HEADER SIGNALING PROTEIN, LIPID BINDING PROTEIN17-AUG-07 2QZQ TITLE CRYSTAL STRUCTURE OF C-TERMINAL OF AIDA COMPND MOL_ID: 1; COMPND 2 MOLECULE: AXIN INTERACTOR, DORSALIZATION ASSOCIATED COMPND 3 PROTEIN; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: C-TERMINAL DOMAIN; COMPND 6 SYNONYM: AXIN INTERACTION PARTNER AND DORSALIZATION COMPND 7 ANTAGONIST; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DANIO RERIO; SOURCE 3 ORGANISM_COMMON: ZEBRAFISH; SOURCE 4 ORGANISM_TAXID: 7955; SOURCE 5 GENE: AIDA; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS BETA SHEET SANDWICH, COILED COIL, SIGNALING PROTEIN, LIPID KEYWDS 2 BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR L.S.ZHENG,J.W.WU REVDAT 2 24-FEB-09 2QZQ 1 VERSN REVDAT 1 23-SEP-08 2QZQ 0 JRNL AUTH L.S.ZHENG JRNL TITL CRYSTAL STRUCTURE OF C-TERMINAL OF AIDA JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.84 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 3 NUMBER OF REFLECTIONS : 18158 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) : 0.197 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.200 REMARK 3 FREE R VALUE TEST SET COUNT : 1858 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1075 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 90.83 REMARK 3 BIN R VALUE (WORKING SET) : 0.2200 REMARK 3 BIN FREE R VALUE SET COUNT : 134 REMARK 3 BIN FREE R VALUE : 0.2630 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1227 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 144 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.23 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.137 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.133 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.085 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.819 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.947 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.922 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1263 ; 0.016 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1704 ; 1.525 ; 2.008 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 151 ; 6.266 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 49 ;30.361 ;24.286 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 244 ;13.567 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 5 ;23.417 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 196 ; 0.103 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 907 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 520 ; 0.216 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 858 ; 0.303 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 115 ; 0.141 ; 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): 34 ; 0.191 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 12 ; 0.216 ; 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): 789 ; 0.975 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1253 ; 1.295 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 525 ; 2.594 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 451 ; 3.552 ; 4.500 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: HYDROGENS HAVE BEEN ADDED IN THE REMARK 3 RIDING POSITIONS REMARK 4 REMARK 4 2QZQ COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-AUG-07. REMARK 100 THE RCSB ID CODE IS RCSB044248. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-DEC-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-6A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9786 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18670 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 47.560 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 20.800 REMARK 200 R MERGE (I) : 0.06700 REMARK 200 R SYM (I) : 0.06400 REMARK 200 FOR THE DATA SET : 33.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 20.50 REMARK 200 R MERGE FOR SHELL (I) : 0.40600 REMARK 200 R SYM FOR SHELL (I) : 0.38700 REMARK 200 FOR SHELL : 9.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.72 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 HEPES NA PH 7.4, 12% PEG 3350, REMARK 280 2% MPD, VAPOR DIFFUSION, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 86.68000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 43.34000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 43.34000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 86.68000 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 LYS A 100 CD CE NZ 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 SER A 20 40.27 -140.89 REMARK 500 GLN A 92 41.17 -87.20 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2QZ5 RELATED DB: PDB DBREF 2QZQ A 19 170 UNP Q6PBN2 AIDA_DANRE 151 302 SEQRES 1 A 152 GLY SER LEU LEU PRO ARG LEU PRO SER GLU PRO GLY MSE SEQRES 2 A 152 THR LEU LEU THR LEU THR ILE GLU LYS ILE GLY LEU LYS SEQRES 3 A 152 ASP ALA GLY GLN CYS ILE ASP PRO TYR ILE THR VAL SER SEQRES 4 A 152 VAL LYS ASP LEU ASN GLY ILE ASP LEU ASN PRO VAL GLN SEQRES 5 A 152 ASP THR PRO VAL ALA THR ARG LYS GLU ASP THR TYR ILE SEQRES 6 A 152 HIS PHE SER VAL ASP VAL GLU ILE GLN ARG HIS LEU GLU SEQRES 7 A 152 LYS LEU PRO LYS GLY ALA ALA ILE PHE PHE GLU PHE LYS SEQRES 8 A 152 HIS TYR LYS PRO LYS LYS ARG PHE THR SER THR LYS CYS SEQRES 9 A 152 PHE ALA PHE MSE GLU MSE ASP GLU ILE LYS PRO GLY PRO SEQRES 10 A 152 ILE VAL ILE GLU LEU TYR LYS LYS PRO THR ASP PHE LYS SEQRES 11 A 152 ARG LYS LYS LEU ASN LEU LEU THR LYS LYS PRO LEU TYR SEQRES 12 A 152 LEU HIS LEU ASN GLN THR LEU HIS LYS MODRES 2QZQ MSE A 31 MET SELENOMETHIONINE MODRES 2QZQ MSE A 126 MET SELENOMETHIONINE MODRES 2QZQ MSE A 128 MET SELENOMETHIONINE HET MSE A 31 8 HET MSE A 126 8 HET MSE A 128 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 3(C5 H11 N O2 SE) FORMUL 2 HOH *144(H2 O) HELIX 1 1 ASP A 45 CYS A 49 5 5 HELIX 2 2 HIS A 94 LEU A 98 5 5 HELIX 3 3 ASP A 129 ILE A 131 5 3 SHEET 1 A 5 ARG A 77 LYS A 78 0 SHEET 2 A 5 TYR A 82 GLU A 90 -1 O HIS A 84 N ARG A 77 SHEET 3 A 5 LEU A 33 GLY A 42 -1 N ILE A 38 O VAL A 87 SHEET 4 A 5 LEU A 162 HIS A 169 -1 O ASN A 165 N THR A 37 SHEET 5 A 5 GLY A 134 ILE A 138 -1 N ILE A 138 O LEU A 162 SHEET 1 B 5 GLN A 70 ASP A 71 0 SHEET 2 B 5 ILE A 50 LYS A 59 -1 N VAL A 56 O GLN A 70 SHEET 3 B 5 ALA A 103 TYR A 111 -1 O LYS A 109 N TYR A 53 SHEET 4 B 5 THR A 118 GLU A 127 -1 O SER A 119 N HIS A 110 SHEET 5 B 5 TYR A 141 LYS A 142 -1 O TYR A 141 N PHE A 123 LINK C GLY A 30 N MSE A 31 1555 1555 1.33 LINK C MSE A 31 N THR A 32 1555 1555 1.33 LINK C PHE A 125 N MSE A 126 1555 1555 1.33 LINK C MSE A 126 N GLU A 127 1555 1555 1.34 LINK C GLU A 127 N MSE A 128 1555 1555 1.33 LINK C MSE A 128 N ASP A 129 1555 1555 1.33 CISPEP 1 LYS A 143 PRO A 144 0 -1.33 CRYST1 54.951 54.951 130.020 90.00 90.00 120.00 P 32 2 1 6 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 0.018198 0.010507 0.000000 0.00000 SCALE2 0.000000 0.021013 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007691 0.00000