HEADER SIGNALING PROTEIN 26-SEP-14 4WIP TITLE DIX DOMAIN OF HUMAN DVL2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SEGMENT POLARITY PROTEIN DISHEVELLED HOMOLOG DVL-2; COMPND 3 CHAIN: A, B, C; COMPND 4 FRAGMENT: UNP RESIDUES 13-105; COMPND 5 SYNONYM: DISHEVELLED-2,DSH HOMOLOG 2; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: DVL2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: CODONPLUS-RIL; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PETM-11 KEYWDS POLYMER SIGNALING UBIQUITIN-LIKE, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.FIEDLER,M.BIENZ,J.MADRZAK,J.W.CHIN REVDAT 1 13-MAY-15 4WIP 0 JRNL AUTH J.MADRZAK,M.FIEDLER,C.M.JOHNSON,R.EWAN,A.KNEBEL,M.BIENZ, JRNL AUTH 2 J.W.CHIN JRNL TITL UBIQUITINATION OF THE DISHEVELLED DIX DOMAIN BLOCKS ITS JRNL TITL 2 HEAD-TO-TAIL POLYMERIZATION. JRNL REF NAT COMMUN V. 6 6718 2015 JRNL REFN ESSN 2041-1723 JRNL PMID 25907794 JRNL DOI 10.1038/NCOMMS7718 REMARK 2 REMARK 2 RESOLUTION. 2.69 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0085 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) : 2.69 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 64.21 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 12778 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) : 0.224 REMARK 3 R VALUE (WORKING SET) : 0.222 REMARK 3 FREE R VALUE : 0.248 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 678 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) : 2.69 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.76 REMARK 3 REFLECTION IN BIN (WORKING SET) : 942 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.70 REMARK 3 BIN R VALUE (WORKING SET) : 0.3480 REMARK 3 BIN FREE R VALUE SET COUNT : 49 REMARK 3 BIN FREE R VALUE : 0.4000 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1933 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 48 REMARK 3 SOLVENT ATOMS : 13 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 48.22 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.47000 REMARK 3 B22 (A**2) : 1.38000 REMARK 3 B33 (A**2) : -1.85000 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): 0.393 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.269 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.213 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 21.557 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.915 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.888 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2020 ; 0.012 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 1948 ; 0.007 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2713 ; 1.807 ; 1.988 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4516 ; 1.405 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 240 ; 7.688 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 93 ;32.847 ;24.516 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 346 ;14.608 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ;13.209 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 294 ; 0.098 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2196 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 426 ; 0.005 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): 969 ; 4.138 ; 2.057 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 968 ; 4.108 ; 2.055 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1206 ; 6.325 ; 3.071 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1207 ; 6.330 ; 3.074 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1051 ; 5.896 ; 2.546 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1051 ; 5.893 ; 2.546 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1508 ; 7.982 ; 3.578 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 1972 ;10.021 ;15.992 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 1972 ;10.019 ;15.988 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 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 3 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 11 91 B 11 91 8856 0.11 0.05 REMARK 3 2 A 12 90 C 12 90 8816 0.10 0.05 REMARK 3 3 B 12 90 C 12 90 8642 0.11 0.05 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 11 A 91 REMARK 3 ORIGIN FOR THE GROUP (A): -5.9660 -21.3960 5.7810 REMARK 3 T TENSOR REMARK 3 T11: 0.1818 T22: 0.0031 REMARK 3 T33: 0.1588 T12: 0.0094 REMARK 3 T13: 0.0329 T23: 0.0035 REMARK 3 L TENSOR REMARK 3 L11: 4.7742 L22: 3.1705 REMARK 3 L33: 2.3521 L12: -0.9631 REMARK 3 L13: -0.0389 L23: 0.3451 REMARK 3 S TENSOR REMARK 3 S11: -0.0752 S12: -0.0820 S13: -0.2530 REMARK 3 S21: 0.1122 S22: 0.0506 S23: 0.0191 REMARK 3 S31: 0.1551 S32: 0.0567 S33: 0.0246 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 11 B 91 REMARK 3 ORIGIN FOR THE GROUP (A): -20.1550 -8.7170 21.5150 REMARK 3 T TENSOR REMARK 3 T11: 0.3286 T22: 0.3270 REMARK 3 T33: 0.3626 T12: -0.0552 REMARK 3 T13: -0.0349 T23: 0.0428 REMARK 3 L TENSOR REMARK 3 L11: 2.4749 L22: 3.5336 REMARK 3 L33: 6.9728 L12: 0.1272 REMARK 3 L13: -0.1036 L23: 4.2997 REMARK 3 S TENSOR REMARK 3 S11: 0.0648 S12: -0.3577 S13: -0.1226 REMARK 3 S21: 0.0410 S22: -0.1696 S23: 0.3128 REMARK 3 S31: 0.2994 S32: -0.6110 S33: 0.1048 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 12 C 92 REMARK 3 ORIGIN FOR THE GROUP (A): -13.5730 6.7190 40.7280 REMARK 3 T TENSOR REMARK 3 T11: 0.1830 T22: 0.0224 REMARK 3 T33: 0.2403 T12: -0.0089 REMARK 3 T13: -0.0206 T23: -0.0590 REMARK 3 L TENSOR REMARK 3 L11: 4.0469 L22: 3.5422 REMARK 3 L33: 3.4688 L12: 0.6777 REMARK 3 L13: 0.3203 L23: 0.1435 REMARK 3 S TENSOR REMARK 3 S11: -0.0166 S12: 0.2241 S13: -0.5041 REMARK 3 S21: -0.0590 S22: -0.0712 S23: 0.0676 REMARK 3 S31: 0.2746 S32: -0.0921 S33: 0.0878 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.10 REMARK 3 ION PROBE RADIUS : 0.90 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 4WIP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-SEP-14. REMARK 100 THE DEPOSITION ID IS D_1000203873. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-AUG-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 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 FR-E+ SUPERBRIGHT REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54178 REMARK 200 MONOCHROMATOR : OSMIC VARIMAX REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS HTC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.21 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13481 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.691 REMARK 200 RESOLUTION RANGE LOW (A) : 98.260 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 3.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.14000 REMARK 200 FOR THE DATA SET : 5.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.69 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.84 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : 0.48000 REMARK 200 R SYM FOR SHELL (I) : 0.48000 REMARK 200 FOR SHELL : 1.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 65.49 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.56 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: GREW IN PEG400 (CRYO CONDITION) OVER REMARK 280 NIGHT, PH 8.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 292K 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 28.15000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 49.13000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 42.41000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 49.13000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.15000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 42.41000 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3640 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14090 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 SER A 92 REMARK 465 ASP A 93 REMARK 465 ASN A 94 REMARK 465 PRO A 95 REMARK 465 GLN A 96 REMARK 465 PRO A 97 REMARK 465 GLU A 98 REMARK 465 MET A 99 REMARK 465 ALA A 100 REMARK 465 PRO A 101 REMARK 465 PRO A 102 REMARK 465 VAL A 103 REMARK 465 HIS A 104 REMARK 465 GLU A 105 REMARK 465 PRO A 106 REMARK 465 ARG A 107 REMARK 465 SER B 92 REMARK 465 ASP B 93 REMARK 465 ASN B 94 REMARK 465 PRO B 95 REMARK 465 GLN B 96 REMARK 465 PRO B 97 REMARK 465 GLU B 98 REMARK 465 MET B 99 REMARK 465 ALA B 100 REMARK 465 PRO B 101 REMARK 465 PRO B 102 REMARK 465 VAL B 103 REMARK 465 HIS B 104 REMARK 465 GLU B 105 REMARK 465 PRO B 106 REMARK 465 ARG B 107 REMARK 465 MET C 11 REMARK 465 ASP C 93 REMARK 465 ASN C 94 REMARK 465 PRO C 95 REMARK 465 GLN C 96 REMARK 465 PRO C 97 REMARK 465 GLU C 98 REMARK 465 MET C 99 REMARK 465 ALA C 100 REMARK 465 PRO C 101 REMARK 465 PRO C 102 REMARK 465 VAL C 103 REMARK 465 HIS C 104 REMARK 465 GLU C 105 REMARK 465 PRO C 106 REMARK 465 ARG C 107 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 O HOH B 301 O HOH C 301 2454 1.74 REMARK 500 O HOH A 301 O HOH A 303 4545 1.81 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 A 77 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 ARG A 77 NE - CZ - NH2 ANGL. DEV. = -4.2 DEGREES 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 ASP A 21 -125.89 45.54 REMARK 500 GLN A 48 71.08 49.79 REMARK 500 ASP B 21 -127.15 44.45 REMARK 500 GLN B 48 91.02 64.91 REMARK 500 ARG B 49 143.68 -37.09 REMARK 500 PRO B 50 -164.45 -66.30 REMARK 500 ALA B 51 73.20 -65.42 REMARK 500 ASP C 21 -126.22 44.93 REMARK 500 GLN C 48 81.08 51.46 REMARK 500 ARG C 49 113.10 -39.07 REMARK 500 PRO C 50 -33.13 -38.01 REMARK 500 ALA C 51 147.25 108.83 REMARK 500 SER C 91 -164.80 -104.73 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 GLN C 48 ARG C 49 -149.55 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 1PE A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 1PE B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 1PE C 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3PZ8 RELATED DB: PDB REMARK 900 3PZ8 CONTAINS THE DIX DOMAIN OF DVL-1. DBREF 4WIP A 12 106 UNP O14641 DVL2_HUMAN 12 106 DBREF 4WIP B 12 106 UNP O14641 DVL2_HUMAN 12 106 DBREF 4WIP C 12 106 UNP O14641 DVL2_HUMAN 12 106 SEQADV 4WIP MET A 11 UNP O14641 INITIATING METHIONINE SEQADV 4WIP ASP A 27 UNP O14641 TYR 27 ENGINEERED MUTATION SEQADV 4WIP ARG A 107 UNP O14641 EXPRESSION TAG SEQADV 4WIP MET B 11 UNP O14641 INITIATING METHIONINE SEQADV 4WIP ASP B 27 UNP O14641 TYR 27 ENGINEERED MUTATION SEQADV 4WIP ARG B 107 UNP O14641 EXPRESSION TAG SEQADV 4WIP MET C 11 UNP O14641 INITIATING METHIONINE SEQADV 4WIP ASP C 27 UNP O14641 TYR 27 ENGINEERED MUTATION SEQADV 4WIP ARG C 107 UNP O14641 EXPRESSION TAG SEQRES 1 A 97 MET GLY GLU THR LYS VAL ILE TYR HIS LEU ASP GLU GLU SEQRES 2 A 97 GLU THR PRO ASP LEU VAL LYS ILE PRO VAL PRO ALA GLU SEQRES 3 A 97 ARG ILE THR LEU GLY ASP PHE LYS SER VAL LEU GLN ARG SEQRES 4 A 97 PRO ALA GLY ALA LYS TYR PHE PHE LYS SER MET ASP GLN SEQRES 5 A 97 ASP PHE GLY VAL VAL LYS GLU GLU ILE SER ASP ASP ASN SEQRES 6 A 97 ALA ARG LEU PRO CYS PHE ASN GLY ARG VAL VAL SER TRP SEQRES 7 A 97 LEU VAL SER SER ASP ASN PRO GLN PRO GLU MET ALA PRO SEQRES 8 A 97 PRO VAL HIS GLU PRO ARG SEQRES 1 B 97 MET GLY GLU THR LYS VAL ILE TYR HIS LEU ASP GLU GLU SEQRES 2 B 97 GLU THR PRO ASP LEU VAL LYS ILE PRO VAL PRO ALA GLU SEQRES 3 B 97 ARG ILE THR LEU GLY ASP PHE LYS SER VAL LEU GLN ARG SEQRES 4 B 97 PRO ALA GLY ALA LYS TYR PHE PHE LYS SER MET ASP GLN SEQRES 5 B 97 ASP PHE GLY VAL VAL LYS GLU GLU ILE SER ASP ASP ASN SEQRES 6 B 97 ALA ARG LEU PRO CYS PHE ASN GLY ARG VAL VAL SER TRP SEQRES 7 B 97 LEU VAL SER SER ASP ASN PRO GLN PRO GLU MET ALA PRO SEQRES 8 B 97 PRO VAL HIS GLU PRO ARG SEQRES 1 C 97 MET GLY GLU THR LYS VAL ILE TYR HIS LEU ASP GLU GLU SEQRES 2 C 97 GLU THR PRO ASP LEU VAL LYS ILE PRO VAL PRO ALA GLU SEQRES 3 C 97 ARG ILE THR LEU GLY ASP PHE LYS SER VAL LEU GLN ARG SEQRES 4 C 97 PRO ALA GLY ALA LYS TYR PHE PHE LYS SER MET ASP GLN SEQRES 5 C 97 ASP PHE GLY VAL VAL LYS GLU GLU ILE SER ASP ASP ASN SEQRES 6 C 97 ALA ARG LEU PRO CYS PHE ASN GLY ARG VAL VAL SER TRP SEQRES 7 C 97 LEU VAL SER SER ASP ASN PRO GLN PRO GLU MET ALA PRO SEQRES 8 C 97 PRO VAL HIS GLU PRO ARG HET 1PE A 201 16 HET 1PE B 201 16 HET 1PE C 201 16 HETNAM 1PE PENTAETHYLENE GLYCOL HETSYN 1PE PEG400 FORMUL 4 1PE 3(C10 H22 O6) FORMUL 7 HOH *13(H2 O) HELIX 1 AA1 THR A 39 GLN A 48 1 10 HELIX 2 AA2 THR B 39 GLN B 48 1 10 HELIX 3 AA3 THR C 39 GLN C 48 1 10 SHEET 1 AA115 ASP A 27 ILE A 31 0 SHEET 2 AA115 THR A 14 LEU A 20 -1 N VAL A 16 O VAL A 29 SHEET 3 AA115 ARG A 84 VAL A 90 1 O VAL A 85 N ILE A 17 SHEET 4 AA115 LYS A 54 ASP A 61 -1 N PHE A 56 O TRP A 88 SHEET 5 AA115 GLY A 65 ILE A 71 -1 O GLU A 69 N PHE A 57 SHEET 6 AA115 ASP B 27 ILE B 31 1 O LEU B 28 N GLU A 70 SHEET 7 AA115 THR B 14 LEU B 20 -1 N VAL B 16 O VAL B 29 SHEET 8 AA115 ARG B 84 VAL B 90 1 O VAL B 85 N ILE B 17 SHEET 9 AA115 LYS B 54 ASP B 61 -1 N PHE B 56 O TRP B 88 SHEET 10 AA115 GLY B 65 GLU B 70 -1 O GLU B 69 N PHE B 57 SHEET 11 AA115 ASP C 27 ILE C 31 1 O LEU C 28 N LYS B 68 SHEET 12 AA115 THR C 14 LEU C 20 -1 N VAL C 16 O VAL C 29 SHEET 13 AA115 ARG C 84 VAL C 90 1 O VAL C 85 N ILE C 17 SHEET 14 AA115 LYS C 54 ASP C 61 -1 N PHE C 56 O TRP C 88 SHEET 15 AA115 GLY C 65 ILE C 71 -1 O GLU C 69 N PHE C 57 CISPEP 1 ALA A 51 GLY A 52 0 28.83 SITE 1 AC1 5 LYS A 58 PHE A 81 ARG A 84 VAL A 86 SITE 2 AC1 5 PHE C 64 SITE 1 AC2 4 LYS B 58 PHE B 81 ARG B 84 VAL B 86 SITE 1 AC3 4 LYS C 58 PHE C 81 ARG C 84 VAL C 86 CRYST1 56.300 84.820 98.260 90.00 90.00 90.00 P 21 21 21 12 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 0.017762 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011790 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010177 0.00000