PDB Short entry for 9ANT HEADER TRANSCRIPTION/DNA 02-JUL-98 9ANT TITLE ANTENNAPEDIA HOMEODOMAIN-DNA COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*AP*GP*AP*AP*AP*GP*CP*CP*AP*TP*TP*AP*GP*AP*G)- COMPND 3 3'); COMPND 4 CHAIN: C, E; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA (5'-D(*TP*CP*TP*CP*TP*AP*AP*TP*GP*GP*CP*TP*TP*TP*C)- COMPND 8 3'); COMPND 9 CHAIN: D, F; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: ANTENNAPEDIA HOMEODOMAIN; COMPND 13 CHAIN: A, B; COMPND 14 FRAGMENT: HOMEODOMAIN; COMPND 15 SYNONYM: HD; COMPND 16 ENGINEERED: YES; COMPND 17 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 MOL_ID: 2; SOURCE 3 MOL_ID: 3; SOURCE 4 ORGANISM_SCIENTIFIC: DROSOPHILA MELANOGASTER; SOURCE 5 ORGANISM_COMMON: FRUIT FLY; SOURCE 6 ORGANISM_TAXID: 7227; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HOMEODOMAIN, DNA-BINDING PROTEIN, COMPLEX (HOMEODOMAIN-DNA), KEYWDS 2 TRANSCRIPTION-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR E.FRAENKEL,C.O.PABO REVDAT 3 03-NOV-21 9ANT 1 REMARK SEQADV LINK REVDAT 2 24-FEB-09 9ANT 1 VERSN REVDAT 1 14-OCT-98 9ANT 0 JRNL AUTH E.FRAENKEL,C.O.PABO JRNL TITL COMPARISON OF X-RAY AND NMR STRUCTURES FOR THE ANTENNAPEDIA JRNL TITL 2 HOMEODOMAIN-DNA COMPLEX. JRNL REF NAT.STRUCT.BIOL. V. 5 692 1998 JRNL REFN ISSN 1072-8368 JRNL PMID 9699632 REMARK 2 REMARK 2 RESOLUTION. 2.40 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) : 2.40 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) (%) : 95.7 REMARK 3 NUMBER OF REFLECTIONS : 17359 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) : 0.218 REMARK 3 FREE R VALUE : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.200 REMARK 3 FREE R VALUE TEST SET COUNT : 1767 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) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.55 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 89.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2361 REMARK 3 BIN R VALUE (WORKING SET) : 0.3360 REMARK 3 BIN FREE R VALUE : 0.3210 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.50 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 276 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.019 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1034 REMARK 3 NUCLEIC ACID ATOMS : 1218 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 38 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) : 0.17000 REMARK 3 B22 (A**2) : -0.26000 REMARK 3 B33 (A**2) : 0.09000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.33 REMARK 3 ESD FROM SIGMAA (A) : 0.44 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) : 0.35 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.38 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.100 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 18.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.120 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) : 2.600 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 3.850 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 4.240 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 6.530 ; 2.500 REMARK 3 REMARK 3 NCS MODEL : NONE 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 9ANT 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_1000180029. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-OCT-97 REMARK 200 TEMPERATURE (KELVIN) : 293 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 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NI FILTER REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17753 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 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: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIR 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 (%): 68.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1-5% MPD 20 MM BIS-TRIS-PROPANE, PH REMARK 280 7.0 10 MM NICL2 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 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 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 47.21000 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 47.21000 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 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 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D, 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: E, F, 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 MET A -1 REMARK 465 GLU A 0 REMARK 465 ARG A 1 REMARK 465 LYS A 2 REMARK 465 ARG A 3 REMARK 465 GLY A 4 REMARK 465 MET B -1 REMARK 465 GLU B 0 REMARK 465 ARG B 1 REMARK 465 LYS B 2 REMARK 465 ARG B 3 REMARK 465 GLY B 4 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT 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 O2 DT D 218 NH2 ARG A 5 2.19 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 DA E 404 0.06 SIDE CHAIN REMARK 500 DC E 407 0.06 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI B 601 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 21 NE2 REMARK 620 2 HIS B 21 NE2 86.2 REMARK 620 3 ASN B 60 ND2 161.4 97.2 REMARK 620 4 ASN B 60 OD1 143.8 101.0 53.6 REMARK 620 5 HOH B 721 O 85.7 84.6 76.5 130.1 REMARK 620 6 HOH B 722 O 84.5 80.5 114.1 62.3 162.6 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI B 601 DBREF 9ANT A 1 60 UNP P02833 ANTP_DROME 1 60 DBREF 9ANT B 1 60 UNP P02833 ANTP_DROME 1 60 DBREF 9ANT C 100 114 PDB 9ANT 9ANT 100 114 DBREF 9ANT D 214 228 PDB 9ANT 9ANT 214 228 DBREF 9ANT E 400 414 PDB 9ANT 9ANT 400 414 DBREF 9ANT F 514 528 PDB 9ANT 9ANT 514 528 SEQADV 9ANT SER A 39 UNP P02833 CYS 39 ENGINEERED MUTATION SEQADV 9ANT SER B 39 UNP P02833 CYS 39 ENGINEERED MUTATION SEQRES 1 C 15 DA DG DA DA DA DG DC DC DA DT DT DA DG SEQRES 2 C 15 DA DG SEQRES 1 D 15 DT DC DT DC DT DA DA DT DG DG DC DT DT SEQRES 2 D 15 DT DC SEQRES 1 E 15 DA DG DA DA DA DG DC DC DA DT DT DA DG SEQRES 2 E 15 DA DG SEQRES 1 F 15 DT DC DT DC DT DA DA DT DG DG DC DT DT SEQRES 2 F 15 DT DC SEQRES 1 A 62 MET GLU ARG LYS ARG GLY ARG GLN THR TYR THR ARG TYR SEQRES 2 A 62 GLN THR LEU GLU LEU GLU LYS GLU PHE HIS PHE ASN ARG SEQRES 3 A 62 TYR LEU THR ARG ARG ARG ARG ILE GLU ILE ALA HIS ALA SEQRES 4 A 62 LEU SER LEU THR GLU ARG GLN ILE LYS ILE TRP PHE GLN SEQRES 5 A 62 ASN ARG ARG MET LYS TRP LYS LYS GLU ASN SEQRES 1 B 62 MET GLU ARG LYS ARG GLY ARG GLN THR TYR THR ARG TYR SEQRES 2 B 62 GLN THR LEU GLU LEU GLU LYS GLU PHE HIS PHE ASN ARG SEQRES 3 B 62 TYR LEU THR ARG ARG ARG ARG ILE GLU ILE ALA HIS ALA SEQRES 4 B 62 LEU SER LEU THR GLU ARG GLN ILE LYS ILE TRP PHE GLN SEQRES 5 B 62 ASN ARG ARG MET LYS TRP LYS LYS GLU ASN HET NI B 601 1 HETNAM NI NICKEL (II) ION FORMUL 7 NI NI 2+ FORMUL 8 HOH *38(H2 O) HELIX 1 1 ARG A 10 PHE A 22 1 13 HELIX 2 2 ARG A 28 LEU A 38 1 11 HELIX 3 3 GLU A 42 LYS A 58 1 17 HELIX 4 4 ARG B 10 PHE B 22 1 13 HELIX 5 5 ARG B 28 LEU B 38 1 11 HELIX 6 6 GLU B 42 LYS B 58 1 17 LINK NE2 HIS A 21 NI NI B 601 3656 1555 2.14 LINK NE2 HIS B 21 NI NI B 601 3655 1555 2.19 LINK ND2 ASN B 60 NI NI B 601 1555 1555 2.36 LINK OD1 ASN B 60 NI NI B 601 1555 1555 2.59 LINK NI NI B 601 O HOH B 721 1555 3655 2.03 LINK NI NI B 601 O HOH B 722 1555 3655 2.10 SITE 1 AC1 5 HIS A 21 HIS B 21 ASN B 60 HOH B 721 SITE 2 AC1 5 HOH B 722 CRYST1 61.050 77.750 94.420 90.00 90.00 90.00 P 2 2 21 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 0.016380 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012862 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010591 0.00000