PDB Short entry for 3A01 HEADER GENE REGULATION/DNA 28-FEB-09 3A01 TITLE CRYSTAL STRUCTURE OF ARISTALESS AND CLAWLESS HOMEODOMAINS BOUND TO DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: HOMEODOMAIN-CONTAINING PROTEIN; COMPND 3 CHAIN: A, E; COMPND 4 FRAGMENT: CLAWLESS HOMEOBOX, RESIDUES 170-261; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: HOMEOBOX PROTEIN ARISTALESS; COMPND 8 CHAIN: B, F; COMPND 9 FRAGMENT: HOMEOBOX, RESIDUES 80-146; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: 5'-D(*GP*GP*CP*TP*TP*AP*AP*TP*TP*AP*AP*TP*TP*GP*CP*GP*G)- COMPND 13 3'; COMPND 14 CHAIN: C, G; COMPND 15 ENGINEERED: YES; COMPND 16 MOL_ID: 4; COMPND 17 MOLECULE: 5'-D(*CP*CP*GP*CP*AP*AP*TP*TP*AP*AP*TP*TP*AP*AP*GP*CP*C)- COMPND 18 3'; COMPND 19 CHAIN: D, H; COMPND 20 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: C15, CG7937; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: DROSOPHILA MELANOGASTER; SOURCE 10 ORGANISM_COMMON: FRUIT FLY; SOURCE 11 ORGANISM_TAXID: 7227; SOURCE 12 GENE: AL, CG3935; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 15 MOL_ID: 3; SOURCE 16 SYNTHETIC: YES; SOURCE 17 MOL_ID: 4; SOURCE 18 SYNTHETIC: YES KEYWDS HOMEODOMAIN, PROTEIN-DNA COMPLEX, DNA-BINDING, HOMEOBOX, NUCLEUS, KEYWDS 2 DEVELOPMENTAL PROTEIN, GENE REGULATION-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR K.MIYAZONO,K.NAGATA,K.SAIGO,T.KOJIMA,M.TANOKURA REVDAT 4 01-NOV-23 3A01 1 SEQADV REVDAT 3 19-MAY-10 3A01 1 JRNL REVDAT 2 28-APR-10 3A01 1 JRNL REVDAT 1 09-MAR-10 3A01 0 JRNL AUTH K.MIYAZONO,Y.ZHI,Y.TAKAMURA,K.NAGATA,K.SAIGO,T.KOJIMA, JRNL AUTH 2 M.TANOKURA JRNL TITL COOPERATIVE DNA-BINDING AND SEQUENCE-RECOGNITION MECHANISM JRNL TITL 2 OF ARISTALESS AND CLAWLESS JRNL REF EMBO J. V. 29 1613 2010 JRNL REFN ISSN 0261-4189 JRNL PMID 20389279 JRNL DOI 10.1038/EMBOJ.2010.53 REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.65 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 17051 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 + TEST SET) : 0.234 REMARK 3 R VALUE (WORKING SET) : 0.228 REMARK 3 FREE R VALUE : 0.283 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.200 REMARK 3 FREE R VALUE TEST SET COUNT : 1943 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.77 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1242 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.3540 REMARK 3 BIN FREE R VALUE SET COUNT : 121 REMARK 3 BIN FREE R VALUE : 0.4080 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2286 REMARK 3 NUCLEIC ACID ATOMS : 1382 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 0 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.793 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.367 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.279 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.936 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.904 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3884 ; 0.011 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5508 ; 1.769 ; 2.389 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 259 ; 5.990 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 131 ;33.494 ;20.840 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 452 ;21.424 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 41 ;16.837 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): NULL ; NULL ; NULL REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2491 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1540 ; 0.220 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2488 ; 0.309 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 133 ; 0.181 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 38 ; 0.151 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 3 ; 0.172 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3A01 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 03-MAR-09. REMARK 100 THE DEPOSITION ID IS D_1000028640. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : AR-NW12A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XSCALE REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18995 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 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 (%) : 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: PDB ENTRIES 3A02, 3A03, AND 1PUF REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.06 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 35.46500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 55.34000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 42.70000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 55.34000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 35.46500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 42.70000 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6760 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13040 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -25.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6190 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12620 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -29.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: E, F, G, H 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 169 REMARK 465 ARG A 248 REMARK 465 GLU A 249 REMARK 465 ALA A 250 REMARK 465 GLU A 251 REMARK 465 ARG A 252 REMARK 465 GLN A 253 REMARK 465 ALA A 254 REMARK 465 ALA A 255 REMARK 465 ASN A 256 REMARK 465 ARG A 257 REMARK 465 LEU A 258 REMARK 465 MET A 259 REMARK 465 LEU A 260 REMARK 465 SER A 261 REMARK 465 ALA B 80 REMARK 465 PRO B 81 REMARK 465 LYS B 82 REMARK 465 ARG B 83 REMARK 465 LYS B 84 REMARK 465 GLN B 85 REMARK 465 GLN B 143 REMARK 465 GLU B 144 REMARK 465 LYS B 145 REMARK 465 VAL B 146 REMARK 465 MET E 169 REMARK 465 ALA E 170 REMARK 465 ARG E 171 REMARK 465 ARG E 172 REMARK 465 ILE E 173 REMARK 465 GLY E 174 REMARK 465 LYS E 184 REMARK 465 ARG E 185 REMARK 465 LYS E 186 REMARK 465 LYS E 187 REMARK 465 PRO E 188 REMARK 465 ARG E 248 REMARK 465 GLU E 249 REMARK 465 ALA E 250 REMARK 465 GLU E 251 REMARK 465 ARG E 252 REMARK 465 GLN E 253 REMARK 465 ALA E 254 REMARK 465 ALA E 255 REMARK 465 ASN E 256 REMARK 465 ARG E 257 REMARK 465 LEU E 258 REMARK 465 MET E 259 REMARK 465 LEU E 260 REMARK 465 SER E 261 REMARK 465 ALA F 80 REMARK 465 PRO F 81 REMARK 465 LYS F 82 REMARK 465 ARG F 83 REMARK 465 LYS F 84 REMARK 465 GLN F 85 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 NH2 ARG F 89 O2 DT G 5 2.15 REMARK 500 OE2 GLU E 201 NH1 ARG E 236 2.15 REMARK 500 NH1 ARG E 215 OP1 DC H 2 2.18 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 C 6 O3' DA C 6 C3' -0.051 REMARK 500 DG C 14 O3' DG C 14 C3' -0.050 REMARK 500 DA D 9 O3' DA D 9 C3' -0.043 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 DG C 1 O4' - C4' - C3' ANGL. DEV. = -2.8 DEGREES REMARK 500 DT C 5 C3' - C2' - C1' ANGL. DEV. = -5.1 DEGREES REMARK 500 DT C 5 O4' - C1' - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 DA C 6 O4' - C1' - N9 ANGL. DEV. = -7.4 DEGREES REMARK 500 DA C 10 O4' - C1' - N9 ANGL. DEV. = -4.5 DEGREES REMARK 500 DA C 10 C3' - O3' - P ANGL. DEV. = 9.2 DEGREES REMARK 500 DT C 13 O4' - C1' - N1 ANGL. DEV. = -5.6 DEGREES REMARK 500 DG C 14 O4' - C1' - N9 ANGL. DEV. = 6.2 DEGREES REMARK 500 DG C 17 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 DG D 3 O4' - C1' - N9 ANGL. DEV. = -5.1 DEGREES REMARK 500 DA D 6 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 DT D 7 O5' - P - OP1 ANGL. DEV. = 8.8 DEGREES REMARK 500 DT D 7 O4' - C4' - C3' ANGL. DEV. = -4.9 DEGREES REMARK 500 DT D 7 C5' - C4' - O4' ANGL. DEV. = 10.8 DEGREES REMARK 500 DT D 7 C1' - O4' - C4' ANGL. DEV. = -7.8 DEGREES REMARK 500 DT D 7 C4' - C3' - C2' ANGL. DEV. = -9.7 DEGREES REMARK 500 DT D 7 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 DT D 8 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 DA D 9 O5' - C5' - C4' ANGL. DEV. = -6.9 DEGREES REMARK 500 DA D 9 O4' - C1' - N9 ANGL. DEV. = -5.2 DEGREES REMARK 500 DA D 10 O4' - C1' - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 DT D 11 C5' - C4' - O4' ANGL. DEV. = 7.5 DEGREES REMARK 500 DT D 11 C1' - O4' - C4' ANGL. DEV. = -8.1 DEGREES REMARK 500 DT D 11 O4' - C1' - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 DT D 11 C4 - C5 - C7 ANGL. DEV. = 4.7 DEGREES REMARK 500 DT D 12 O4' - C1' - N1 ANGL. DEV. = -5.9 DEGREES REMARK 500 DA D 13 C3' - C2' - C1' ANGL. DEV. = -5.0 DEGREES REMARK 500 DA D 14 O4' - C1' - N9 ANGL. DEV. = -6.5 DEGREES REMARK 500 DG D 15 C3' - C2' - C1' ANGL. DEV. = -6.3 DEGREES REMARK 500 DG D 15 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 DC D 17 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 DT G 5 O4' - C1' - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 DT G 5 C4 - C5 - C7 ANGL. DEV. = 3.9 DEGREES REMARK 500 DT G 5 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 DA G 6 O4' - C1' - N9 ANGL. DEV. = -5.5 DEGREES REMARK 500 DT G 8 N3 - C2 - O2 ANGL. DEV. = -3.6 DEGREES REMARK 500 DA G 11 O4' - C4' - C3' ANGL. DEV. = -5.1 DEGREES REMARK 500 DA G 11 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 DG G 14 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 DC G 15 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 DG G 16 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 DC H 1 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 DT H 7 O4' - C4' - C3' ANGL. DEV. = -5.6 DEGREES REMARK 500 DT H 7 C1' - O4' - C4' ANGL. DEV. = -10.2 DEGREES REMARK 500 DT H 7 C4' - C3' - C2' ANGL. DEV. = -8.1 DEGREES REMARK 500 DT H 7 O4' - C1' - N1 ANGL. DEV. = 5.5 DEGREES REMARK 500 DA H 9 O5' - C5' - C4' ANGL. DEV. = -6.6 DEGREES REMARK 500 DA H 10 C1' - O4' - C4' ANGL. DEV. = -7.0 DEGREES REMARK 500 DA H 10 O4' - C1' - C2' ANGL. DEV. = -5.2 DEGREES REMARK 500 DA H 10 O4' - C1' - N9 ANGL. DEV. = 6.8 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 57 ANGLE DEVIATIONS. 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 ARG A 171 -36.01 -154.07 REMARK 500 ARG A 172 59.29 37.51 REMARK 500 LYS A 187 -55.96 -164.26 REMARK 500 THR A 244 -81.25 -39.41 REMARK 500 ARG B 106 -74.37 -67.37 REMARK 500 GLN E 207 102.49 -164.28 REMARK 500 TYR F 109 66.05 -116.22 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 LYS A 187 PRO A 188 -142.41 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3A02 RELATED DB: PDB REMARK 900 ARISTALESS HOMEODOMAIN REMARK 900 RELATED ID: 3A03 RELATED DB: PDB REMARK 900 HOX11L1 HOMEODOMAIN DBREF 3A01 A 170 261 UNP Q9VD99 Q9VD99_DROME 170 261 DBREF 3A01 B 80 146 UNP Q06453 AL_DROME 80 146 DBREF 3A01 E 170 261 UNP Q9VD99 Q9VD99_DROME 170 261 DBREF 3A01 F 80 146 UNP Q06453 AL_DROME 80 146 DBREF 3A01 C 1 17 PDB 3A01 3A01 1 17 DBREF 3A01 G 1 17 PDB 3A01 3A01 1 17 DBREF 3A01 D 1 17 PDB 3A01 3A01 1 17 DBREF 3A01 H 1 17 PDB 3A01 3A01 1 17 SEQADV 3A01 MET A 169 UNP Q9VD99 INITIATING METHIONINE SEQADV 3A01 MET E 169 UNP Q9VD99 INITIATING METHIONINE SEQRES 1 A 93 MET ALA ARG ARG ILE GLY HIS PRO TYR GLN ASN ARG THR SEQRES 2 A 93 PRO PRO LYS ARG LYS LYS PRO ARG THR SER PHE THR ARG SEQRES 3 A 93 ILE GLN VAL ALA GLU LEU GLU LYS ARG PHE HIS LYS GLN SEQRES 4 A 93 LYS TYR LEU ALA SER ALA GLU ARG ALA ALA LEU ALA ARG SEQRES 5 A 93 GLY LEU LYS MET THR ASP ALA GLN VAL LYS THR TRP PHE SEQRES 6 A 93 GLN ASN ARG ARG THR LYS TRP ARG ARG GLN THR ALA GLU SEQRES 7 A 93 GLU ARG GLU ALA GLU ARG GLN ALA ALA ASN ARG LEU MET SEQRES 8 A 93 LEU SER SEQRES 1 B 67 ALA PRO LYS ARG LYS GLN ARG ARG TYR ARG THR THR PHE SEQRES 2 B 67 THR SER PHE GLN LEU GLU GLU LEU GLU LYS ALA PHE SER SEQRES 3 B 67 ARG THR HIS TYR PRO ASP VAL PHE THR ARG GLU GLU LEU SEQRES 4 B 67 ALA MET LYS ILE GLY LEU THR GLU ALA ARG ILE GLN VAL SEQRES 5 B 67 TRP PHE GLN ASN ARG ARG ALA LYS TRP ARG LYS GLN GLU SEQRES 6 B 67 LYS VAL SEQRES 1 C 17 DG DG DC DT DT DA DA DT DT DA DA DT DT SEQRES 2 C 17 DG DC DG DG SEQRES 1 D 17 DC DC DG DC DA DA DT DT DA DA DT DT DA SEQRES 2 D 17 DA DG DC DC SEQRES 1 E 93 MET ALA ARG ARG ILE GLY HIS PRO TYR GLN ASN ARG THR SEQRES 2 E 93 PRO PRO LYS ARG LYS LYS PRO ARG THR SER PHE THR ARG SEQRES 3 E 93 ILE GLN VAL ALA GLU LEU GLU LYS ARG PHE HIS LYS GLN SEQRES 4 E 93 LYS TYR LEU ALA SER ALA GLU ARG ALA ALA LEU ALA ARG SEQRES 5 E 93 GLY LEU LYS MET THR ASP ALA GLN VAL LYS THR TRP PHE SEQRES 6 E 93 GLN ASN ARG ARG THR LYS TRP ARG ARG GLN THR ALA GLU SEQRES 7 E 93 GLU ARG GLU ALA GLU ARG GLN ALA ALA ASN ARG LEU MET SEQRES 8 E 93 LEU SER SEQRES 1 F 67 ALA PRO LYS ARG LYS GLN ARG ARG TYR ARG THR THR PHE SEQRES 2 F 67 THR SER PHE GLN LEU GLU GLU LEU GLU LYS ALA PHE SER SEQRES 3 F 67 ARG THR HIS TYR PRO ASP VAL PHE THR ARG GLU GLU LEU SEQRES 4 F 67 ALA MET LYS ILE GLY LEU THR GLU ALA ARG ILE GLN VAL SEQRES 5 F 67 TRP PHE GLN ASN ARG ARG ALA LYS TRP ARG LYS GLN GLU SEQRES 6 F 67 LYS VAL SEQRES 1 G 17 DG DG DC DT DT DA DA DT DT DA DA DT DT SEQRES 2 G 17 DG DC DG DG SEQRES 1 H 17 DC DC DG DC DA DA DT DT DA DA DT DT DA SEQRES 2 H 17 DA DG DC DC HELIX 1 1 THR A 193 GLN A 207 1 15 HELIX 2 2 ALA A 211 GLY A 221 1 11 HELIX 3 3 THR A 225 ALA A 245 1 21 HELIX 4 4 THR B 93 THR B 107 1 15 HELIX 5 5 ASP B 111 GLY B 123 1 13 HELIX 6 6 THR B 125 LYS B 142 1 18 HELIX 7 7 PRO E 176 ARG E 180 5 5 HELIX 8 8 THR E 193 GLN E 207 1 15 HELIX 9 9 ALA E 211 LEU E 222 1 12 HELIX 10 10 THR E 225 ALA E 245 1 21 HELIX 11 11 THR F 93 THR F 107 1 15 HELIX 12 12 ASP F 111 GLY F 123 1 13 HELIX 13 13 THR F 125 GLU F 144 1 20 CISPEP 1 LYS A 186 LYS A 187 0 -15.21 CISPEP 2 ARG E 189 THR E 190 0 3.83 CRYST1 70.930 85.400 110.680 90.00 90.00 90.00 P 21 21 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 0.014098 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011710 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009035 0.00000