGREES REMARK 500 DA D 10 P - O5' - C5' ANGL. DEV. = -9.9 DEGREES REMARK 500 DA D 10 O4' - C1' - N9 ANGL. DEV. = 8.6 DEGREES REMARK 500 DT D 11 C4 - C5 - C6 ANGL. DEV. = 4.2 DEGREES REMARK 500 DT D 11 C6 - C5 - C7 ANGL. DEV. = -4.5 DEGREES REMARK 500 DT D 12 C4 - C5 - C6 ANGL. DEV. = 3.6 DEGREES REMARK 500 DA D 13 C3' - C2' - C1' ANGL. DEV. = -5.3 DEGREES REMARK 500 DA D 13 O4' - C1' - C2' ANGL. DEV. = -5.9 DEGREES REMARK 500 DC D 14 O4' - C1' - C2' ANGL. DEV. = -7.9 DEGREES REMARK 500 DC D 14 O4' - C1' - N1 ANGL. DEV. = 7.1 DEGREES REMARK 500 DT E 1 C6 - C5 - C7 ANGL. DEV. = -5.5 DEGREES REMARK 500 DT E 1 C3' - O3' - P ANGL. DEV. = -10.1 DEGREES REMARK 500 DA E 1 C3' - O3' - P ANGL. DEV. = -15.4 DEGREES REMARK 500 DG E 2 O4' - C1' - C2' ANGL. DEV. = 3.1 DEGREES REMARK 500 DG E 2 C3' - O3' - P ANGL. DEV. = 8.3 DEGREES REMARK 500 DT E 3 O4' - C1' - N1 ANGL. DEV. = 6.8 DEGREES REMARK 500 DT E 3 C6 - C5 - C7 ANGL. DEV. = -4.7 DEGREES REMARK 500 DA E 4 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 DA E 5 O4' - C1' - C2' ANGL. DEV. = -7.7 DEGREES REMARK 500 DT E 6 C1' - O4' - C4' ANGL. DEV. = -8.6 DEGREES REMARK 500 DT E 6 O4' - C1' - C2' ANGL. DEV. = -5.5 DEGREES REMARK 500 DT E 6 C4 - C5 - C6 ANGL. DEV. = 4.8 DEGREES REMARK 500 DT E 6 C6 - C5 - C7 ANGL. DEV. = -5.1 DEGREES REMARK 500 DC E 7 C1' - O4' - C4' ANGL. DEV. = -8.5 DEGREES REMARK 500 DC E 7 C3' - O3' - P ANGL. DEV. = 7.8 DEGREES REMARK 500 DC E 7 C3' - O3' - P ANGL. DEV. = -9.0 DEGREES REMARK 500 DT E 8 N3 - C2 - O2 ANGL. DEV. = -3.8 DEGREES REMARK 500 DT E 8 C6 - C5 - C7 ANGL. DEV. = -4.5 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 107 ANGLE DEVIATIONS. 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 DT E 12 0.06 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE STANDARD HOMEODOMAIN NUMBERING SYSTEM (SEE, FOR REMARK 999 EXAMPLE, KISSINGER, C.R., LIU, B., MARTIN-BLANCO, E., REMARK 999 KORNBERG, T.B. AND PABO, C.O. (1990). CELL 63, 357 - 590) REMARK 999 RELATES TO THE NUMBERING OF THE RESIDUES OF THE THREE REMARK 999 HOMEODOMAINS IN THIS STRUCTURE IN THE FOLLOWING WAY: THE REMARK 999 HOMEODOMAIN IS A 60 AMINO ACID MOTIF AND IS REFERRED TO REMARK 999 HEREAFTER AS THE "HOMEODOMAIN PROPER". REMARK 999 REMARK 999 THE PROTEIN THAT WAS CRYSTALLIZED CONTAINS 17 ENDOGENOUS REMARK 999 AMINO ACIDS UPSTREAM AND 4 AMINO ACIDS DOWNSTREAM OF THE 60 REMARK 999 AMINO ACID HOMEODOMAIN PROPER. FOR EACH OF THE REMARK 999 HOMEODOMAINS, THE RESIDUES ARE NUMBERED AS FOLLOWS, WITH REMARK 999 SEGMENT IDENTIFIERS AS INDICATED: REMARK 999 REMARK 999 HOMEODOMAIN NO. 1: RESIDUES A 0 - A 64, WHERE RESIDUES A 1 REMARK 999 - A 60 CORRESPOND TO THE HOMEODOMAIN PROPER. REMARK 999 REMARK 999 HOMEODOMAIN NO. 2: RESIDUES B 1 - B 58, WHERE RESIDUES B 1 REMARK 999 - B 58 CORRESPOND TO THE HOMEODOMAIN PROPER (THE LAST 2 REMARK 999 RESIDUES ARE DISORDERED AND SO NOT IN THE MODEL). REMARK 999 REMARK 999 HOMEODOMAIN NO. 3: RESIDUES C 0 - C 58, WHERE RESIDUES C 1 REMARK 999 - C 58 CORRESPOND TO THE HOMEODOMAIN PROPER (THE LAST 2 REMARK 999 RESIDUES ARE DISORDERED AND SO NOT IN THE MODEL). DBREF 1FJL A -16 64 UNP P06601 PRD_DROME 196 276 DBREF 1FJL B -16 64 UNP P06601 PRD_DROME 196 276 DBREF 1FJL C -16 64 UNP P06601 PRD_DROME 196 276 DBREF 1FJL D 1 14 PDB 1FJL 1FJL 1 14 DBREF 1FJL E 1 14 PDB 1FJL 1FJL 1 14 DBREF 1FJL F 1 14 PDB 1FJL 1FJL 1 14 SEQADV 1FJL SER A 4 UNP P06601 CYS 216 ENGINEERED MUTATION SEQADV 1FJL GLN A 50 UNP P06601 SER 262 ENGINEERED MUTATION SEQADV 1FJL SER B 4 UNP P06601 CYS 216 ENGINEERED MUTATION SEQADV 1FJL GLN B 50 UNP P06601 SER 262 ENGINEERED MUTATION SEQADV 1FJL SER C 4 UNP P06601 CYS 216 ENGINEERED MUTATION SEQADV 1FJL GLN C 50 UNP P06601 SER 262 ENGINEERED MUTATION SEQRES 1 A 81 GLU ASP ILE SER ASP CYS GLU SER GLU PRO GLY ILE ALA SEQRES 2 A 81 LEU LYS ARG LYS GLN ARG ARG SER ARG THR THR PHE SER SEQRES 3 A 81 ALA SER GLN LEU ASP GLU LEU GLU ARG ALA PHE GLU ARG SEQRES 4 A 81 THR GLN TYR PRO ASP ILE TYR THR ARG GLU GLU LEU ALA SEQRES 5 A 81 GLN ARG THR ASN LEU THR GLU ALA ARG ILE GLN VAL TRP SEQRES 6 A 81 PHE GLN ASN ARG ARG ALA ARG LEU ARG LYS GLN HIS THR SEQRES 7 A 81 SER VAL SER SEQRES 1 B 81 GLU ASP ILE SER ASP CYS GLU SER GLU PRO GLY ILE ALA SEQRES 2 B 81 LEU LYS ARG LYS GLN ARG ARG SER ARG THR THR PHE SER SEQRES 3 B 81 ALA SER GLN LEU ASP GLU LEU GLU ARG ALA PHE GLU ARG SEQRES 4 B 81 THR GLN TYR PRO ASP ILE TYR THR ARG GLU GLU LEU ALA SEQRES 5 B 81 GLN ARG THR ASN LEU THR GLU ALA ARG ILE GLN VAL TRP SEQRES 6 B 81 PHE GLN ASN ARG ARG ALA ARG LEU ARG LYS GLN HIS THR SEQRES 7 B 81 SER VAL SER SEQRES 1 C 81 GLU ASP ILE SER ASP CYS GLU SER GLU PRO GLY ILE ALA SEQRES 2 C 81 LEU LYS ARG LYS GLN ARG ARG SER ARG THR THR PHE SER SEQRES 3 C 81 ALA SER GLN LEU ASP GLU LEU GLU ARG ALA PHE GLU ARG SEQRES 4 C 81 THR GLN TYR PRO ASP ILE TYR THR ARG GLU GLU LEU ALA SEQRES 5 C 81 GLN ARG THR ASN LEU THR GLU ALA ARG ILE GLN VAL TRP SEQRES 6 C 81 PHE GLN ASN ARG ARG ALA ARG LEU ARG LYS GLN HIS THR SEQRES 7 C 81 SER VAL SER SEQRES 1 D 14 DA DA DT DA DA DT DC DT DG DA DT DT DA SEQRES 2 D 14 DC SEQRES 1 E 14 DT DG DT DA DA DT DC DA DG DA DT DT DA SEQRES 2 E 14 DT SEQRES 1 F 14 DT DG DT DA DA DT DC DT DG DA DT DT DA SEQRES 2 F 14 DC FORMUL 7 HOH *243(H2 O) HELIX 1 1 ALA A 10 ARG A 22 1 13 HELIX 2 2 ILE A 28 THR A 38 1 11 HELIX 3 3 GLU A 42 VAL A 63 1 22 HELIX 4 4 ALA B 10 ARG B 22 1 13 HELIX 5 5 ILE B 28 THR B 38 1 11 HELIX 6 6 GLU B 42 ARG B 57 1 16 HELIX 7 7 ALA C 10 ARG C 22 1 13 HELIX 8 8 ILE C 28 THR C 38 1 11 HELIX 9 9 GLU C 42 ARG C 57 1 16 CRYST1 72.210 146.890 77.230 90.00 90.00 90.00 C 2 2 21 24 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 0.013848 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006808 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012948 0.00000